all_inputs.tsv

Terra Task Name	Variable	Type	Description	Default Value	Terra Status	Workflow	Classification	Manual Override
amr_search_workflow	amr_search_database	String	NCBI taxon code of samples known taxonomy, see above supported species		Required	AMR_Search	general	
amr_search_workflow	input_fasta	File	A microbial assembly file		Required	AMR_Search	general	
amr_search_workflow	samplename	String	The name of the sample being analyzed		Required	AMR_Search	general	
amrfinderplus_wf	assembly	File	The assembly file for your sample in FASTA format		Required	AMRFinderPlus	general	
amrfinderplus_wf	samplename	String	The name of the sample being analyzed		Required	AMRFinderPlus	general	
assembly_fetch	samplename	String	The name of the sample being analyzed		Required	Assembly_Fetch	general	
augur	assembly_fastas	Array[File]+	The assembly files for your samples in FASTA format		Required	Augur	general	
augur	build_name	String	Name to give to the Augur build		Required	Augur	general	
augur_prep	assembly	File	The assembly file for your sample in FASTA format		Required	Augur_Prep	general	
basespace_fetch	access_token	String	The access token is used in place of a username and password to allow the workflow to access the user account in BaseSpace from which the data is to be transferred. It is an alphanumeric string that is 32 characters in length. Example: 9e08a96471df44579b72abf277e113b7		Required	BaseSpace_Fetch	general	
basespace_fetch	basespace_collection_id	String	The collection ID is the BaseSpace Run or Project where the data to be transferred is stored.		Required	BaseSpace_Fetch	general	
basespace_fetch	basespace_sample_name	String	The BaseSpace sample name is the sample identifier used in BaseSpace. This identifier is set on the sample sheet at the onset of an Illumina sequencing run.		Required	BaseSpace_Fetch	general	
basespace_fetch	sample_name	String	The sample name is the sample identifier used in the Terra.bio data table corresponding to the metadata associated with the sample to be transferred from BaseSpace		Required	BaseSpace_Fetch	general	
cauris_cladetyper	assembly_fasta	File	The assembly file for your sample in FASTA format		Required	Cauris_CladeTyper	general	
cauris_cladetyper	samplename	String	The name of the sample being analyzed		Required	Cauris_CladeTyper	general	
clair3_variants_ont	read1	File	ONT read file in FASTQ file format (compression optional)		Required	Clair3_Variants_ONT	general	
clair3_variants_ont	reference_genome_file	File	Reference genome in FASTA format		Required	Clair3_Variants_ONT	general	
clair3_variants_ont	samplename	String	The name of the sample being analyzed		Required	Clair3_Variants_ONT	general	
concatenate_column_content	concatenated_file_name	String	The name of the output file. Include the extension, such as ".fasta" or ".txt".		Required	Concatenate_Column_Content	general	
concatenate_column_content	files_to_cat	Array[File]	The column that has the files you want to concatenate.		Required	Concatenate_Column_Content	general	
concatenate_illumina_lanes	read1_lane1	File	The first lane for the forward reads		Required	Concatenate_Illumina_Lanes	general	
concatenate_illumina_lanes	read1_lane2	File	The second lane for the forward reads		Required	Concatenate_Illumina_Lanes	general	
concatenate_illumina_lanes	samplename	String	The name of the sample being analyzed		Required	Concatenate_Illumina_Lanes	general	
core_gene_snp_workflow	cluster_name	String	Name of sample set		Required	Core_Gene_SNP	general	
core_gene_snp_workflow	gff3	Array[File]	Array of gff3 files to include in analysis, output gff files from both prokka and bakta using TheiaProk workflows are compatible		Required	Core_Gene_SNP	general	
create_terra_table	assembly_data	Boolean	Set to true if your data is in FASTA format; set to false if your data is FASTQ format		Required	Create_Terra_Table	general	
create_terra_table	data_location_path	String	The full path to your data's Google bucket folder location, including the gs://; can be easily copied by right-clicking and copying the link address in the header after navigating to the folder in the "Files" section of the "Data" tab on Terra (see above for examples)		Required	Create_Terra_Table	general	
create_terra_table	new_table_name	String	The name of the new Terra table you want to create		Required	Create_Terra_Table	general	
create_terra_table	paired_end	Boolean	Set to true if your data is paired-end FASTQ files; set to false if not		Required	Create_Terra_Table	general	
create_terra_table	terra_project	String	The name of the Terra project where your data table will be created		Required	Create_Terra_Table	general	
create_terra_table	terra_workspace	String	The name of the Terra workspace where your data table will be created		Required	Create_Terra_Table	general	
czgenepi_prep	assembly_fasta_column_name	String	The column name where the sample's assembly file can be found		Required	CZGenEpi_Prep	general	
czgenepi_prep	collection_date_column_name	String	The column name where the sample's collection date can be found		Required	CZGenEpi_Prep	general	
czgenepi_prep	continent_column_name	String	The column name where the sample's originating continent can be found		Required	CZGenEpi_Prep	general	
czgenepi_prep	country_column_name	String	The column name where the sample's originating country can be found		Required	CZGenEpi_Prep	general	
czgenepi_prep	county_column_name	String	The column name where the samples' originating county can be found		Required	CZGenEpi_Prep	general	
czgenepi_prep	sample_names	Array[String]	The array of sample ids you want to prepare for CZ GEN EPI		Required	CZGenEpi_Prep	general	
czgenepi_prep	state_column_name	String	The column name where the sample's originating state can be found		Required	CZGenEpi_Prep	general	
czgenepi_prep	terra_project_name	String	The name of the Terra project where the data is hosted		Required	CZGenEpi_Prep	general	
czgenepi_prep	terra_table_name	String	The name of the Terra table where the data is hosted		Required	CZGenEpi_Prep	general	
czgenepi_prep	terra_workspace_name	String	The name of the Terra workspace where the data is hosted		Required	CZGenEpi_Prep	general	
dehost_pe	read1	File	FASTQ file containing read1 sequences		Required	NCBI_Scrub_PE	general	
dehost_pe	read2	File	FASTQ file containing read2 sequences		Required	NCBI_Scrub_PE	general	
dehost_pe	samplename	String	The name of the sample being analyzed		Required	NCBI_Scrub_PE	general	
dehost_se	read1	File	FASTQ file containing read1 sequences		Required	NCBI_Scrub_SE	general	
dehost_se	samplename	String	The name of the sample being analyzed		Required	NCBI_Scrub_SE	general	
dorado_basecalling	kit_name	String	Sequencing kit name used (e.g., SQK-RPB114-24); see above for all available options.		Required	Dorado_Basecalling	general	
dorado_basecalling	new_table_name	String	The desired name for a newly created Terra table that will contain the basecalled FASTQ files. This value should be the name as you want the table to appear as in the sidebar on the lefthand side of the Terra Data tab.		Required	Dorado_Basecalling	general	
dorado_basecalling	output_file_prefix	String	Prefix for naming output FASTQ files		Required	Dorado_Basecalling	general	
dorado_basecalling	pod5_bucket_path	String	GCS path of the bucket containing POD5 files.		Required	Dorado_Basecalling	general	
dorado_basecalling	terra_project	String	The name of your Terra project. You can find this information in the URL of the webpage of your Terra dashboard. For example, if your URL contains #workspaces/example/my_workspace/ then your project name is example		Required	Dorado_Basecalling	general	
dorado_basecalling	terra_workspace	String	The name of your Terra workspace where your samples can be found. For example, if your URL contains #workspaces/example/my_workspace/ then your workspace name is my_workspace		Required	Dorado_Basecalling	general	
fetch_sra_to_fastq	accession	String	SRA, ENA, or DRA accession number		Required	SRA_Fetch	general	
fetch_srr_accession	sample_accession	String	SRA-compatible accession, such as a BioSample ID (e.g., "SAMN00000000") or SRA Experiment ID (e.g., "SRX000000"), used to retrieve SRR metadata.		Required	Fetch_SRR_Accession	general	
freyja_dashboard	collection_date	Array[String]	An array containing the collection dates for the sample (YYYY-MM-DD format)		Required	Freyja_Dashboard	general	
freyja_dashboard	freyja_dashboard_title	String	The name of the dashboard to be produced. Example: "my-freyja-dashboard"		Required	Freyja_Dashboard	general	
freyja_dashboard	freyja_demixed	Array[File]	An array containing the output files (freyja_demixed) made by Freyja_FASTQ workflow		Required	Freyja_Dashboard	general	
freyja_dashboard	samplename	Array[String]	The names of the samples being analyzed		Required	Freyja_Dashboard	general	
freyja_dashboard	viral_load	Array[String]	An array containing the number of viral copies per liter		Required	Freyja_Dashboard	general	
freyja_fastq	read1	File	FASTQ file containing read1 sequences (Illumina or (ONT)		Required	Freyja_FASTQ	general	
freyja_fastq	reference_genome	File	The reference genome to use; should match the reference used for alignment (Wuhan-Hu-1)		Required	Freyja_FASTQ	general	
freyja_fastq	samplename	String	The name of the sample being analyzed		Required	Freyja_FASTQ	general	
freyja_plot	freyja_demixed	Array[File]	An array containing the output files (freyja_demixed) made by Freyja_FASTQ		Required	Freyja_Plot	general	
freyja_plot	freyja_plot_name	String	The name of the plot to be produced. Example: "my-freyja-plot"		Required	Freyja_Plot	general	
freyja_plot	samplename	Array[String]	The names of the samples being analyzed		Required	Freyja_Plot	general	
gambit_query	assembly_fasta	File	The assembly file for your sample in FASTA format		Required	Gambit_Query	general	
gambit_query	samplename	String	The name of the sample being analyzed		Required	Gambit_Query	general	
kraken2_pe_wf	kraken2_db	File	A Kraken2 database in .tar.gz format		Required	Kraken_PE	general	
kraken2_pe_wf	read1	File	Forward read in FASTQ file format (compression optional)		Required	Kraken_PE	general	
kraken2_pe_wf	read2	File	Illumina reverse read file in FASTQ file format (compression optional)		Required	Kraken_PE	general	
kraken2_pe_wf	samplename	String	The name of the sample being analyzed		Required	Kraken_PE	general	
kraken2_se_wf	kraken2_db	File	A Kraken2 database in .tar.gz format		Required	Kraken_SE	general	
kraken2_se_wf	read1	File	Forward read in FASTQ file format (compression optional)		Required	Kraken_SE	general	
kraken2_se_wf	samplename	String	The name of the sample being analyzed		Required	Kraken_SE	general	
ksnp3_workflow	assembly_fasta	Array[File]	The assembly files for your samples in FASTA format		Required	kSNP3	general	
ksnp3_workflow	cluster_name	String	Free text string used to label output files		Required	kSNP3	general	
ksnp3_workflow	samplename	Array[String]	The names of the samples being analyzed		Required	kSNP3	general	
ksnp4_workflow	assembly_fasta	Array[File]	The assembly files for your samples in FASTA format		Required	kSNP4	general	
ksnp4_workflow	cluster_name	String	Free text string used to label output files		Required	kSNP4	general	
ksnp4_workflow	samplename	Array[String]	The names of the samples being analyzed		Required	kSNP4	general	
lyveset_workflow	dataset_name	String	Free text string used to label output files		Required	Lyve_SET	general	
lyveset_workflow	read1	Array[File]	FASTQ files containing read1 sequences; we recommend using cleaned reads instead of raw reads		Required	Lyve_SET	general	
lyveset_workflow	read2	Array[File]	FASTQ files containing read2 sequences; we recommend using cleaned reads instead of raw reads		Required	Lyve_SET	general	
lyveset_workflow	reference_genome	File	Path to reference genome in a Terra-accessible Google bucket. For considerations when choosing a reference genome, see: <https://github.com/lskatz/lyve-SET/blob/master/docs/FAQ.md>		Required	Lyve_SET	general	
lyveset_workflow	samplename	Array[String]	The names of the samples being analyzed		Required	Lyve_SET	general	
mashtree_fasta	assembly_fasta	Array[File]	The assembly files for your samples in FASTA format		Required	MashTree_FASTA	general	
mashtree_fasta	cluster_name	String	Free text string used to label output files		Required	MashTree_FASTA	general	
mercury_prep_n_batch	gcp_bucket_uri	String	Google bucket where your SRA reads will be temporarily stored before transferring to SRA. Example: "gs://theiagen_sra_transfer"		Required	Mercury_Prep_N_Batch	general	
mercury_prep_n_batch	sample_names	Array[String]	The samples you want to submit		Required	Mercury_Prep_N_Batch	general	
mercury_prep_n_batch	terra_project_name	String	The name of your Terra project. You can find this information in the URL of the webpage of your Terra dashboard. For example, if your URL contains #workspaces/example/my_workspace/ then your project name is example		Required	Mercury_Prep_N_Batch	general	
mercury_prep_n_batch	terra_table_name	String	The name of the Terra table where your samples can be found. Do not include the entity: prefix, the _id suffix, or the _set_id suffix, just the name of the sample-level data table as listed in the sidebar on lefthand side of the Terra Data tab.		Required	Mercury_Prep_N_Batch	general	
mercury_prep_n_batch	terra_workspace_name	String	The name of your Terra workspace where your samples can be found. For example, if your URL contains #workspaces/example/my_workspace/ then your project name is my_workspace		Required	Mercury_Prep_N_Batch	general	
metabuli_wf	metabuli_db	File			Required	Metabuli	general	
metabuli_wf	read1	File	FASTQ file containing read1 sequences		Required	Metabuli	general	
metabuli_wf	samplename	String	The name of the sample being analyzed		Required	Metabuli	general	
nextclade_batch	assembly_fastas	Array[File]	The assembly files for your samples in FASTA format		Required	Nextclade_Batch	general	
nextclade_batch	dataset_name	String	What nextclade dataset name to run nextclade on; some options are: "sars-cov-2", "flu_h1n1pdm_ha", "flu_h1n1pdm_na", "flu_h3n2_ha", "flu_h3n2_na", "flu_vic_ha", "flu_vic_na", "flu_yam_ha", "hMPXV", "hMPXV_B1", "MPXV", "rsv_a" and "rsv_b"		Required	Nextclade_Batch	general	
ont_barcode_concatenation	input_bucket_path	String	The full path to your **unconcatenated** data's Google bucket folder location, including the gs://; can be easily copied by right-clicking and copying the link address in the header after navigating to the folder in the "Files" section of the "Data" tab on Terra (see above for examples)		Required	ONT_Barcode_Concatenation	general	
ont_barcode_concatenation	new_table_name	String	The name of the Terra table where you want the **concatenated** data to be added to; can be new or pre-existing		Required	ONT_Barcode_Concatenation	general	
ont_barcode_concatenation	output_bucket_path	String	The full path to where you want the **concatenated** data to be stored as a Google bucket folder location, including the gs://; can be easily copied by right-clicking and copying the link address in the header after navigating to the desired folder in the "Files" section of the "Data" tab on Terra (see above for examples)		Required	ONT_Barcode_Concatenation	general	
ont_barcode_concatenation	terra_project	String	The name of the Terra project where your data table will be located		Required	ONT_Barcode_Concatenation	general	
ont_barcode_concatenation	terra_workspace	String	The name of the Terra workspace where your data table will be located		Required	ONT_Barcode_Concatenation	general	
pangolin_update	assembly_fasta	File	The assembly file for your sample in FASTA format		Required	Pangolin_Update	general	
pangolin_update	old_lineage	String	The Pangolin lineage previously assigned to the sample		Required	Pangolin_Update	general	
pangolin_update	old_pangolin_assignment_version	String	Version of the Pangolin software previously used for lineage assignment.		Required	Pangolin_Update	general	
pangolin_update	old_pangolin_docker	String	The Pangolin docker image previously used for lineage assignment.		Required	Pangolin_Update	general	
pangolin_update	old_pangolin_versions	String	All pangolin software and database versions previously used for lineage assignment.		Required	Pangolin_Update	general	
pangolin_update	samplename	String	The name of the sample being analyzed		Required	Pangolin_Update	general	
phylocompare	tree1	File	Path to a newick-formatted phylogenetic tree in an accessible bucket		Required	PhyloCompare	general	
phylocompare	tree2	File	Path to a newick-formatted phylogenetic tree in an accessible bucket		Required	PhyloCompare	general	
rasusa_workflow	coverage	Float	Use to specify the desired coverage of reads after downsampling; actual coverage of subsampled reads will not be exact and may be slightly higher; always check the estimated clean coverage after performing downstream workflows to verify coverage values, when necessary		Required	RASUSA	general	
rasusa_workflow	genome_length	String	Input the approximate genome size expected in quotations; this is used to determine the number of bases required to achieve the desired coverage; acceptable metric suffixes include: b, k, m, g, and t for base, kilo, mega, giga, and tera, respectively		Required	RASUSA	general	
rasusa_workflow	read1	File	FASTQ file containing read1 sequences		Required	RASUSA	general	
rasusa_workflow	samplename	String	The name of the sample being analyzed		Required	RASUSA	general	
rename_fastq_files	new_filename	String	New name for the FASTQ file(s)		Required	Rename_FASTQ	general	
rename_fastq_files	read1	File	FASTQ file containing read1 sequences		Required	Rename_FASTQ	general	
shared_variants_wf	concatenated_file_name	String	String of your choice to prefix output files		Required	Find_Shared_Variants	general	
shared_variants_wf	samplenames	Array[String]	The names of the samples being analyzed		Required	Find_Shared_Variants	general	
shared_variants_wf	variants_to_cat	Array[File]	The result file from the Snippy_Variants workflow		Required	Find_Shared_Variants	general	
snippy_streamline	read1	Array[File]	FASTQ files containing read1 sequences		Required	Snippy_Streamline	general	
snippy_streamline	read2	Array[File]	FASTQ files containing read2 sequences		Required	Snippy_Streamline	general	
snippy_streamline	samplenames	Array[String]	The names of the samples being analyzed		Required	Snippy_Streamline	general	
snippy_streamline	tree_name	String	String of your choice to prefix output files		Required	Snippy_Streamline	general	
snippy_streamline_fasta	assembly_fasta	Array[File]	The assembly files for your samples in FASTA format		Required	Snippy_Streamline_FASTA	general	
snippy_streamline_fasta	samplenames	Array[String]	The names of the samples being analyzed		Required	Snippy_Streamline_FASTA	general	
snippy_streamline_fasta	tree_name	String	String of your choice to prefix output files		Required	Snippy_Streamline_FASTA	general	
snippy_tree_wf	reference_genome_file	File	Reference genome in FASTA or GENBANK format (must be the same reference used in Snippy_Variants workflow)		Required	Snippy_Tree	general	
snippy_tree_wf	samplenames	Array[String]	The names of the samples being analyzed		Required	Snippy_Tree	general	
snippy_tree_wf	snippy_variants_outdir_tarball	Array[File]	Output from the Snippy_Variants workflow		Required	Snippy_Tree	general	
snippy_tree_wf	tree_name	String	String of your choice to prefix output files		Required	Snippy_Tree	general	
snippy_variants_wf	reference_genome_file	File	Reference genome (GenBank file or fasta)		Required	Snippy_Variants	general	
snippy_variants_wf	samplename	String	The name of the sample being analyzed		Required	Snippy_Variants	general	
tbprofiler_tngs	read1	File	Illumina forward read file in FASTQ file format (compression optional)		Required	TBProfiler_tNGS	general	
tbprofiler_tngs	read2	File	Illumina reverse read file in FASTQ file format (compression optional)		Required	TBProfiler_tNGS	general	
tbprofiler_tngs	samplename	String	The name of the sample being analyzed		Required	TBProfiler_tNGS	general	
Terra_2_ENA	ena_password	String	ENA password to authenticate submission		Required	Terra_2_ENA	general	
Terra_2_ENA	ena_username	String	ENA username to authenticate submission		Required	Terra_2_ENA	general	
Terra_2_ENA	sample_id_column	String	The column name in the Terra data table containing sample IDs		Required	Terra_2_ENA	general	
Terra_2_ENA	sample_type	String	Type of sample being submitted ("prokaryotic_pathogen" or "virus_pathogen")		Required	Terra_2_ENA	general	
Terra_2_ENA	samples	Array[String]	Array of sample IDs to submit		Required	Terra_2_ENA	general	
Terra_2_ENA	study_accession	String	ENA study accession number to associate submissions with		Required	Terra_2_ENA	general	
Terra_2_ENA	terra_project_name	String	The Terra project containing the data table		Required	Terra_2_ENA	general	
Terra_2_ENA	terra_table_name	String	The name of the Terra data table containing sample data		Required	Terra_2_ENA	general	
Terra_2_ENA	terra_workspace_name	String	The Terra workspace containing the data table		Required	Terra_2_ENA	general	
Terra_2_GISAID	client_id	String	This value should be filled with the client-ID provided by GISAID		Required	Terra_2_GISAID	general	
Terra_2_GISAID	concatenated_fastas	File	The GISAID FASTA file generated by Mercury_Prep_N_Batch (or Mercury_Prep)		Required	Terra_2_GISAID	general	
Terra_2_GISAID	concatenated_metadata	File	The GISAID metadata file generated by Mercury_Prep_N_Batch (or Mercury_Prep)		Required	Terra_2_GISAID	general	
Terra_2_NCBI	bioproject	String	BioProject accession that the samples will be submitted to		Required	Terra_2_NCBI	general	
Terra_2_NCBI	biosample_package	String	The BioSample package that the samples will be submitted under		Required	Terra_2_NCBI	general	
Terra_2_NCBI	ncbi_config_js	File	Configuration file that contains your username and password for the NCBI FTP		Required	Terra_2_NCBI	general	
Terra_2_NCBI	project_name	String	The name of your Terra project. You can find this information in the url of the webpage you are on. It is the section right after "#workspaces/"		Required	Terra_2_NCBI	general	
Terra_2_NCBI	sample_names	Array[String]	The list of samples you want to submit		Required	Terra_2_NCBI	general	
Terra_2_NCBI	sra_transfer_gcp_bucket	String	Google bucket where your SRA reads will be temporarily stored before transferring to SRA		Required	Terra_2_NCBI	general	
Terra_2_NCBI	table_name	String	The name of the Terra table where your samples are found		Required	Terra_2_NCBI	general	
Terra_2_NCBI	workspace_name	String	The name of the workspace where your samples are found		Required	Terra_2_NCBI	general	
theiacov_clearlabs	primer_bed	File	The bed file containing the primers used when sequencing was performed		Required	TheiaCoV_ClearLabs	general	
theiacov_clearlabs	read1	File	Clear Dx-produced read file in FASTQ file format (compression optional)		Required	TheiaCoV_ClearLabs	general	
theiacov_clearlabs	samplename	String	The name of the sample being analyzed		Required	TheiaCoV_ClearLabs	general	
theiacov_fasta	assembly_fasta	File	Input assembly FASTA file. Must contain either all 8 influenza genome segments or a single segment provided in multi-FASTA format.		Required	TheiaCoV_FASTA	general	
theiacov_fasta	input_assembly_method	String	Method used to generate the assembly file		Required	TheiaCoV_FASTA	general	
theiacov_fasta	samplename	String	The name of the sample being analyzed		Required	TheiaCoV_FASTA	general	
theiacov_fasta	seq_method	String	The sequencing methodology used to generate the input read data		Required	TheiaCoV_FASTA	general	
theiacov_fasta_batch	assembly_fastas	Array[File]	The assembly files for your samples in FASTA format		Required	TheiaCoV_FASTA_Batch	general	
theiacov_fasta_batch	bucket_name	String	The GCP bucket for the workspace where the TheiaCoV_FASTA_Batch output files are saved. We recommend using a unique GSURI for the bucket associated with your Terra workspace. The root GSURI is accessible in the Dashboard page of your workspace in the "Cloud Information" section.Do not include the prefix gs:// in the stringExample: ""fc-c526190d-4332-409b-8086-be7e1af9a0b6/theiacov_fasta_batch-2024-04-15-seq-run-1/		Required	TheiaCoV_FASTA_Batch	general	
theiacov_fasta_batch	project_name	String	The name of the Terra project where the data can be found. Example: "my-terra-project"		Required	TheiaCoV_FASTA_Batch	general	
theiacov_fasta_batch	samplenames	Array[String]	The names of the samples being analyzed		Required	TheiaCoV_FASTA_Batch	general	
theiacov_fasta_batch	table_name	String	The name of the Terra table where the data can be found. Example: "sars-cov-2-sample"		Required	TheiaCoV_FASTA_Batch	general	
theiacov_fasta_batch	workspace_name	String	The name of the Terra workspace where the data can be found. Example "my-terra-workspace"		Required	TheiaCoV_FASTA_Batch	general	
theiacov_illumina_pe	read1	File	Illumina forward read file in FASTQ file format (compression optional)		Required	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	read2	File	Illumina reverse read file in FASTQ file format (compression optional)		Required	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	samplename	String	The name of the sample being analyzed		Required	TheiaCoV_Illumina_PE	general	
theiacov_illumina_se	read1	File	Illumina forward read file in FASTQ file format (compression optional)		Required	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	samplename	String	The name of the sample being analyzed		Required	TheiaCoV_Illumina_SE	general	
theiacov_ont	read1	File	ONT read file in FASTQ file format (compression optional)		Required	TheiaCoV_ONT	general	
theiacov_ont	samplename	String	The name of the sample being analyzed		Required	TheiaCoV_ONT	general	
theiaeuk_illumina_pe	read1	File	FASTQ file containing read1 sequences		Required	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	read2	File	FASTQ file containing read2 sequences		Required	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	samplename	String	Sample name for the analysis		Required	TheiaEuk_Illumina_PE	general	
theiaeuk_ont	read1	File	ONT read file in FASTQ file format (compression optional)		Required	TheiaEuk_ONT	general	
theiaeuk_ont	samplename	String	The name of the sample being analyzed		Required	TheiaEuk_ONT	general	
theiameta_illumina_pe	read1	File	Illumina forward read file in FASTQ file format (compression optional)		Required	TheiaMeta_Illumina_PE	general	
theiameta_illumina_pe	read2	File	Illumina reverse read file in FASTQ file format (compression optional)		Required	TheiaMeta_Illumina_PE	general	
theiameta_illumina_pe	samplename	String	The name of the sample being analyzed		Required	TheiaMeta_Illumina_PE	general	
theiaprok_fasta	assembly_fasta	File	The assembly file for your sample in FASTA format		Required	TheiaProk_FASTA	general	
theiaprok_fasta	samplename	String	The name of the sample being analyzed		Required	TheiaProk_FASTA	general	
theiaprok_illumina_pe	read1	File	Illumina forward read file in FASTQ file format (compression optional)		Required	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	read2	File	Illumina reverse read file in FASTQ file format (compression optional)		Required	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	samplename	String	The name of the sample being analyzed		Required	TheiaProk_Illumina_PE	general	
theiaprok_illumina_se	read1	File	Illumina forward read file in FASTQ file format (compression optional)		Required	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	samplename	String	The name of the sample being analyzed		Required	TheiaProk_Illumina_SE	general	
theiaprok_ont	read1	File	ONT read file in FASTQ file format (compression optional)		Required	TheiaProk_ONT	general	
theiaprok_ont	samplename	String	The name of the sample being analyzed		Required	TheiaProk_ONT	general	
theiavalidate	columns_to_compare	String	A comma-separated list of the columns the user wants to compare. Do not include whitespace.		Required	TheiaValidate	general	
theiavalidate	output_prefix	String	The prefix for the output files		Required	TheiaValidate	general	
theiavalidate	table1_name	String	The name of the first table		Required	TheiaValidate	general	
theiavalidate	table2_name	String	The name of the second table		Required	TheiaValidate	general	
theiavalidate	terra_project1_name	String	The name of the Terra project where table1_name can be found		Required	TheiaValidate	general	
theiavalidate	terra_workspace1_name	String	The name of the Terra workspace where table1_name can be found		Required	TheiaValidate	general	
theiaviral_illumina_pe	read1	File	llumina forward read file in FASTQ file format (compression optional)		Required	TheiaViral_Illumina_PE	general	
theiaviral_illumina_pe	read2	File	llumina reverse read file in FASTQ file format (compression optional)		Required	TheiaViral_Illumina_PE	general	
theiaviral_illumina_pe	samplename	String	Nme of the sample being analyzed		Required	TheiaViral_Illumina_PE	general	
theiaviral_illumina_pe	taxon	String	Taxon ID or organism name of interest		Required	TheiaViral_Illumina_PE	general	
theiaviral_ont	read1	File	Base-called ONT read file in FASTQ file format (compression optional)		Required	TheiaViral_ONT	general	
theiaviral_ont	samplename	String	Name of the sample being analyzed		Required	TheiaViral_ONT	general	
theiaviral_ont	taxon	String	Taxon ID or organism name of interest		Required	TheiaViral_ONT	general	
theiaviral_panel	read1	File	Illumina forward read file in FASTQ file format (compression optional)		Required	TheiaViral_Panel	general	
theiaviral_panel	read2	File	Illumina reverse read file in FASTQ file format (compression optional)		Required	TheiaViral_Panel	general	
theiaviral_panel	samplename	String	Name of the sample being analyzed		Required	TheiaViral_Panel	general	
theiaviral_panel	source_table_name	String	Name of the Terra table the source reads originate from. This is used for identifying originating location of extracted assemblies once added to output tables.		Required	TheiaViral_Panel	general	
theiaviral_panel	terra_project	String	The Terra project containing the data table		Required	TheiaViral_Panel	general	
theiaviral_panel	terra_workspace	String	The Terra workspace containing the data table		Required	TheiaViral_Panel	general	
transfer_column_content	files_to_transfer	Array[String]	The column that has the files you want to transfer.		Required	Transfer_Column_Content	general	
transfer_column_content	target_bucket	String	The GS URI[^1] of the target storage bucket. Note: Do not include spaces, but do include the gs:// at the beginning of the bucket URI		Required	Transfer_Column_Content	general	
usher_workflow	assembly_fasta	Array[File]	The assembly files for your samples in FASTA format; can either be a set of samples, an individual sample, or multiple individual samples		Required	Usher	general	
usher_workflow	organism	String	What organism to run UShER on; the following organism have default global phylogenies and reference files provided: sars-cov-2, mpox, RSV-A, RSV-B.		Required	Usher	general	
usher_workflow	tree_name	String	The output prefix for the uncondensed tree output and the clades output.		Required	Usher	general	
vadr_update	genome_fasta	File	Consensus genome assembly		Required	VADR_Update	general	
wf_microreact_export	id_column	String	Column used as the unique identifier for Microreact		Required	Microreact_Export	general	
wf_microreact_export	project_name	String	Name of the project to be uploaded to Microreact		Required	Microreact_Export	general	
wf_microreact_export	set_id	String	ID column of the set being run		Required	Microreact_Export	general	
wf_microreact_export	terra_project_name	String	Terra project location where metadata Terra table is housed		Required	Microreact_Export	general	
wf_microreact_export	terra_table_name	String	Name of the Terra table used as the Microreact metadata table		Required	Microreact_Export	general	
wf_microreact_export	terra_workspace_name	String	Terra workspace location where metadata Terra table is housed		Required	Microreact_Export	general	
zip_column_content	files_to_zip	Array[File]	The column that has the files you want to zip.		Required	Zip_Column_Content	general	
zip_column_content	zipped_file_name	String	The name you want your zipped file to have. The .zip file extension will be added to this name.		Required	Zip_Column_Content	general	
abricate	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
abricate	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
abricate	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-abaum-plasmid	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
abricate	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
abricate	min_percent_coverage	Int	Minimum DNA %coverage for the Abricate task	80	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
abricate	min_percent_identity	Int	Minimum DNA %identity for the Abricate task	80	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
add_biosample_accessions	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Terra_2_NCBI	runtime	
add_biosample_accessions	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Terra_2_NCBI	runtime	
add_biosample_accessions	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16	Optional	Terra_2_NCBI	docker	
add_biosample_accessions	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Terra_2_NCBI	runtime	
amr_search	cpu	Int	Number of CPUs to allocate to the task	2	Optional	AMR_Search	runtime	
amr_search	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	AMR_Search	runtime	
amr_search	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.1	Optional	AMR_Search	docker	
amr_search	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	AMR_Search	runtime	
amrfinderplus_nuc	annotation_assembly	File	Assembly file from annotation software such as Prokka or Bakta, used for utilizing protein fasta and GFF files.		Optional	AMRFinderPlus	general	
amrfinderplus_nuc	annotation_format	String	The format of the annotation files		Optional	AMRFinderPlus	general	
amrfinderplus_nuc	cpu	Int	Number of CPUs to allocate to the task	2	Optional	AMRFinderPlus	runtime	
amrfinderplus_nuc	detailed_drug_class	Boolean	If set to true, amrfinderplus_amr_classes and amrfinderplus_amr_subclasses outputs will be created	False	Optional	AMRFinderPlus	general	
amrfinderplus_nuc	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	AMRFinderPlus	runtime	
amrfinderplus_nuc	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:4.0.23-2025-07-16.1	Optional	AMRFinderPlus	docker	
amrfinderplus_nuc	gff	File	GFF file provided by Prokka or Bakta when amrfinder_use_gff is set to true. This file is used to determine the location of AMR genes in the genome.		Optional	AMRFinderPlus	general	
amrfinderplus_nuc	hide_point_mutations	Boolean	If set to true, the output File amrfinderplus_all_report will not include any POINT mutations identified by AMRFinderPlus.	False	Optional	AMRFinderPlus	general	
amrfinderplus_nuc	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	AMRFinderPlus	runtime	
amrfinderplus_nuc	min_percent_coverage	Float	Minimum proportion of reference gene covered for a BLAST-based hit (Methods BLAST or PARTIAL). Attribute should be a float ranging from 0-1, such as 0.6 (equal to 60% coverage)	0.5	Optional	AMRFinderPlus	general	
amrfinderplus_nuc	min_percent_identity	Float	Minimum identity for a blast-based hit hit (Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs. Attribute should be a float ranging from 0-1, such as 0.95 (equal to 95% identity)	0.9	Optional	AMRFinderPlus	general	
amrfinderplus_nuc	organism	String	If provided, this input will override the taxonomic assignment made by GAMBIT and launch the relevant taxon-specific submodules. It will also modify the organism flag used by AMRFinderPlus. Example format: "Salmonella enterica"		Optional	AMRFinderPlus	general	
amrfinderplus_nuc	protein_fasta	File	Protein FASTA from annotation software such as Prokka or Bakta. Utilized when amrfinder_use_gff is set to true		Optional	AMRFinderPlus	general	
amrfinderplus_nuc	separate_betalactam_genes	Boolean	Report beta-Lactam AMR genes separated out by all beta-lactam and the respective beta-lactam subclasses	False	Optional	AMRFinderPlus	general	
amrfinderplus_nuc	use_gff	Boolean	Whether or not to use the GFF and protein FASTA files for AMRFinderPlus	False	Optional	AMRFinderPlus	general	
amrfinderplus_task	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
amrfinderplus_task	detailed_drug_class	Boolean	If set to true, amrfinderplus_amr_classes and amrfinderplus_amr_subclasses outputs will be created	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
amrfinderplus_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
amrfinderplus_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:4.0.23-2025-07-16.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
amrfinderplus_task	hide_point_mutations	Boolean	If set to true, point mutations are not reported	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
amrfinderplus_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
amrfinderplus_task	min_percent_coverage	Float	Minimum proportion of reference gene covered for a BLAST-based hit (Methods BLAST or PARTIAL)." Attribute should be a float ranging from 0-1, such as 0.6 (equal to 60% coverage)	0.5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
amrfinderplus_task	min_percent_identity	Float	Minimum identity for a blast-based hit hit (Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs. Attribute should be a float ranging from 0-1, such as 0.95 (equal to 95% identity)	0.9	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
amrfinderplus_task	separate_betalactam_genes	Boolean	Report beta-Lactam AMR genes separated out by all beta-lactam and the respective beta-lactam subclasses	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
ani	ani_threshold	Float	ANI value threshold must be surpassed in order to output the ani_top_species_match. If a genome does not surpass this threshold (and the percent_bases_aligned_threshold) then the ani_top_species_match output String will show a warning instead of a genus & species.	80.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
ani	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
ani	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
ani	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mummer:4.0.0-rgdv2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
ani	mash_filter	Float	Mash distance threshold over which ANI is not calculated	0.9	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
ani	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
ani	percent_bases_aligned_threshold	Float	Threshold regarding the proportion of bases aligned between the query genome and reference genome. If a genome does not surpass this threshold (and the ani_threshold) then the ani_top_species_match output String will show a warning instead of a genus & species.	70.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
ani	ref_genome	File	If not set, uses all 43 genomes in RGDv2		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
arln_stats	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
arln_stats	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
arln_stats	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/arln_stats:1.0.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
arln_stats	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
arln_stats	read1_clean	File	Internal component, do not modify		Optional	TheiaProk_FASTA	general	
arln_stats	read1_raw	File	Internal component, do not modify		Optional	TheiaProk_FASTA	general	
arln_stats	read2_clean	File	Internal component, do not modify		Optional	TheiaProk_FASTA, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
arln_stats	read2_raw	File	Internal component, do not modify		Optional	TheiaProk_FASTA, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
assembled_reads_percent	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
assembled_reads_percent	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
assembled_reads_percent	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17	Optional	TheiaMeta_Illumina_PE	docker	
assembled_reads_percent	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
assembly_fetch	assembly_fasta	File	The assembly file for your sample in FASTA format		Optional	Assembly_Fetch	general	
assembly_fetch	ncbi_accession	String	NCBI accession passed to the NCBI datasets task to be downloaded. Example: GCF_000006945.2 (Salmonella enterica subsp. enterica, serovar Typhimurium str. LT2 reference genome)		Optional	Assembly_Fetch	general	
augur	alignment_fasta	File	The alignment fasta file in Augur		Optional	Augur	general	
augur	augur_id_column	String	Column name of sequence IDs	strain	Optional	Augur	general	
augur	augur_trait_columns	String	Comma-separated list of columns to use for trait analysis in Augur		Optional	Augur	general	
augur	auspice_config	File	Auspice config file for customizing visualizations; takes priority over the other customization values available for augur_export	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, a minimal auspice config file is provided to prevent workflow failure, "gs://theiagen-public-resources-rp/empty_files/minimal-auspice-config.json", but will not be as useful as an organism specific config file.	Optional	Augur	general	True
augur	clades_tsv	File	TSV file containing clade mutation positions in four columns	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, an empty clades file is provided to prevent workflow failure, "gs://theiagen-public-resources-rp/empty_files/minimal-clades.tsv", but will not be as useful as an organism specific clades file.	Optional, Required	Augur	general	True
augur	extract_clade_mutations	Boolean	Generate a "clades.tsv" using "clade_membership" column metadata (overrides clades_tsv)	False	Optional	Augur	general	
augur	flu_segment	String	Required if organism = "flu". The name of the segment to be analyzed; options: "HA" or "NA"	HA	Optional	Augur	general	
augur	flu_subtype	String	Required if organism = "flu". The subtype of the flu samples being analyzed; options: "H1N1", "H3N2", "Victoria", "Yamagata", "H5N1"	N/A	Optional, Required	Augur	general	True
augur	lat_longs_tsv	File	Tab-delimited file of geographic location names with corresponding latitude and longitude values	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, a minimal lat-long file is provided to prevent workflow failure, "gs://theiagen-public-resources-rp/empty_files/minimal-lat-longs.tsv", but will not be as useful as a detailed lat-longs file covering all the locations for the samples to be visualized.	Optional	Augur	general	True
augur	midpoint_root_tree	Boolean	Boolean variable that will instruct the workflow to reroot the tree at the midpoint	True	Optional	Augur	general	
augur	min_date	Float	Minimum date to begin filtering or frequencies calculations	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, the default value is 0.0	Optional	Augur	general	True
augur	min_num_unambig	Int	Minimum number of called bases in genome to pass prefilter	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, the default value is 0	Optional	Augur	general	True
augur	narrow_bandwidth	Float	The bandwidth for the narrow KDE	0.08333	Optional	Augur	general	True
augur	organism	String	Organism used to preselect default values; options: "sars-cov-2", "flu", "mpxv", "rsv-a", "rsv-b"	sars-cov-2	Optional	Augur	general	
augur	outgroup_root	String	Tip name to root phylogenetic tree upon (overrides midpoint root)		Optional	Augur	general	
augur	pivot_interval	Int	Number of units between pivots	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, the default value is 3	Optional	Augur	general	True
augur	proportion_wide	Float	The proportion of the wide bandwidth to use in the KDE mixture model	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, the default value is 0.2	Optional	Augur	general	True
augur	reference_fasta	File	The reference FASTA file used to align the genomes and build the trees	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, a reference fasta file must be provided otherwise the workflow fails.	Optional, Required	Augur	reference	True
augur	reference_genbank	File	The GenBank .gb file for the same reference genome used for the reference_fasta	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>.	Optional, Required	Augur	reference	True
augur	remove_reference	Boolean	Whether or not to remove the reference in Augur	False	Optional	Augur	general	True
augur	sample_metadata_tsvs	Array[File]	An array of the metadata files produced in Augur_Prep_PHB		Optional	Augur	general	
augur_align	cpu	Int	Number of CPUs to allocate to the task	64	Optional	Augur	runtime	
augur_align	disk_size	Int	Amount of storage (in GB) to allocate to the task	750	Optional	Augur	runtime	
augur_align	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/augur:31.5.0	Optional	Augur	docker	
augur_align	fill_gaps	Boolean	If true, gaps represent missing data rather than true indels and so are replaced by N after aligning.	False	Optional	Augur	general	
augur_align	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	128	Optional	Augur	runtime	
augur_ancestral	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Augur	runtime	
augur_ancestral	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Augur	runtime	
augur_ancestral	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/augur:31.5.0	Optional	Augur	docker	
augur_ancestral	infer_ambiguous	Boolean	If true, infer nucleotides and ambiguous sites and replace with most likely	False	Optional	Augur	general	
augur_ancestral	inference	String	Calculate joint or marginal maximum likelihood ancestral sequence states; options: "joint", "marginal"	joint	Optional	Augur	general	
augur_ancestral	keep_ambiguous	Boolean	If true, do not infer nucleotides at ambiguous (N) sides	False	Optional	Augur	general	
augur_ancestral	keep_overhangs	Boolean	If true, do not infer nucleotides for gaps on either side of the alignment	False	Optional	Augur	general	
augur_ancestral	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	50	Optional	Augur	runtime	
augur_clades	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur	runtime	
augur_clades	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Augur	runtime	
augur_clades	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/augur:31.5.0	Optional	Augur	docker	
augur_clades	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Augur	runtime	
augur_export	colors_tsv	File	Custom color defintiions, one per line in the format TRAIT_TYPE\tTRAIT_VALUE\tHEX_CODE		Optional	Augur	general	
augur_export	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Augur	runtime	
augur_export	description_md	File	Markdown file with description of build and/or acknowledgements		Optional	Augur	general	
augur_export	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Augur	runtime	
augur_export	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/augur:31.5.0	Optional	Augur	docker	
augur_export	include_root_sequence	Boolean	Export an additional JSON containing the root sequence used to identify mutations	False	Optional	Augur	general	
augur_export	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	64	Optional	Augur	runtime	
augur_export	title	String	The title to be displayed by auspice		Optional	Augur	general	
augur_prep	clade	String	Clade membership metadata		Optional	Augur_Prep	general	
augur_prep	collection_date	String	Collection date of the sample		Optional	Augur_Prep	general	
augur_prep	country	String	Country where sample was collected		Optional	Augur_Prep	general	
augur_prep	division	String	Sub-national location (e.g. state/province) where sample was collected		Optional	Augur_Prep	general	
augur_prep	location	String	Sub-divisional location (e.g. county) where sample was collected 		Optional	Augur_Prep	general	
augur_prep	pango_lineage	String	The Pangolin lineage of the sample		Optional	Augur_Prep	general	
augur_prep	region	String	Continental/regional location where sample was collected		Optional	Augur_Prep	general	
augur_refine	branch_length_inference	String	Branch length mode of timetree to use; options: "auto", "joint", "marginal", "input"	auto	Optional	Augur	general	
augur_refine	clock_filter_iqd	Int	Remove tips that deviate more than n_iqd interquartile ranges from the root-to-tip vs time regression	4	Optional	Augur	general	
augur_refine	clock_rate	Float	Fixed clock rate to use for time tree calculations		Optional	Augur	general	
augur_refine	clock_std_dev	Float	Standard deviation of the fixed clock_rate estimate		Optional	Augur	general	
augur_refine	coalescent	String	Coalescent time scale in units of inverse clock rate (float), optimize as scalar ("opt") or skyline ("skyline")		Optional	Augur	general	
augur_refine	covariance	Boolean	If true, account for covariation when estimating rates and/or rerooting	True	Optional	Augur	general	
augur_refine	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Augur	runtime	
augur_refine	date_confidence	Boolean	If true, calculate confidence intervals for node dates	True	Optional	Augur	general	
augur_refine	date_inference	String	Assign internal nodes to their marginally most likely dates; options: "joint", "marginal"	marginal	Optional	Augur	general	
augur_refine	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Augur	runtime	
augur_refine	divergence_units	String	Units in which sequence divergences is exported; options: "mutations" or "mutations-per-site"	mutations	Optional	Augur	general	
augur_refine	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/augur:31.5.0	Optional	Augur	docker	
augur_refine	gen_per_year	Int	Number of generations per year	50	Optional	Augur	general	
augur_refine	keep_polytomies	Boolean	If true, don't attempt to resolve polytomies	False	Optional	Augur	general	
augur_refine	keep_root	Boolean	If true, do not reroot the tree; use it as-is (overrides anything specified by root)	True	Optional	Augur	general	
augur_refine	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	50	Optional	Augur	runtime	
augur_refine	precision	Int	Precision used by TreeTime to determine the number of grid points that are used for the evaluation of the branch length interpolation objects. Values range from 0 (rough) to 3 (ultra fine) and default to 'auto'	'auto'	Optional	Augur	general	True
augur_refine	root	String	Rooting mechanism; options: "best", "least-squares", "min_dev", "oldest", etc.		Optional	Augur	general	
augur_traits	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Augur	runtime	
augur_traits	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Augur	runtime	
augur_traits	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/augur:31.5.0	Optional	Augur	docker	
augur_traits	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	30	Optional	Augur	runtime	
augur_traits	metadata_id_columns	String	The names of possible metadata columns containing identifier information, ordered by priority	'strain' 'name'	Optional	Augur	general	
augur_traits	weights	File	a dictionary of key/value mappings in JSON format used to weight KDE tip frequencies		Optional	Augur	general	
augur_translate	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur	runtime	
augur_translate	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Augur	runtime	
augur_translate	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/augur:31.5.0	Optional	Augur	docker	
augur_translate	genes	File	A file containing a list of genes to translate (from nucleotides to amino acids)		Optional	Augur	general	
augur_translate	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Augur	runtime	
augur_tree	cpu	Int	Number of CPUs to allocate to the task	64	Optional	Augur	runtime	
augur_tree	disk_size	Int	Amount of storage (in GB) to allocate to the task	750	Optional	Augur	runtime	
augur_tree	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/augur:31.5.0	Optional	Augur	docker	
augur_tree	exclude_sites	File	File of one-based sites to exclude for raw tree building (BED format in .bed files, DRM format in tab-delimited files, or one position per line)		Optional	Augur	general	
augur_tree	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Augur	runtime	
augur_tree	method	String	The method used to build the tree. Options: "fasttree", "raxml", "iqtree" (default)	iqtree	Optional	Augur	general	
augur_tree	override_default_args	Boolean	If true, override default tree builder arguments instead of augmenting them	False	Optional	Augur	general	
augur_tree	substitution_model	String	The substitution model to use; only available for iqtree. Specify "auto" to run ModelTest; model options can be found here	GTR	Optional	Augur	general	
augur_tree	tree_builder_args	String	Additional tree builder arguments either augmenting or overriding the default arguments. FastTree defaults: "-nt -nosupport". RAxML defaults: "-f d -m GTRCAT -c 25 -p 235813". IQ-TREE defaults: "-ninit 2 -n 2 -me 0.05 -nt AUTO -redo"		Optional	Augur	general	
bakta	bakta_opts	String	Parameters to pass to bakta from <https://github.com/oschwengers/bakta#usage>		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
bakta	compliant	Boolean	If true, forces Genbank/ENA/DDJB compliant headers in Bakta output files	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
bakta	cpu	Int	Number of CPUs to allocate to the task	8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
bakta	disk_size	Int	Amount of storage (in GB) to allocate to the task	200	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
bakta	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/bakta:1.10.3	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
bakta	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	24	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
bakta	prodigal_tf	File	Prodigal training file to use for CDS prediction by bakta		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
bakta	proteins	File	Fasta file of trusted protein sequences for CDS annotation		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
basespace_fetch	api_server	String	The API server is the web address to which data transfer requests can be sent by the workflow.	https://api.basespace.illumina.com	Optional	BaseSpace_Fetch	general	
basespace_fetch	basespace_sample_id	String	The BaseSpace sample ID is an optional additional identifier used in BaseSpace. If a sample has a BaseSpace sample ID it should be available on the sample sheet and must be included in the metadata sheet upload prior to running BaseSpace_Fetch.		Optional	BaseSpace_Fetch	general	
bbduk	adapters_fasta	File	FASTA with adapter sequences to be removed		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
bbduk	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
bbduk	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
bbduk	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/bbtools:39.38_python	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	docker	
bbduk	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
bbduk	phix_fasta	File	FASTA file with phiX sequences to be removed		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
bbduk	primers_fasta	File	FASTA file with primer sequences to be removed		Optional	TheiaViral_Illumina_PE	general	
bbduk	primers_fasta	File	Internal component, do not modify		Optional	TheiaViral_Panel	general	
bbduk	primers_hamming_distance	Int	Hamming distance allowed for primer matching	1	Optional	TheiaViral_Illumina_PE	general	
bbduk	primers_hamming_distance	Int	Internal component, do not modify	1	Optional	TheiaViral_Panel	general	
bbduk	primers_literal	String	Comma-delimited list of primer sequences		Optional	TheiaViral_Illumina_PE	general	
bbduk	primers_literal	String	Internal component, do not modify		Optional	TheiaViral_Panel	general	
bbduk	primers_mask_middle	Boolean	Treat the middle base of a primer kmer as a wildcard to increase sensitivity in the presence of errors	False	Optional	TheiaViral_Illumina_PE	general	
bbduk	primers_mask_middle	Boolean	Internal component, do not modify	False	Optional	TheiaViral_Panel	general	
bbduk	primers_max_start_offset	Int	Maximum offset from edge of read for primers to begin	10	Optional	TheiaViral_Illumina_PE	general	
bbduk	primers_max_start_offset	Int	Internal component, do not modify	10	Optional	TheiaViral_Panel	general	
bbduk	primers_reverse_complement	Boolean	Whether to search for reverse complement primers	True	Optional	TheiaViral_Illumina_PE	general	
bbduk	primers_reverse_complement	Boolean	Internal component, do not modify	True	Optional	TheiaViral_Panel	general	
bcftools_consensus	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_ONT	runtime	
bcftools_consensus	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
bcftools_consensus	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/bcftools:1.20	Optional	TheiaViral_ONT	docker	
bcftools_consensus	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaViral_ONT	runtime	
biosample_submit_tsv_ftp_upload	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Terra_2_NCBI	runtime	
biosample_submit_tsv_ftp_upload	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Terra_2_NCBI	runtime	
biosample_submit_tsv_ftp_upload	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/broadinstitute/ncbi-tools:2.10.7.10	Optional	Terra_2_NCBI	docker	
biosample_submit_tsv_ftp_upload	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Terra_2_NCBI	runtime	
busco	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
busco	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
busco	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.7.1_cv1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
busco	eukaryote	Boolean	Assesses eukaryotic organisms, rather than prokaryotic organisms	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
busco	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
bwa	cpu	Int	Number of CPUs to allocate to the task	6	Optional	Freyja_FASTQ, TheiaMeta_Illumina_PE, TheiaViral_Illumina_PE	runtime	
bwa	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ, TheiaMeta_Illumina_PE, TheiaViral_Illumina_PE	runtime	
bwa	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan	Optional	Freyja_FASTQ, TheiaMeta_Illumina_PE, TheiaViral_Illumina_PE	docker	
bwa	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Freyja_FASTQ, TheiaMeta_Illumina_PE, TheiaViral_Illumina_PE	runtime	
calculate_coverage	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
calculate_coverage	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
calculate_coverage	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/bedtools:2.31.0	Optional	TheiaMeta_Illumina_PE	docker	
calculate_coverage	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
calculate_coverage_paf	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
calculate_coverage_paf	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
calculate_coverage_paf	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/quay/ubuntu:latest	Optional	TheiaMeta_Illumina_PE	docker	
calculate_coverage_paf	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
cat_files	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Augur, Concatenate_Column_Content	runtime	
cat_files	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Augur, Concatenate_Column_Content	runtime	
cat_files	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	Augur, Concatenate_Column_Content	docker	
cat_files	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Augur, Concatenate_Column_Content	runtime	
cat_files	skip_extra_headers	Boolean	If the files you are concatenating have identical headers, you can include only the first instance of the header and skip all of the others so they do not appear duplicated in the concatenated file. To activate this, set to true.	False	Optional	Concatenate_Column_Content	general	
cat_files_fasta	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_FASTA_Batch	runtime	
cat_files_fasta	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_FASTA_Batch	runtime	
cat_files_fasta	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	TheiaCoV_FASTA_Batch	docker	
cat_files_fasta	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_FASTA_Batch	runtime	
cat_lanes	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Concatenate_Illumina_Lanes, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
cat_lanes	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Concatenate_Illumina_Lanes, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
cat_lanes	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.2	Optional	Concatenate_Illumina_Lanes, TheiaViral_Illumina_PE, TheiaViral_Panel	docker	
cat_lanes	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Concatenate_Illumina_Lanes, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
cat_lanes	read1_lane3	File	Internal component, do not modify		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
cat_lanes	read1_lane4	File	Internal component, do not modify		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
cat_lanes	read2_lane3	File	Internal component, do not modify		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
cat_lanes	read2_lane4	File	Internal component, do not modify		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
cat_ont_barcodes	cpu	Int	Number of CPUs to allocate to the task	2	Optional	ONT_Barcode_Concatenation	runtime	
cat_ont_barcodes	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	ONT_Barcode_Concatenation	runtime	
cat_ont_barcodes	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/ont-barcodes:0.0.2	Optional	ONT_Barcode_Concatenation	docker	
cat_ont_barcodes	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	ONT_Barcode_Concatenation	runtime	
cat_variants	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	Find_Shared_Variants	docker	
centroid	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Snippy_Streamline, Snippy_Streamline_FASTA	runtime	
centroid	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Snippy_Streamline, Snippy_Streamline_FASTA	runtime	
centroid	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/centroid:0.1.0	Optional	Snippy_Streamline, Snippy_Streamline_FASTA	docker	
centroid	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Snippy_Streamline, Snippy_Streamline_FASTA	runtime	
cg_pipeline_clean	cg_pipe_opts	String	Options to pass to CG-Pipeline for clean read assessment	--fast	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
cg_pipeline_clean	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
cg_pipeline_clean	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
cg_pipeline_clean	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/lyveset:1.1.4f	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	docker	
cg_pipeline_clean	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
cg_pipeline_clean	read2	File	Internal component, do not modify		Optional	TheiaProk_Illumina_SE	general	
cg_pipeline_raw	cg_pipe_opts	String	Options to pass to CG-Pipeline for raw read assessment	--fast	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
cg_pipeline_raw	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
cg_pipeline_raw	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
cg_pipeline_raw	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/lyveset:1.1.4f	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	docker	
cg_pipeline_raw	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
cg_pipeline_raw	read2	File	Internal component, do not modify		Optional	TheiaProk_Illumina_SE	general	
cg_reorder_matrix	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Snippy_Tree	runtime	
cg_reorder_matrix	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Tree	runtime	
cg_reorder_matrix	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1	Optional	Snippy_Tree	docker	
cg_reorder_matrix	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Snippy_Tree	runtime	
cg_reorder_matrix	outgroup_root	String	Tip name to root phylogenetic tree upon (overrides midpoint root)		Optional	Snippy_Tree	general	
checkv_consensus	checkv_db	File	CheckV database file	gs://theiagen-public-resources-rp/reference_data/databases/checkv/checkv-db-v1.5.tar.gz	Optional	TheiaViral_ONT	database	
checkv_consensus	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
checkv_consensus	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
checkv_consensus	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/checkv:1.0.3	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
checkv_consensus	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
checkv_denovo	checkv_db	File	CheckV database file	gs://theiagen-public-resources-rp/reference_data/databases/checkv/checkv-db-v1.5.tar.gz	Optional	TheiaViral_ONT	database	
checkv_denovo	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
checkv_denovo	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
checkv_denovo	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/checkv:1.0.3	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
checkv_denovo	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
chunk_files	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Dorado_Basecalling	runtime	
chunk_files	disk_size	Int	Amount of storage (in GB) to allocate to the task	25	Optional	Dorado_Basecalling	runtime	
chunk_files	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	Dorado_Basecalling	docker	
chunk_files	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Dorado_Basecalling	runtime	
clade_extraction_task	allow_missing_tips	Boolean	Generate clades if metadata is missing for some tips	True	Optional	Augur	general	
clade_extraction_task	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur	runtime	
clade_extraction_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	Augur	runtime	
clade_extraction_task	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/extract_clade_mutations:0.0.1	Optional	Augur	docker	
clade_extraction_task	memory	Int	Amount of memory (in GB) to allocate to the task	4	Optional	Augur	runtime	
clade_extraction_task	skip_singleton_clades	Boolean	Skip extracting sequence signatures for clades with a single tip	True	Optional	Augur	general	
cladetyper	cpu	Int	Number of CPUs to allocate to the task	8	Optional	Cauris_CladeTyper	runtime	
cladetyper	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Cauris_CladeTyper	runtime	
cladetyper	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0	Optional	Cauris_CladeTyper	docker	
cladetyper	kmer_size	Int	The kmer size to use for generating the GAMBIT signatures file; see GAMBIT documentation for more details	11	Optional	Cauris_CladeTyper	general	
cladetyper	max_distance	Float	The maximum GAMBIT distance to report a clade hit	0.1	Optional	Cauris_CladeTyper	general	
cladetyper	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Cauris_CladeTyper	runtime	
cladetyper	ref_clade1	File	The reference assembly for clade 1	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.3_Cand_auris_B8441_V3_genomic.fasta	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade1_annotated	String	The path to the annotated reference for clade 1	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.3_Cand_auris_B8441_V3_genomic.gbff	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade2	File	The reference assembly for clade 2	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.fasta	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade2_annotated	String	The path to the annotated reference for clade 2	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.gbff	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade3	File	The reference assembly for clade 3	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.fasta	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade3_annotated	String	The path to the annotated reference for clade 3	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.gbff	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade4	File	The reference assembly for clade 4	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.fasta	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade4_annotated	String	The path to the annotated reference for clade 4	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.gbff	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade5	File	The reference assembly for clade 5	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.fasta	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade5_annotated	String	The path to the annotated reference for clade 5	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.gbff	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade6	File	The reference assembly for clade 6	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade6_GCA_032714025.1_ASM3271402v1_genomic.fasta	Optional	Cauris_CladeTyper	reference	
cladetyper	ref_clade6_annotated	String	The path to the annotated reference for clade 6		Optional	Cauris_CladeTyper	general	
clair3	clair3_model	String	Model to be used by Clair3	r1041_e82_400bps_sup_v500	Optional	TheiaViral_ONT	general	
clair3	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_ONT	runtime	
clair3	disable_phasing	Boolean	True/False that determines if variants should be called without whatshap phasing in full alignment calling	True	Optional	TheiaViral_ONT	general	
clair3	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
clair3	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/clair3-extra-models:1.0.10	Optional	TheiaViral_ONT	docker	
clair3	enable_gvcf	Boolean	True/False that determines if an additional GVCF output should generated	False	Optional	TheiaViral_ONT	general	
clair3	enable_haploid_precise	Boolean	True/False that determines haploid calling mode where only 1/1 is considered as a variant	True	Optional	TheiaViral_ONT	general	
clair3	include_all_contigs	Boolean	True/False that determines if all contigs should be included in the output	True	Optional	TheiaViral_ONT	general	
clair3	indel_min_af	Float	Minimum Indel AF required for a candidate variant	Default values are dependent on the sequencing platform. For ONT, 0.15	Optional	TheiaViral_ONT	general	True
clair3	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_ONT	runtime	
clair3	snp_min_af	Float	Minimum SNP allele frequency required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy	0.08	Optional	TheiaViral_ONT	general	
clair3	variant_quality	Int	If set, variants with >$qual will be marked PASS, or LowQual otherwise	2	Optional	TheiaViral_ONT	general	
clair3_variants	indel_min_af	Float	Minimum Indel AF required for a candidate variant		Optional	Clair3_Variants_ONT	general	
clair3_variants	snp_min_af	Float	Minimum SNP AF required for a candidate variant	0.08	Optional	Clair3_Variants_ONT	general	
clair3_variants_ont	clair3_cpu	Int	Number of CPUs to allocate to the task	4	Optional	Clair3_Variants_ONT	runtime	
clair3_variants_ont	clair3_disable_phasing	Boolean	Disable whatshap phasing	True	Optional	Clair3_Variants_ONT	general	
clair3_variants_ont	clair3_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Clair3_Variants_ONT	runtime	
clair3_variants_ont	clair3_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/clair3-extra-models:1.0.10	Optional	Clair3_Variants_ONT	docker	
clair3_variants_ont	clair3_enable_gvcf	Boolean	Output gVCF format	False	Optional	Clair3_Variants_ONT	general	
clair3_variants_ont	clair3_enable_haploid_precise	Boolean	Enable haploid precise calling, only 1/1 is considered as a variant	True	Optional	Clair3_Variants_ONT	general	
clair3_variants_ont	clair3_enable_long_indel	Boolean	Enable long indel calling	False	Optional	Clair3_Variants_ONT	general	
clair3_variants_ont	clair3_include_all_contigs	Boolean	Call variants on all contigs, should always be true for non-human samples	True	Optional	Clair3_Variants_ONT	general	
clair3_variants_ont	clair3_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Clair3_Variants_ONT	runtime	
clair3_variants_ont	clair3_model	String	Model name for variant calling (see supported models for available options)	r1041_e82_400bps_sup_v500	Optional	Clair3_Variants_ONT	general	
clair3_variants_ont	clair3_variant_quality	Int	Minimum variant quality score	2	Optional	Clair3_Variants_ONT	general	
clean_check_reads	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
clean_check_reads	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
clean_check_reads	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/bactopia/gather_samples:2.0.2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
clean_check_reads	max_genome_length	Int	Maximum genome length able to pass read screening	2673870	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
clean_check_reads	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
clean_check_reads	min_basepairs	Int	Minimum base pairs to pass read screening	15000	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
clean_check_reads	min_coverage	Int	Minimum coverage to pass read screening	10	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
clean_check_reads	min_genome_length	Int	Minimum genome length to pass read screening	1500	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
clean_check_reads	min_proportion	Int	Minimum read proportion to pass read screening	40	Optional	TheiaViral_Illumina_PE	general	
clean_check_reads	min_reads	Int	Minimum reads to pass read screening	50	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
clean_check_reads	workflow_series	String	Internal component, do not modify	theiaviral	Optional	TheiaEuk_ONT	general	
clockwork_decon_reads	cpu	Int	Number of CPUs to allocate to the task	16	Optional	TBProfiler_tNGS	runtime	
clockwork_decon_reads	disk_size	Int	Amount of storage (in GB) to allocate to the task	200	Optional	TBProfiler_tNGS	runtime	
clockwork_decon_reads	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/cdcgov/varpipe_wgs_with_refs:2bc7234074bd53d9e92a1048b0485763cd9bbf6f4d12d5a1cc82bfec8ca7d75e	Optional	TBProfiler_tNGS	docker	
clockwork_decon_reads	memory	Int	Amount of memory (in GB) to allocate to the task	64	Optional	TBProfiler_tNGS	runtime	
compare_two_tsvs	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaValidate	runtime	
compare_two_tsvs	debug_output	Boolean	Set to true to enable more outputs; useful when debugging	False	Optional	TheiaValidate	general	
compare_two_tsvs	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	TheiaValidate	runtime	
compare_two_tsvs	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/theiavalidate:1.1.2	Optional	TheiaValidate	docker	
compare_two_tsvs	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaValidate	runtime	
compare_two_tsvs	na_values	String	If the user knows a particular value in either table that they would like to be considered N/A, they can indicate those values in a comma-separated list here. Any changes here will overwrite the default and not append to the default list. Do not include whitespace.	-1.#IND,1.#QNAN,1.#IND,-1.#QNAN,#N/A,N/A,n/a,,#NA,NULL,null,NaN,-NaN,nan,-nan,None	Optional	TheiaValidate	general	True
concatenate_illumina_lanes	read1_lane3	File	The third lane for the forward reads		Optional	Concatenate_Illumina_Lanes	general	
concatenate_illumina_lanes	read1_lane4	File	The fourth lane for the forward reads		Optional	Concatenate_Illumina_Lanes	general	
concatenate_illumina_lanes	read2_lane1	File	The first lane for the reverse reads		Optional	Concatenate_Illumina_Lanes	general	
concatenate_illumina_lanes	read2_lane1	File	Internal component, do not modify		Optional	TheiaProk_Illumina_SE	general	
concatenate_illumina_lanes	read2_lane2	File	The second lane for the reverse reads		Optional	Concatenate_Illumina_Lanes	general	
concatenate_illumina_lanes	read2_lane2	File	Internal component, do not modify		Optional	TheiaProk_Illumina_SE	general	
concatenate_illumina_lanes	read2_lane3	File	The third lane for the reverse reads		Optional	Concatenate_Illumina_Lanes	general	
concatenate_illumina_lanes	read2_lane3	File	Internal component, do not modify		Optional	TheiaProk_Illumina_SE	general	
concatenate_illumina_lanes	read2_lane4	File	The fourth lane for the reverse reads		Optional	Concatenate_Illumina_Lanes	general	
concatenate_illumina_lanes	read2_lane4	File	Internal component, do not modify		Optional	TheiaProk_Illumina_SE	general	
concatenate_qc_metrics	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Snippy_Tree	runtime	
concatenate_qc_metrics	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Tree	runtime	
concatenate_qc_metrics	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	Snippy_Tree	docker	
concatenate_qc_metrics	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Snippy_Tree	runtime	
concatenate_variants	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	Snippy_Tree	docker	
consensus	char_unknown	String	Character used to represent unknown bases in the consensus sequence	N	Optional	TheiaViral_Illumina_PE	general	
consensus	count_orphans	Boolean	True/False that determines if anomalous read pairs are NOT skipped in variant calling. Anomalous read pairs are those marked in the FLAG field as paired in sequencing but without the properly-paired flag set.	True	Optional	TheiaViral_Illumina_PE	general	
consensus	cpu	Int	Number of CPUs to allocate to the task	8	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	runtime	
consensus	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Illumina_PE	runtime	
consensus	disable_baq	Boolean	True/False that determines if base alignment quality (BAQ) computation should be disabled during samtools mpileup before consensus generation	True	Optional	TheiaViral_Illumina_PE	general	
consensus	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT, TheiaViral_Illumina_PE	runtime	
consensus	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019-epi2me	Optional	TheiaCoV_ONT	docker	
consensus	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan	Optional	TheiaViral_Illumina_PE	docker	
consensus	max_depth	Int	For a given position, read at maximum INT number of reads per input file during samtools mpileup before consensus generation	600000	Optional	TheiaViral_Illumina_PE	general	
consensus	medaka_model	String	In order to obtain the best results, the appropriate model must be set to match the sequencer's basecaller model; this string takes the format of {pore}{device}{caller variant}_{caller_version}. See also <https://github.com/nanoporetech/medaka?tab=readme-ov-file#models>.	r941_min_high_g360	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	general	
consensus	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	runtime	
consensus	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_Illumina_PE	runtime	
consensus	min_bq	Int	Minimum base quality required for a base to be considered during samtools mpileup before consensus generation	0	Optional	TheiaViral_Illumina_PE	general	
consensus	skip_N	Boolean	True/False that determines if "N" bases should be skipped in the consensus sequence	False	Optional	TheiaViral_Illumina_PE	general	
consensus_qc	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT, VADR_Update	runtime	
consensus_qc	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT, VADR_Update	runtime	
consensus_qc	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT, VADR_Update	docker	
consensus_qc	genome_length	Int	Internal component, do not modify		Optional	TheiaCoV_ClearLabs, TheiaCoV_Illumina_SE, VADR_Update	general	
consensus_qc	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT, VADR_Update	runtime	
consensus_qc	reference_genome	File	Internal component, do not modify		Optional	VADR_Update	general	
cophylo_task	cpu	Int	Number of CPUs to allocate to the task	1	Optional	PhyloCompare	runtime	
cophylo_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	PhyloCompare	runtime	
cophylo_task	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/theiaphylo:0.2.0	Optional	PhyloCompare	docker	
cophylo_task	memory	Int	Amount of memory (in GB) to allocate to the task	4	Optional	PhyloCompare	runtime	
core_gene_snp_workflow	align	Boolean	Boolean variable that instructs the workflow to generate core and pangenome alignments if "true". If "false", the workflow will produce only a pangenome summary.	True	Optional	Core_Gene_SNP	general	
core_gene_snp_workflow	core_tree	Boolean	Boolean variable that instructs the workflow to create a phylogenetic tree and SNP distance matrix from the core gene alignment. Align must also be set to true.	True	Optional	Core_Gene_SNP	general	
core_gene_snp_workflow	data_summary_column_names	String	A comma-separated list of the column names from the sample-level data table for generating a data summary (presence/absence .csv matrix); e.g., "amrfinderplus_amr_genes,amrfinderplus_virulence_genes"		Optional	Core_Gene_SNP	general	
core_gene_snp_workflow	data_summary_terra_project	String	The billing project for your current workspace. This can be found after the "#workspaces/" section in the workspace's URL		Optional	Core_Gene_SNP	general	
core_gene_snp_workflow	data_summary_terra_table	String	The name of the sample-level Terra data table that will be used for generating a data summary		Optional	Core_Gene_SNP	general	
core_gene_snp_workflow	data_summary_terra_workspace	String	The name of the Terra workspace you are in. This can be found at the top of the webpage, or in the URL after the billing project.		Optional	Core_Gene_SNP	general	
core_gene_snp_workflow	midpoint_root_tree	Boolean	Boolean variable that will instruct the workflow to reroot the tree at the midpoint	True	Optional	Core_Gene_SNP	general	
core_gene_snp_workflow	pan_tree	Boolean	Boolean variable that instructs the workflow to create a phylogenetic tree and SNP distance matrix from the pangenome alignment. Align must also be set to true.	False	Optional	Core_Gene_SNP	general	
core_gene_snp_workflow	phandango_coloring	Boolean	Boolean variable that tells the data summary task and the reorder matrix task to include a suffix that enables consistent coloring on Phandango; by default, this suffix is not added. To add this suffix set this variable to true.	False	Optional	Core_Gene_SNP	general	
core_gene_snp_workflow	sample_names	Array[String]	Array of sample_ids from the data table used		Optional	Core_Gene_SNP	general	
core_iqtree	alrt	Int	Number of replicates to use for the SH-like approximate likelihood ratio test (Minimum recommended= 1000). Follows IQ-TREE "-alrt" option	1000	Optional	Core_Gene_SNP	general	
core_iqtree	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Core_Gene_SNP	runtime	
core_iqtree	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Core_Gene_SNP	runtime	
core_iqtree	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/iqtree:1.6.7	Optional	Core_Gene_SNP	docker	
core_iqtree	iqtree_model	String	Substitution model, frequency type (optional) and rate heterogeneity type (optional) used by IQ-TREE. This string follows the IQ-TREE "-m" option. For comparison to other tools use HKY for Bactopia, GTR+F+I for Grandeur, GTR+G4 for Nullarbor, GTR+G for Dryad	GTR+I+G	Optional	Core_Gene_SNP	general	
core_iqtree	iqtree_opts	String	Additional options for IQ-TREE, see <http://www.iqtree.org/doc/Command-Reference>		Optional	Core_Gene_SNP	general	
core_iqtree	iqtree_ultrafast_bootstraps	Int	Number of ultrafast bootstrap replicates. Follows IQ-TREE "-bb" option.	1000	Optional	Core_Gene_SNP	general	
core_iqtree	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Core_Gene_SNP	runtime	
core_ksnp3_shared_snps_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	kSNP3	runtime	
core_ksnp4_shared_snps_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	kSNP4	runtime	
core_reorder_matrix	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
core_reorder_matrix	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
core_reorder_matrix	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1	Optional	Core_Gene_SNP, kSNP3, kSNP4	docker	
core_reorder_matrix	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
core_reorder_matrix	outgroup_root	String	Tip name to root phylogenetic tree upon (overrides midpoint root)		Optional	Core_Gene_SNP, kSNP3, kSNP4	general	
core_snp_dists	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
core_snp_dists	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
core_snp_dists	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2	Optional	Core_Gene_SNP, kSNP3, kSNP4	docker	
core_snp_dists	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
core_snp_sites	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Core_Gene_SNP	runtime	
core_snp_sites	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Core_Gene_SNP	runtime	
core_snp_sites	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snp-sites:2.5.1	Optional	Core_Gene_SNP	docker	
core_snp_sites	memory	Int	Amount of memory (in GB) to allocate to the task	2	Optional	Core_Gene_SNP	runtime	
create_microreact_project	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Microreact_Export	runtime	
create_microreact_project	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	Microreact_Export	runtime	
create_microreact_project	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/microreact_export:1.0.0	Optional	Microreact_Export	docker	
create_microreact_project	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Microreact_Export	runtime	
create_table_from_array	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Dorado_Basecalling	runtime	
create_table_from_array	disk_size	Int	Amount of storage (in GB) to allocate to the task	25	Optional	Dorado_Basecalling	runtime	
create_table_from_array	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	Dorado_Basecalling	docker	
create_table_from_array	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Dorado_Basecalling	runtime	
create_terra_table	cpu	Int	Number of CPUs to allocate to the task	1	Optional	ONT_Barcode_Concatenation	runtime	
create_terra_table	disk_size	Int	Amount of storage (in GB) to allocate to the task	25	Optional	ONT_Barcode_Concatenation	runtime	
create_terra_table	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	ONT_Barcode_Concatenation	docker	
create_terra_table	file_ending	String	Use to provide file ending(s) to determine what should be dropped from the filename to determine the name of the sample (see above for more information)		Optional	Create_Terra_Table	general	
create_terra_table	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	ONT_Barcode_Concatenation	runtime	
czgenepi_prep	genbank_accession_column_name	String	The column name where the genbank accession for the sample can be found	genbank_accession	Optional	CZGenEpi_Prep	general	
czgenepi_prep	is_private	Boolean	Sets whether sample status is provate, or not	True	Optional	CZGenEpi_Prep	general	
czgenepi_prep	organism	String	The organism for data preparation. Options: "mpox" or "sars-cov-2"	sars-cov-2	Optional	CZGenEpi_Prep	general	
czgenepi_prep	private_id_column_name	String	The column name where the Private ID for the sample can be found	terra_table_name_id	Optional	CZGenEpi_Prep	general	
czgenepi_prep	sequencing_date_column_name	String	The column name where the sample's sequencing data can be found	sequencing_date	Optional	CZGenEpi_Prep	general	
czgenepi_wrangling	cpu	Int	Number of CPUs to allocate to the task	1	Optional	CZGenEpi_Prep	runtime	
czgenepi_wrangling	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	CZGenEpi_Prep	runtime	
czgenepi_wrangling	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-08-08-2	Optional	CZGenEpi_Prep	docker	
czgenepi_wrangling	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	CZGenEpi_Prep	runtime	
dehost_pe	target_organism	String	Target organism for Kraken2 reporting	Severe acute respiratory syndrome coronavirus 2	Optional	NCBI_Scrub_PE	general	
dehost_se	target_organism	String	Target organism for Kraken2 reporting	Severe acute respiratory syndrome coronavirus 2	Optional	NCBI_Scrub_SE	general	
digger_denovo	assembler	String	Assembler to use (spades, skesa, megahit)	skesa	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	assembler_options	String	Assembler-specific options that you might choose for the selected assembler		Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	bwa_cpu	Int	Number of CPUs to allocate to the task	6	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	bwa_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	bwa_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	docker	
digger_denovo	bwa_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	call_pilon	Boolean	Whether to run Pilon polishing after assembly	False	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	filter_contigs_cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	filter_contigs_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	filter_contigs_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/shovilter:0.2	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	docker	
digger_denovo	filter_contigs_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	filter_contigs_min_coverage	Float	Minimum coverage threshold for contig filtering	2.0	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	filter_contigs_min_length	Int	Minimum length threshold for contig filtering	200	Optional	TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	filter_contigs_skip_coverage_filter	Boolean	Skip filtering contigs based on coverage	False	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	filter_contigs_skip_homopolymer_filter	Boolean	Skip filtering contigs containing homopolymers	False	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	filter_contigs_skip_length_filter	Boolean	Skip filtering contigs based on length	False	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	kmers	String	K-mer sizes for assembly (comma-separated)		Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	megahit_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	megahit_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	megahit_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/megahit:1.2.9	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	docker	
digger_denovo	megahit_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	min_contig_length	Int	Minimum contig length to retain in final assembly	200	Optional	TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	pilon_cpu	Int	Number of CPUs to allocate to the task	8	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	pilon_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	pilon_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/pilon:1.24--hdfd78af_0	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	docker	
digger_denovo	pilon_fix	String	Potential issues with assembly to try and automatically fix (snps, indels, gaps, local, all, bases, none)	bases	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	pilon_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	pilon_min_base_quality	Int	Minimum base quality to keep	3	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	pilon_min_depth	Float	Minimum coverage threshold for variant calling: when set to a value ≥1, it requires that absolute depth of coverage; when set to a fraction <1, it requires coverage at least that fraction of the mean coverage for the region	0.25	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	pilon_min_mapping_quality	Int	Minimum mapping quality for a read to count in pileups	60	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	read2	File	Internal component, do not modify		Optional	TheiaProk_Illumina_SE	general	
digger_denovo	run_filter_contigs	Boolean	Whether to run contig filtering step	True	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
digger_denovo	skesa_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	skesa_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	skesa_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/skesa:2.4.0	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	docker	
digger_denovo	skesa_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	spades_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	spades_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	spades_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/spades:4.1.0	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	docker	
digger_denovo	spades_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
digger_denovo	spades_type	String	SPAdes assembly mode (isolate, meta, rna, etc.), more can be found [here](https://ablab.github.io/spades/running.html)	isolate	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
dorado_basecall	cpu	Int	Number of CPUs to allocate to the task	8	Optional	Dorado_Basecalling	runtime	
dorado_basecall	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Dorado_Basecalling	runtime	
dorado_basecall	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/dorado:0.9.0-cuda12.2.0	Optional	Dorado_Basecalling	docker	
dorado_basecall	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Dorado_Basecalling	runtime	
dorado_basecalling	custom_primers	File	A FASTA file containing custom primer sequences for PCR primer trimming during demultiplexing.		Optional	Dorado_Basecalling	general	
dorado_basecalling	demux_no_trim	Boolean	Set to true to disable barcode trimming during demultiplexing.	False	Optional	Dorado_Basecalling	general	
dorado_basecalling	dorado_model	String	The model to use during basecalling ('sup' for super accuracy, 'hac' for high accuracy, or 'fast' for high speed). Users may also specify a full model name (see above for more details).	sup	Optional	Dorado_Basecalling	general	
dorado_basecalling	number_chunks	Int	The number of chunks to split the input files into for basecalling; increasing chunk size can decrease runtime, though too high of a chunk size will be detrimental instead of beneficial due to resource allocation and quota limits	4	Optional	Dorado_Basecalling	general	
dorado_demux	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Dorado_Basecalling	runtime	
dorado_demux	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Dorado_Basecalling	runtime	
dorado_demux	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/dorado:0.9.0-cuda12.2.0	Optional	Dorado_Basecalling	docker	
dorado_demux	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Dorado_Basecalling	runtime	
dorado_trim	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Dorado_Basecalling	runtime	
dorado_trim	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Dorado_Basecalling	runtime	
dorado_trim	docker	String	The Docker container to use for the task. This is not the most up-to-date image since there is a bug with this Dorado subcommand in v0.9.0	us-docker.pkg.dev/general-theiagen/staphb/dorado:0.8.3	Optional	Dorado_Basecalling	docker	
dorado_trim	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Dorado_Basecalling	runtime	
download_terra_table	cpu	Int	Number of CPUs to allocate to the task	1	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Microreact_Export, Terra_2_ENA	runtime	
download_terra_table	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Microreact_Export, Terra_2_ENA	runtime	
download_terra_table	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Microreact_Export, Terra_2_ENA	docker	
download_terra_table	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Microreact_Export, Terra_2_ENA	runtime	
est_genome_length	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
est_genome_length	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
est_genome_length	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/ncbi-datasets:18.9.0-python-jq	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
est_genome_length	memory	Int	Amount of memory (in GB) to allocate to the task	4	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
est_genome_length	summary_limit	Int	Maximum number of genomes to query	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
ete4_identify	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel	runtime	
ete4_identify	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel	runtime	
ete4_identify	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/ete4:4.3.0	Optional	Metabuli	docker	
ete4_identify	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/ete4:4.3.0	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel	docker	
ete4_identify	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Metabuli	runtime	
ete4_identify	memory	Int	Amount of memory (in GB) to allocate to the task	4	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel	runtime	
ete4_identify	rank	String	Internal component, do not modify		Optional	Metabuli, TheiaViral_Panel	general	
export_taxon_table	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Panel	runtime	
export_taxon_table	disk_size	Int	Amount of storage (in GB) to allocate to the task	25	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Panel	runtime	
export_taxon_table	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Panel	docker	
export_taxon_table	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaViral_Panel	runtime	
export_taxon_table	theiaviral_panel	Boolean	Internal component, do not modify	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
export_two_tsvs	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaValidate	runtime	
export_two_tsvs	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	TheiaValidate	runtime	
export_two_tsvs	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16	Optional	TheiaValidate	docker	
export_two_tsvs	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	1	Optional	TheiaValidate	runtime	
fasta_to_ids	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur	runtime	
fasta_to_ids	disk_size	Int	Amount of storage (in GB) to allocate to the task	375	Optional	Augur	runtime	
fasta_to_ids	docker	String	The Docker container to use for the task	ubuntu	Optional	Augur	docker	
fasta_to_ids	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	1	Optional	Augur	runtime	
fasta_utilities	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaViral_ONT	runtime	
fasta_utilities	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
fasta_utilities	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17	Optional	TheiaViral_ONT	docker	
fasta_utilities	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_ONT	runtime	
fastp	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
fastp	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
fastp	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/fastp:1.1.0	Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_Panel	docker	
fastp	fastp_adapter_fasta	File	FASTA of adapters to replace Fastp's default adapter search		Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_Panel	general	
fastp	fastp_args	String	Additional arguments to use with fastp		Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_Panel	general	
fastp	fastp_min_length	Int	Minimum read length	15	Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_Panel	general	
fastp	fastp_quality_trim_score	Int	Minimum mean base quality relative to window size	20	Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_Panel	general	
fastp	fastp_trim_adapters	Boolean	Enable adapter trimming via Fastp	True	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
fastp	fastp_window_size	Int	Sliding window size for surveying read quality	4	Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_Panel	general	
fastp	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Metabuli, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
fastplong	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Metabuli	runtime	
fastplong	cut_front	Boolean	Apply trimming options from 5' to 3'	False	Optional	Metabuli	general	
fastplong	cut_tail	Boolean	Apply trimming options from 3' to 5'	False	Optional	Metabuli	general	
fastplong	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Metabuli	runtime	
fastplong	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/fastplong:0.4.1	Optional	Metabuli	docker	
fastplong	fastplong_adapter_fasta	File	FASTA of adapter sequences to trim		Optional	Metabuli	general	
fastplong	fastplong_args	String	Additional arguments to use with fastplong		Optional	Metabuli	general	
fastplong	fastplong_end_adapter	String	Adapter sequence to trim from the 3' end		Optional	Metabuli	general	
fastplong	fastplong_min_length	Int	Minimum read length	15	Optional	Metabuli	general	
fastplong	fastplong_quality_trim_score	Int	Minimum mean base quality relative to window size	20	Optional	Metabuli	general	
fastplong	fastplong_start_adapter	String	Adapter sequence to trim from the 5' end		Optional	Metabuli	general	
fastplong	fastplong_trim_adapters	Boolean	Enable adapter trimming via fastplong	True	Optional	Metabuli	general	
fastplong	fastplong_window_size	Int	Sliding window size for surveying read quality	4	Optional	Metabuli	general	
fastplong	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Metabuli	runtime	
fastq_scan_clean	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
fastq_scan_clean	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
fastq_scan_clean	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3	Optional	TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel	docker	
fastq_scan_clean	memory	Int	Amount of memory (in GB) to allocate to the task	4	Optional	TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
fastq_scan_clean_reads	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaCoV_ClearLabs	runtime	
fastq_scan_clean_reads	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaCoV_ClearLabs	runtime	
fastq_scan_clean_reads	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3	Optional	TheiaCoV_ClearLabs	docker	
fastq_scan_clean_reads	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaCoV_ClearLabs	runtime	
fastq_scan_raw	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
fastq_scan_raw	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
fastq_scan_raw	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3	Optional	TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel	docker	
fastq_scan_raw	memory	Int	Amount of memory (in GB) to allocate to the task	4	Optional	TBProfiler_tNGS, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
fastq_scan_raw_reads	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaCoV_ClearLabs	runtime	
fastq_scan_raw_reads	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaCoV_ClearLabs	runtime	
fastq_scan_raw_reads	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3	Optional	TheiaCoV_ClearLabs	docker	
fastq_scan_raw_reads	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaCoV_ClearLabs	runtime	
fetch_bs	cpu	Int	Number of CPUs to allocate to the task	2	Optional	BaseSpace_Fetch	runtime	
fetch_bs	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	BaseSpace_Fetch	runtime	
fetch_bs	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/basespace_cli:1.2.1	Optional	BaseSpace_Fetch	docker	
fetch_bs	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	BaseSpace_Fetch	runtime	
fetch_sra_to_fastq	cpu	Int	Number of CPUs to allocate to the task	2	Optional	SRA_Fetch	runtime	
fetch_sra_to_fastq	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	SRA_Fetch	runtime	
fetch_sra_to_fastq	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0	Optional	SRA_Fetch	docker	
fetch_sra_to_fastq	fastq_dl_opts	String	Additional parameters to pass to fastq_dl from here	--provider sra	Optional	SRA_Fetch	general	
fetch_sra_to_fastq	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	SRA_Fetch	runtime	
fetch_srr	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Fetch_SRR_Accession	runtime	
fetch_srr	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	Fetch_SRR_Accession	runtime	
fetch_srr	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0	Optional	Fetch_SRR_Accession	docker	
fetch_srr	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Fetch_SRR_Accession	runtime	
filter_sequences_by_length	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur	runtime	
filter_sequences_by_length	disk_size	Int	Amount of storage (in GB) to allocate to the task	300	Optional	Augur	runtime	
filter_sequences_by_length	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/broadinstitute/viral-core:2.1.33	Optional	Augur	docker	
filter_sequences_by_length	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	1	Optional	Augur	runtime	
find_files	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Dorado_Basecalling	runtime	
find_files	disk_size	Int	Amount of storage (in GB) to allocate to the task	25	Optional	Dorado_Basecalling	runtime	
find_files	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/cloudsdktool/google-cloud-cli:427.0.0-alpine	Optional	Dorado_Basecalling	docker	
find_files	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Dorado_Basecalling	runtime	
flu_track	abricate_flu_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	abricate_flu_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	abricate_flu_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-insaflu-220727	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	docker	
flu_track	abricate_flu_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	abricate_flu_min_percent_coverage	Int	Minimum DNA percent coverage	60	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	abricate_flu_min_percent_identity	Int	Minimum DNA percent identity	70	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	antiviral_aa_subs	String	Additional list of antiviral resistance associated amino acid substitutions of interest to be searched against those called on the sample segments. They take the format of :, e.g. NA:A26V		Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	assembly_fasta	File	Internal component, do not modify		Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	assembly_metrics_cpu	Int	Internal component, do not modify	2	Optional	TheiaCoV_FASTA	general	
flu_track	assembly_metrics_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	assembly_metrics_disk_size	Int	Internal component, do not modify	100	Optional	TheiaCoV_FASTA	general	
flu_track	assembly_metrics_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	assembly_metrics_docker	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.23	Optional	TheiaCoV_FASTA	general	
flu_track	assembly_metrics_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.23	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	docker	
flu_track	assembly_metrics_memory	Int	Internal component, do not modify	8	Optional	TheiaCoV_FASTA	general	
flu_track	assembly_metrics_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	flu_h1_ha_ref	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/viral/flu/reference_h1_ha.fasta	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	flu_h1n1_m2_ref	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/viral/flu/reference_h1n1_m2.fasta	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	flu_h3_ha_ref	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/viral/flu/reference_h3_ha.fasta	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	flu_h3n2_m2_ref	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/viral/flu/reference_h3n2_m2.fasta	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	flu_n1_na_ref	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/viral/flu/reference_n1_na.fasta	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	flu_n2_na_ref	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/viral/flu/reference_n2_na.fasta	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	flu_pa_ref	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/viral/flu/reference_pa.fasta	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	flu_pb1_ref	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/viral/flu/reference_pb1.fasta	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	flu_pb2_ref	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/viral/flu/reference_pb2.fasta	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	flu_subtype	String	The influenza subtype being analyzed. Used for picking nextclade datasets. Options: "Yamagata", "Victoria", "H1N1", "H3N2", "H5N1". Only use to override the subtype call from IRMA and ABRicate.		Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	genoflu_cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	genoflu_cross_reference	File	An Excel file to cross-reference BLAST findings; probably useful if novel genotypes are not in the default file used by genoflu.py		Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	genoflu_disk_size	Int	Amount of storage (in GB) to allocate to the task	25	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	genoflu_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/genoflu:1.06	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	docker	
flu_track	genoflu_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	genoflu_min_percent_identity	Float	Percent identity threshold used for calling matches for each genome segment that make up the final GenoFlu genotype	98	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	irma_cpu	Int	Internal component, do not modify	4	Optional	TheiaCoV_FASTA	general	
flu_track	irma_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	irma_disk_size	Int	Internal component, do not modify	100	Optional	TheiaCoV_FASTA	general	
flu_track	irma_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	irma_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/irma:1.3.1	Optional	TheiaCoV_FASTA	general	
flu_track	irma_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/irma:1.3.1	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	docker	
flu_track	irma_keep_ref_deletions	Boolean	Internal component, do not modify	True	Optional	TheiaCoV_FASTA	general	
flu_track	irma_keep_ref_deletions	Boolean	True/False variable that determines if sites missed (i.e. 0 reads for a site in the reference genome) during read gathering should be deleted by ambiguation by inserting N's or deleting the sequence entirely. False sets this IRMA paramater to "DEL" and true sets it to "NNN"	True	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	True
flu_track	irma_memory	Int	Internal component, do not modify	16	Optional	TheiaCoV_FASTA	general	
flu_track	irma_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	irma_min_ambiguous_threshold	Float	Internal component, do not modify	0.25	Optional	TheiaCoV_FASTA	general	
flu_track	irma_min_ambiguous_threshold	Float	Minimum called Single Nucleotide Variant (SNV) frequency for mixed based calls in the output consensus assembly (AKA amended consensus).	0.25	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	irma_min_avg_consensus_allele_quality	Int	Internal component, do not modify	10	Optional	TheiaCoV_FASTA	general	
flu_track	irma_min_avg_consensus_allele_quality	Int	Minimum allele coverage depth to call plurality consensus, otherwise calls "N". Setting this value too high can negatively impact final amended consensus.	10	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	irma_min_consensus_support	Int	Internal component, do not modify	50	Optional	TheiaCoV_FASTA	general	
flu_track	irma_min_read_length	Int	Internal component, do not modify	75	Optional	TheiaCoV_FASTA	general	
flu_track	irma_min_read_length	Int	Minimum read length to include reads in read gathering step in IRMA. This value should not be greater than the typical read length.	75	Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flu_track	nextclade_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	nextclade_custom_input_dataset	File	For H5N1 flu samples only. A custom Nextclade dataset in JSON format. If provided, this dataset will be used to process any H5N1 flu samples. If not provided, a custom dataset will be selected depending on the GenoFLU Genotype.	Defaults are GenoFLU Genotype specific. Please find these default values here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	True
flu_track	nextclade_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	nextclade_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.16.0	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	docker	
flu_track	nextclade_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	nextclade_output_parser_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	nextclade_output_parser_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	nextclade_output_parser_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/python/python:3.8.18-slim	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	docker	
flu_track	nextclade_output_parser_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_ONT	runtime	
flu_track	read1	File	Internal component, do not modify		Optional	TheiaCoV_FASTA	general	
flu_track	read2	File	Internal component, do not modify		Optional	TheiaCoV_FASTA, TheiaCoV_ONT	general	
flu_track	vadr_outputs_tgz	File	Internal component, do not modify		Optional	TheiaCoV_Illumina_PE, TheiaCoV_ONT	general	
flye	additional_parameters	String	Additional parameters for Flye assembler		Optional	TheiaViral_ONT	general	
flye	asm_coverage	Int	Reduced coverage for initial disjointig assembly		Optional	TheiaViral_ONT	general	
flye	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_ONT	runtime	
flye	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
flye	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/flye:2.9.4	Optional	TheiaViral_ONT	docker	
flye	flye_polishing_iterations	Int	Number of polishing iterations	1	Optional	TheiaViral_ONT	general	
flye	genome_length	Int	Expected genome length for assembly - requires asm_coverage		Optional	TheiaViral_ONT	general	
flye	keep_haplotypes	Boolean	True/False to prevent collapsing alternative haplotypes	False	Optional	TheiaViral_ONT	general	
flye	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaViral_ONT	runtime	
flye	minimum_overlap	Int	Minimum overlap between reads		Optional	TheiaViral_ONT	general	
flye	no_alt_contigs	Boolean	True/False to disable alternative contig generation	False	Optional	TheiaViral_ONT	general	
flye	read_error_rate	Float	Expected error rate in reads		Optional	TheiaViral_ONT	general	
flye	read_type	String	Type of read data for Flye	--nano-hq	Optional	TheiaViral_ONT	general	
flye	scaffold	Boolean	True/False to enable scaffolding using graph	False	Optional	TheiaViral_ONT	general	
flye_denovo	auto_medaka_model	Boolean	If true, medaka will automatically select the best Medaka model for assembly	True	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	bandage_cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	bandage_disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	bandage_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	dnaapler_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	dnaapler_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	dnaapler_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	dnaapler_mode	String	Dnaapler-specific inputs	all	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	filter_contigs_cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	filter_contigs_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	filter_contigs_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	filter_contigs_min_length	Int	Minimum contig length to keep	1000	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_additional_parameters	String	Any extra Flye-specific parameters		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_asm_coverage	Int	Reduced coverage for initial disjointig assembly		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	flye_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	flye_genome_length	Int	User-specified expected genome length to be used in genome statistics calculations		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_keep_haplotypes	Boolean	If true keep haplotypes	False	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	flye_minimum_overlap	Int	Minimum overlap between reads		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_no_alt_contigs	Boolean	If true, do not generate alternative contigs	False	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_polishing_iterations	Int	Default polishing iterations	1	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_read_error_rate	Float	Maximum expected read error rate		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_read_type	String	Specifies the type of sequencing reads. Options: --nano-hq (default), --nano-corr, --nano-raw, --pacbio-raw, --pacbio-corr, --pacbio-hifi. Refer to Flye documentation for details on each type.	--nano-hq	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_scaffold	Boolean	If true, scaffolding is enabled using graph	False	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	flye_uneven_coverage_mode	Boolean	sets the --meta option in the case of uneven coverage (or metagenomics)	False	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	illumina_read1	File	If Illumina reads are provided, flye_denovo subworkflow will perform Illumina polishing		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	illumina_read2	File	If Illumina reads are provided, flye_denovo subworkflow will perform Illumina polishing		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	medaka_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	medaka_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	medaka_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	medaka_model	String	In order to obtain the best results, the appropriate model must be set to match the sequencer's basecaller model; this string takes the format of {pore}{device}{caller variant}_{caller_version}. See also <https://github.com/nanoporetech/medaka?tab=readme-ov-file#models>. If this is being run on legacy data it is likely to be r941_min_hac_g507.	r1041_e82_400bps_sup_v5.0.0	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polish_rounds	Int	The number of polishing rounds to conduct for medaka or racon (without Illumina)	1	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polisher	String	The polishing tool to use for assembly	medaka	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polypolish_careful	Boolean	Polypolish-specific inputs	False	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polypolish_cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	polypolish_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	polypolish_fraction_invalid	Float	Polypolish-specific inputs		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polypolish_fraction_valid	Float	Polypolish-specific inputs		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polypolish_high_percentile_threshold	Float	Polypolish-specific inputs		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polypolish_low_percentile_threshold	Float	Polypolish-specific inputs		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polypolish_maximum_errors	Int	Polypolish-specific inputs		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polypolish_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	polypolish_minimum_depth	Int	Polypolish-specific inputs		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	polypolish_pair_orientation	String	Polypolish-specific inputs		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	porechop_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	porechop_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	porechop_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	porechop_trimopts	String	Options to pass to Porechop for trimming		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	racon_cpu	Int	Number of CPUs to allocate to the task	8	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	racon_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	racon_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
flye_denovo	run_porechop	Boolean	If true, trims reads before assembly using Porechop	False	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
flye_denovo	skip_polishing	Boolean	If true, skips polishing	False	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
freyja	adapt	Float	adaptive lasso penalty parameter	0.0	Optional	Freyja_FASTQ	general	
freyja	auto_adapt	Boolean	When set to true will use error profile to set adapt value	False	Optional	Freyja_FASTQ	general	
freyja	bootstrap	Boolean	Perform bootstrapping	False	Optional	Freyja_FASTQ	general	
freyja	confirmed_only	Boolean	Include only confirmed SARS-CoV-2 lineages	False	Optional	Freyja_FASTQ	general	
freyja	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Freyja_FASTQ	runtime	
freyja	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ	runtime	
freyja	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/freyja:2.0.1	Optional	Freyja_FASTQ	docker	
freyja	eps	Float	The minimum lineage abundance cut-off value	0.001	Optional	Freyja_FASTQ	general	
freyja	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Freyja_FASTQ	runtime	
freyja	number_bootstraps	Int	The number of bootstraps to perform (only used if bootstrap = true)	100	Optional	Freyja_FASTQ	general	
freyja	update_db	Boolean	Updates the Freyja reference files (the usher barcodes and lineage metadata files) but will not save them as output (use Freyja_Update for that purpose). If set to true, the freyja_lineage_metadata and freyja_barcodes files are not required.	False	Optional	Freyja_FASTQ	general	True
freyja_dashboard	dashboard_intro_text	File	A file containing the text to be contained at the top of the dashboard.	SARS-CoV-2 lineage de-convolution performed by the Freyja workflow (<https://github.com/andersen-lab/Freyja>).	Optional	Freyja_Dashboard	general	True
freyja_dashboard_task	config	File	(found in the optional section, but is required) A yaml file that applies various configurations to the dashboard, such as grouping lineages together, applying colorings, etc. See also <https://github.com/andersen-lab/Freyja/blob/main/freyja/data/plot_config.yml>.		Optional, Required	Freyja_Dashboard	general	True
freyja_dashboard_task	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Freyja_Dashboard	runtime	
freyja_dashboard_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_Dashboard	runtime	
freyja_dashboard_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/freyja:2.0.1	Optional	Freyja_Dashboard	docker	
freyja_dashboard_task	headerColor	String	A hex color code to change the color of the header		Optional	Freyja_Dashboard	general	
freyja_dashboard_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Freyja_Dashboard	runtime	
freyja_dashboard_task	mincov	Float	The minimum genome coverage used as a cut-off of data to include in the dashboard. Default is set to 60 by the freyja command-line tool (not a WDL task default, per se)		Optional	Freyja_Dashboard	general	
freyja_dashboard_task	scale_by_viral_load	Boolean	If set to true, averages samples taken the same day while taking viral load into account	False	Optional	Freyja_Dashboard	general	
freyja_dashboard_task	thresh	Float	The minimum lineage abundance cut-off value		Optional	Freyja_Dashboard	general	
freyja_fastq	depth_cutoff	Int	The minimum coverage depth with which to exclude sites below this value and group identical barcodes -- THIS MAY NOT WORK FOR NON-SARS-COV-2 ORGANISMS!		Optional	Freyja_FASTQ	general	
freyja_fastq	freyja_barcodes	File	Custom barcode file. Does not need to be provided if update_db is true if the freyja_pathogen is provided.		Optional	Freyja_FASTQ	general	
freyja_fastq	freyja_lineage_metadata	File	File containing the lineage metadata; the "curated_lineages.json" file found <https://github.com/andersen-lab/Freyja/tree/main/freyja/data> can be used for this variable. Does not need to be provided if update_db is true or if the freyja_pathogen is provided.		Optional, Required	Freyja_FASTQ	general	True
freyja_fastq	freyja_pathogen	String	Pathogen to be used by Freyja	SARS-CoV-2	Optional	Freyja_FASTQ	general	
freyja_fastq	kraken2_target_organism	String	The organism whose abundance the user wants to check in their reads. This should be a proper taxonomic name recognized by the Kraken database.	Severe acute respiratory syndrome coronavirus 2	Optional	Freyja_FASTQ	general	
freyja_fastq	ont	Boolean	Indicates if the input data is derived from an ONT instrument.	False	Optional	Freyja_FASTQ	general	
freyja_fastq	primer_bed	File	The bed file containing the primers used when sequencing was performed		Optional	Freyja_FASTQ	general	
freyja_fastq	qc_check_table	File	TSV containing values to check quality control metrics		Optional	Freyja_FASTQ	general	
freyja_fastq	read2	File	Illumina reverse read file in FASTQ file format (compression optional)		Optional	Freyja_FASTQ	general	
freyja_fastq	reference_gff	File	The GFF file for reference; should match the reference used for alignment (Wuhan-Hu-1)		Optional	Freyja_FASTQ	general	
freyja_fastq	run_qualimap	Boolean	When set to true, will run qualimap and provide custom visuals	True	Optional	Freyja_FASTQ	general	
freyja_fastq	trimmomatic_min_length	Int	The minimum length cut-off when performing read cleaning	25	Optional	Freyja_FASTQ	general	
freyja_plot	collection_date	Array[String]	An array containing the collection dates for the sample (YYYY-MM-DD format)		Optional	Freyja_Plot	general	
freyja_plot_task	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Freyja_Plot	runtime	
freyja_plot_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_Plot	runtime	
freyja_plot_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/freyja:2.0.1	Optional	Freyja_Plot	docker	
freyja_plot_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Freyja_Plot	runtime	
freyja_plot_task	mincov	Int	The minimum genome coverage used as a cut-off of data to include in the plot	60	Optional	Freyja_Plot	general	
freyja_plot_task	plot_day_window	Int	The width of the rolling average window; only used if plot_time_interval is "D"	14	Optional	Freyja_Plot	general	
freyja_plot_task	plot_lineages	Boolean	If true, will plot a lineage-specific breakdown	False	Optional	Freyja_Plot	general	
freyja_plot_task	plot_time	Boolean	If true, will plot sample collection time information (requires the collection_date input variable)	False	Optional	Freyja_Plot	general	
freyja_plot_task	plot_time_interval	String	Options: "MS" for month, "D" for day	MS	Optional	Freyja_Plot	general	
gambit	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Gambit_Query, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
gambit	disk_size	Int	Amount of storage (in GB) to allocate to the task	20	Optional	Gambit_Query, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
gambit	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0	Optional	Gambit_Query, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
gambit	gambit_db_genomes	File	Database of metadata for assembled query genomes; requires complementary signatures file. If not provided, uses default database "/gambit-db"	gs://gambit-databases-rp/2.1.0/gambit-metadata-2.1.0-20250808.gdb	Optional	Gambit_Query, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	
gambit	gambit_db_signatures	File	Signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used.	gs://gambit-databases-rp/2.1.0/gambit-signatures-2.1.0-20250808.gs	Optional	Gambit_Query, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	
gambit	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Gambit_Query, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
gamma	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
gamma	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
gamma	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/gamma:2.2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
gamma	extended_output	Boolean	GAMMA will provide the extended output when set to true	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
gamma	gamma_db	File	Multifasta sequence database GAMMA is to use for gene matching	gs://theiagen-public-resources-rp/reference_data/databases/gamma/default_ResFinderDB_Combined_05-06-20.fsa	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	
gamma	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
gamma	min_length_percent_gammas	Int	Threshold of match length percent used by GAMMA-s	20	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
gamma	min_percent_identity	Int	Threshold of identity for gene matches in percent	90	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
gamma	output_fasta	Boolean	Allows GAMMA to output gene matches in FASTA format	True	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
gamma	output_gff	Boolean	Allows GAMMA to output gene matches in GFF format	True	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
gamma	run_gammas	Boolean	Turns on GAMMA-S which runs GAMMA on nucleotide sequences rather than translating input sequences and matches	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
gene_coverage	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Freyja_FASTQ	runtime	
gene_coverage	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ	runtime	
gene_coverage	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15	Optional	Freyja_FASTQ	docker	
gene_coverage	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Freyja_FASTQ	runtime	
gene_coverage	min_depth	Int	Minimum depth for coverage	10	Optional	Freyja_FASTQ	general	
gene_coverage	sc2_s_gene_start	Int	Where the S gene starts	21563	Optional	Freyja_FASTQ	general	
gene_coverage	sc2_s_gene_stop	Int	Where the S gene stops	25384	Optional	Freyja_FASTQ	general	
get_fasta_genome_size	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Freyja_FASTQ	runtime	
get_fasta_genome_size	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	Freyja_FASTQ	runtime	
get_fasta_genome_size	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/seqkit:2.4.0--h9ee0642_0	Optional	Freyja_FASTQ	docker	
get_fasta_genome_size	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Freyja_FASTQ	runtime	
gisaid_upload	authentication_file	File	[EITHER] The GISAID authentication file generated by running cli3 authenticate for the submitter.		Optional, Required	Terra_2_GISAID	general	True
gisaid_upload	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Terra_2_GISAID	runtime	
gisaid_upload	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Terra_2_GISAID	runtime	
gisaid_upload	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/broadinstitute/gisaid-cli:3.0	Optional	Terra_2_GISAID	docker	
gisaid_upload	frameshift_notification	String	See top of inputs section for explanation; the notification preference regarding frameshifts in your submission	catch_novel	Optional	Terra_2_GISAID	general	
gisaid_upload	gisaid_credentials	File	[EITHER] A tab-delimited file containing the submitter's GISAID username followed by their password, used to generate the GISAID authentication file.		Optional, Required	Terra_2_GISAID	general	True
gisaid_upload	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Terra_2_GISAID	runtime	
gubbins	filter_percent	Int	Maximum % gaps to include a sample in gubbins analysis and downstream analyses	25	Optional	Snippy_Tree	general	
gubbins	iterations	Int	Maximum number of trees to iteratively build to remove recombination	5	Optional	Snippy_Tree	general	
gubbins	nuc_subst_model	String	Nucleotide substitution model to use with Gubbins: "JC", "K2P", "HKY", "GTR", "GTRGAMMA" or "GTRCAT" (see <https://github.com/nickjcroucher/gubbins/blob/v3.3/docs/gubbins_manual.md#nucleotide-substitution-model-options>)	GTRGAMMA	Optional	Snippy_Tree	general	
gubbins	tree_args	String	Quoted string of further arguments passed to tree building algorithm		Optional	Snippy_Tree	general	
gubbins	tree_builder	String	Application to use for Gubbins tree building algorithm: "raxml", "raxmlng", "iqtree", "iqtree-fast", "fasttree", "hybrid" (fasttree is used for the first tree, and raxml is used for later iterations), "rapidnj"	raxml	Optional	Snippy_Tree	general	
host_decontaminate	complete_only	Boolean	Only download genomes labeled "complete"	False	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel	general	
host_decontaminate	is_accession	Boolean	Inputted "host" is an accession	False	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel	general	
host_decontaminate	is_genome	Boolean	Inputted "host" is an assembly FASTA	False	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel	general	
host_decontaminate	minimap2_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel	runtime	
host_decontaminate	read2	File	Internal component, do not modify		Optional	TheiaViral_ONT	general	
host_decontaminate	refseq	Boolean	Only download RefSeq genomes	True	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel	general	
iqtree2	alrt	Int	Number of replicates to use for the SH-like approximate likelihood ratio test (Minimum recommended= 1000). Follows IQ-TREE "-alrt" option	1000	Optional	Snippy_Tree	general	
ivar_consensus	ivar_bwa_cpu	Int	Number of CPUs to allocate to the task	6	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_bwa_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_bwa_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	docker	
ivar_consensus	ivar_bwa_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_consensus_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_consensus_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_consensus_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	docker	
ivar_consensus	ivar_consensus_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_trim_primers_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_trim_primers_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_trim_primers_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	docker	
ivar_consensus	ivar_trim_primers_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_variant_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_variant_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	ivar_variant_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	docker	
ivar_consensus	ivar_variant_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	read2	File	Internal component, do not modify		Optional	TheiaCoV_Illumina_SE	general	
ivar_consensus	skip_N	Boolean	True/False variable that determines if regions with depth less than minimum depth should not be added to the consensus sequence	False	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	general	
ivar_consensus	stats_n_coverage_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	stats_n_coverage_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	stats_n_coverage_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.23	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	docker	
ivar_consensus	stats_n_coverage_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	stats_n_coverage_primtrim_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	stats_n_coverage_primtrim_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_consensus	stats_n_coverage_primtrim_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.23	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	docker	
ivar_consensus	stats_n_coverage_primtrim_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	runtime	
ivar_variants	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Illumina_PE	runtime	
ivar_variants	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE	runtime	
ivar_variants	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan	Optional	TheiaViral_Illumina_PE	docker	
ivar_variants	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_Illumina_PE	runtime	
ivar_variants	reference_gff	File	A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs) so iVar can identify codons and translate variants into amino acids		Optional	TheiaViral_Illumina_PE	general	
kmerfinder	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
kmerfinder	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
kmerfinder	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/kmerfinder:3.0.2--hdfd78af_0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
kmerfinder	kmerfinder_args	String	Kmerfinder additional arguments		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
kmerfinder	kmerfinder_db	File	Bacterial database for KmerFinder	gs://theiagen-public-resources-rp/reference_data/databases/kmerfinder/kmerfinder_bacteria_20230911.tar.gz	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	
kmerfinder	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
kraken2	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database 		Optional	NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaViral_Illumina_PE	general	
kraken2	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaViral_Illumina_PE	general	
kraken2	classified_out	String	Allows user to rename the classified FASTQ files output. Must include .fastq as the suffix	classified#.fastq	Optional	NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaViral_Illumina_PE	general	
kraken2	cpu	Int	Number of CPUs to allocate to the task	4	Optional	NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaViral_Illumina_PE	runtime	
kraken2	disk_size	Int	Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database)	100	Optional	NCBI_Scrub_PE, NCBI_Scrub_SE	runtime	
kraken2	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE	runtime	
kraken2	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/kraken2:2.17.1	Optional	NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaViral_Illumina_PE	docker	
kraken2	kraken2_args	String	Allows a user to supply additional kraken2 command-line arguments		Optional	NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaViral_Illumina_PE	general	
kraken2	kraken2_db	File	The database used to run Kraken2	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz	Optional	NCBI_Scrub_PE, NCBI_Scrub_SE	database	
kraken2	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaViral_Illumina_PE	runtime	
kraken2	read2	File	Internal component, do not modify		Optional	NCBI_Scrub_SE	general	
kraken2	unclassified_out	String	Allows user to rename unclassified FASTQ files output. Must include .fastq as the suffix	unclassified#.fastq	Optional	NCBI_Scrub_PE, NCBI_Scrub_SE, TheiaViral_Illumina_PE	general	
kraken2_clean	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database		Optional	TheiaMeta_Illumina_PE, TheiaViral_Panel	general	
kraken2_clean	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	TheiaViral_Panel	general	
kraken2_clean	classified_out	String	Internal component, do not modify	classified#.fastq	Optional	TheiaViral_Panel	general	
kraken2_clean	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaMeta_Illumina_PE, TheiaViral_Panel	runtime	
kraken2_clean	disk_size	Int	Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database)	100	Optional	TheiaMeta_Illumina_PE	runtime	
kraken2_clean	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Panel	runtime	
kraken2_clean	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/kraken2:2.17.1	Optional	TheiaMeta_Illumina_PE, TheiaViral_Panel	docker	
kraken2_clean	kraken2_args	String	Additional kraken2 arguments		Optional	TheiaViral_Panel	general	
kraken2_clean	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaMeta_Illumina_PE, TheiaViral_Panel	runtime	
kraken2_clean	target_organism	String	Target organism for reporting percent identified		Optional	TheiaMeta_Illumina_PE, TheiaViral_Panel	general	
kraken2_clean	unclassified_out	String	Internal component, do not modify	unclassified#.fastq	Optional	TheiaViral_Panel	general	
kraken2_dehosted	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database		Optional	TheiaCoV_ClearLabs	general	
kraken2_dehosted	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	TheiaCoV_ClearLabs	general	
kraken2_dehosted	classified_out	String	Internal component, do not modify	classified#.fastq	Optional	TheiaCoV_ClearLabs	general	
kraken2_dehosted	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaCoV_ClearLabs	runtime	
kraken2_dehosted	disk_size	Int	Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database)	100	Optional	TheiaCoV_ClearLabs	runtime	
kraken2_dehosted	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/kraken2:2.17.1	Optional	TheiaCoV_ClearLabs	docker	
kraken2_dehosted	kraken2_args	String	Additional kraken2 arguments		Optional	TheiaCoV_ClearLabs	general	
kraken2_dehosted	kraken2_db	File	The database used to run Kraken2. Must contain viral and human sequences.	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz	Optional	TheiaCoV_ClearLabs	database	
kraken2_dehosted	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaCoV_ClearLabs	runtime	
kraken2_dehosted	read2	File	Internal component, do not modify		Optional	TheiaCoV_ClearLabs	general	
kraken2_dehosted	unclassified_out	String	Internal component, do not modify	unclassified#.fastq	Optional	TheiaCoV_ClearLabs	general	
kraken2_extract	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaViral_Illumina_PE	runtime	
kraken2_extract	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE	runtime	
kraken2_extract	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/krakentools:d4a2fbe	Optional	TheiaViral_Illumina_PE	docker	
kraken2_extract	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaViral_Illumina_PE	runtime	
kraken2_pe	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database		Optional	Kraken_PE	general	
kraken2_pe	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	Kraken_PE	general	
kraken2_pe	classified_out	String	Allows user to rename the classified FASTQ files output. Must include .fastq as the suffix	classified#.fastq	Optional	Kraken_PE	general	
kraken2_pe	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Kraken_PE	runtime	
kraken2_pe	disk_size	Int	Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database)	100	Optional	Kraken_PE	runtime	
kraken2_pe	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/kraken2:2.17.1	Optional	Kraken_PE	docker	
kraken2_pe	kraken2_args	String	Allows a user to supply additional kraken2 command-line arguments		Optional	Kraken_PE	general	
kraken2_pe	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Kraken_PE	runtime	
kraken2_pe	target_organism	String	Target organism for reporting percent identified		Optional	Kraken_PE	general	
kraken2_pe	unclassified_out	String	Allows user to rename unclassified FASTQ files output. Must include .fastq as the suffix	unclassified#.fastq	Optional	Kraken_PE	general	
kraken2_raw	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database		Optional	TheiaCoV_ClearLabs, TheiaMeta_Illumina_PE, TheiaViral_Panel	general	
kraken2_raw	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	TheiaCoV_ClearLabs	general	
kraken2_raw	classified_out	String	Internal component, do not modify	classified#.fastq	Optional	TheiaCoV_ClearLabs, TheiaViral_Panel	general	
kraken2_raw	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaCoV_ClearLabs, TheiaMeta_Illumina_PE, TheiaViral_Panel	runtime	
kraken2_raw	disk_size	Int	Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database)	100	Optional	TheiaCoV_ClearLabs, TheiaMeta_Illumina_PE	runtime	
kraken2_raw	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Panel	runtime	
kraken2_raw	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/kraken2:2.17.1	Optional	TheiaCoV_ClearLabs, TheiaMeta_Illumina_PE, TheiaViral_Panel	docker	
kraken2_raw	kraken2_args	String	Additional kraken2 arguments		Optional	TheiaCoV_ClearLabs, TheiaViral_Panel	general	
kraken2_raw	kraken2_db	File	The database used to run Kraken2. Must contain viral and human sequences.	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz	Optional	TheiaCoV_ClearLabs	database	
kraken2_raw	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaCoV_ClearLabs, TheiaMeta_Illumina_PE, TheiaViral_Panel	runtime	
kraken2_raw	read2	File	Internal component, do not modify		Optional	TheiaCoV_ClearLabs	general	
kraken2_raw	target_organism	String	Target organism for reporting percent identified		Optional	TheiaMeta_Illumina_PE, TheiaViral_Panel	general	
kraken2_raw	unclassified_out	String	Internal component, do not modify	unclassified#.fastq	Optional	TheiaCoV_ClearLabs, TheiaViral_Panel	general	
kraken2_se	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database		Optional	Kraken_SE	general	
kraken2_se	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	Kraken_SE	general	
kraken2_se	classified_out	String	Allows user to rename the classified FASTQ files output. Must include .fastq as the suffix	classified#.fastq	Optional	Kraken_SE	general	
kraken2_se	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Kraken_SE	runtime	
kraken2_se	disk_size	Int	Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database)	100	Optional	Kraken_SE	runtime	
kraken2_se	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/kraken2:2.17.1	Optional	Kraken_SE	docker	
kraken2_se	kraken2_args	String	Allows a user to supply additional kraken2 command-line arguments		Optional	Kraken_SE	general	
kraken2_se	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Kraken_SE	runtime	
kraken2_se	read2	File	Internal component, do not modify		Optional	Kraken_SE	general	
kraken2_se	target_organism	String	Target organism for reporting percent identified		Optional	Kraken_SE	general	
kraken2_se	unclassified_out	String	Allows user to rename unclassified FASTQ files output. Must include .fastq as the suffix	unclassified#.fastq	Optional	Kraken_SE	general	
kraken2_taxon	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database		Optional	TheiaViral_Panel	general	
kraken2_taxon	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	TheiaViral_Panel	general	
kraken2_taxon	classified_out	String	Internal component, do not modify	classified#.fastq	Optional	TheiaViral_Panel	general	
kraken2_taxon	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_Panel	runtime	
kraken2_taxon	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Panel	runtime	
kraken2_taxon	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/kraken2:2.17.1	Optional	TheiaViral_Panel	docker	
kraken2_taxon	kraken2_args	String	Additional kraken2 arguments		Optional	TheiaViral_Panel	general	
kraken2_taxon	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaViral_Panel	runtime	
kraken2_taxon	unclassified_out	String	Internal component, do not modify	unclassified#.fastq	Optional	TheiaViral_Panel	general	
kraken_parser	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Panel	runtime	
kraken_parser	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Panel	runtime	
kraken_parser	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/krakentools:d4a2fbe	Optional	TheiaViral_Panel	docker	
kraken_parser	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaViral_Panel	runtime	
krakentools	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaViral_Panel	runtime	
krakentools	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Panel	runtime	
krakentools	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/krakentools:d4a2fbe	Optional	TheiaViral_Panel	docker	
krakentools	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaViral_Panel	runtime	
krona	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Kraken_PE, Kraken_SE	runtime	
krona	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Kraken_PE, Kraken_SE	runtime	
krona	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1	Optional	Kraken_PE, Kraken_SE	docker	
krona	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Kraken_PE, Kraken_SE	runtime	
krona_clean	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
krona_clean	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
krona_clean	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1	Optional	TheiaMeta_Illumina_PE	docker	
krona_clean	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
krona_raw	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
krona_raw	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
krona_raw	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1	Optional	TheiaMeta_Illumina_PE	docker	
krona_raw	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
ksnp3_task	cpu	Int	Number of CPUs to allocate to the task	2	Optional	kSNP3	runtime	
ksnp3_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	kSNP3	runtime	
ksnp3_task	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ksnp3:3.1	Optional	kSNP3	docker	
ksnp3_task	kmer_size	Int	The length of kmer containing the SNP you want kSNP3 to use	19	Optional	kSNP3	general	
ksnp3_task	ksnp3_args	String	Additional arguments you want kSNP3 to use; e.g., "-ML" or "-NJ"		Optional	kSNP3	general	
ksnp3_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	kSNP3	runtime	
ksnp3_task	previous_ksnp3_snps	File	File with existing SNPs for the current run to be appended to.		Optional	kSNP3	general	
ksnp3_workflow	cluster_name_updated	String	Internal component, do not modify	cluster_name where ' ' is substituted with '_'	Optional	kSNP3	general	
ksnp3_workflow	data_summary_column_names	String	A comma-separated list of the column names from the sample-level data table for generating a data summary (presence/absence .csv matrix); e.g., "amrfinderplus_amr_genes,amrfinderplus_virulence_genes"		Optional	kSNP3	general	
ksnp3_workflow	data_summary_terra_project	String	The billing project for your current workspace. This can be found after the "#workspaces/" section in the workspace's URL		Optional	kSNP3	general	
ksnp3_workflow	data_summary_terra_table	String	The name of the sample-level Terra data table that will be used for generating a data summary		Optional	kSNP3	general	
ksnp3_workflow	data_summary_terra_workspace	String	The name of the Terra workspace you are in. This can be found at the top of the webpage, or in the URL after the billing project.		Optional	kSNP3	general	
ksnp3_workflow	midpoint_root_tree	Boolean	If true, midpoint root the final tree	True	Optional	kSNP3	general	
ksnp3_workflow	phandango_coloring	Boolean	Boolean variable that tells the data summary task and the reorder matrix task to include a suffix that enables consistent coloring on Phandango; by default, this suffix is not added. To add this suffix set this variable to true.	False	Optional	kSNP3	general	
ksnp4_task	cpu	Int	Number of CPUs to allocate to the task	2	Optional	kSNP4	runtime	
ksnp4_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	kSNP4	runtime	
ksnp4_task	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ksnp4:4.1	Optional	kSNP4	docker	
ksnp4_task	kmer_size	Int	The length of kmer containing the SNP you want ksnp4 to use	19	Optional	kSNP4	general	
ksnp4_task	ksnp4_args	String	Additional arguments you want kSNP4 to use; e.g., "-ML" or "-NJ"		Optional	kSNP4	general	
ksnp4_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	kSNP4	runtime	
ksnp4_task	previous_ksnp4_snps	File	File with existing SNPs for the current run to be appended to.		Optional	kSNP4	general	
ksnp4_workflow	cluster_name_updated	String	Internal component, do not modify	cluster_name where ' ' is substituted with '_'	Optional	kSNP4	general	
ksnp4_workflow	data_summary_column_names	String	A comma-separated list of the column names from the sample-level data table for generating a data summary (presence/absence .csv matrix); e.g., "amrfinderplus_amr_genes,amrfinderplus_virulence_genes"		Optional	kSNP4	general	
ksnp4_workflow	data_summary_terra_project	String	The billing project for your current workspace. This can be found after the "#workspaces/" section in the workspace's URL		Optional	kSNP4	general	
ksnp4_workflow	data_summary_terra_table	String	The name of the sample-level Terra data table that will be used for generating a data summary		Optional	kSNP4	general	
ksnp4_workflow	data_summary_terra_workspace	String	The name of the Terra workspace you are in. This can be found at the top of the webpage, or in the URL after the billing project.		Optional	kSNP4	general	
ksnp4_workflow	midpoint_root_tree	Boolean	If true, midpoint root the final tree	True	Optional	kSNP4	general	
ksnp4_workflow	phandango_coloring	Boolean	Boolean variable that tells the data summary task and the reorder matrix task to include a suffix that enables consistent coloring on Phandango; by default, this suffix is not added. To add this suffix set this variable to true.	False	Optional	kSNP4	general	
lyveset	allowedFlanking	Int	Allowed flanking distance in base pairs. Nucleotides this close together cannot be considered as high-quality.	0	Optional	Lyve_SET	general	
lyveset	cpu	Int	Number of CPUs to allocate to the task	16	Optional	Lyve_SET	runtime	
lyveset	disk_size	Int	Amount of storage (in GB) to allocate to the task	250	Optional	Lyve_SET	runtime	
lyveset	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/lyveset:1.1.4f	Optional	Lyve_SET	docker	
lyveset	downsample	Boolean	If true, downsample all reads to 50x. Approximated according to the ref genome assembly	False	Optional	Lyve_SET	general	
lyveset	fast	Boolean	Shorthand for --downsample --mapper snap --nomask-phages --nomask-cliffs --sample-sites	False	Optional	Lyve_SET	general	
lyveset	mapper	String	Which mapper? Choices: "smalt", "snap"	smalt	Optional	Lyve_SET	general	
lyveset	mask_cliffs	Boolean	If true, search for and mask 'Cliffs' in pileups	False	Optional	Lyve_SET	general	
lyveset	mask_phages	Boolean	If true, search for and mask phages in the reference genome	False	Optional	Lyve_SET	general	
lyveset	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	64	Optional	Lyve_SET	runtime	
lyveset	min_alt_frac	Float	The percent consensus that needs to be reached before a SNP is called. Otherwise, 'N'	0.75	Optional	Lyve_SET	general	
lyveset	min_coverage	Int	Minimum coverage needed before a SNP is called. Otherwise, 'N'	10	Optional	Lyve_SET	general	
lyveset	nomatrix	Boolean	If true, do not create an hqSNP matrix	False	Optional	Lyve_SET	general	
lyveset	nomsa	Boolean	If true, do not make a multiple sequence alignment	False	Optional	Lyve_SET	general	
lyveset	notrees	Boolean	If true, do not make phylogenies	False	Optional	Lyve_SET	general	
lyveset	presets	String	See presets.conf for more information		Optional	Lyve_SET	general	
lyveset	read_cleaner	String	Which read cleaner? Choices: "none", "CGP", "BayesHammer"	CGP	Optional	Lyve_SET	general	
lyveset	sample_sites	Boolean	If true, randomly choose a genome and find SNPs in a quick and dirty way. Then on the SNP-calling stage, only interrogate those sites for SNPs for each genome (including the randomly-sampled genome).	False	Optional	Lyve_SET	general	
lyveset	snpcaller	String	Which SNP caller? Choices: "varscan", "vcftools"	varscan	Optional	Lyve_SET	general	
make_table	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Create_Terra_Table	runtime	
make_table	disk_size	Int	Amount of storage (in GB) to allocate to the task	25	Optional	Create_Terra_Table	runtime	
make_table	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	Create_Terra_Table	docker	
make_table	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Create_Terra_Table	runtime	
make_table	responsible_workflow	String	Internal component, do not modify	Create_Terra_Table_PHB	Optional	Create_Terra_Table	general	
mashtree_fasta	data_summary_column_names	String	A comma-separated list of the column names from the sample-level data table for generating a data summary (presence/absence .csv matrix); e.g., "amrfinderplus_amr_genes,amrfinderplus_virulence_genes"		Optional	MashTree_FASTA	general	
mashtree_fasta	data_summary_terra_project	String	The billing project for your current workspace. This can be found after the "#workspaces/" section in the workspace's URL		Optional	MashTree_FASTA	general	
mashtree_fasta	data_summary_terra_table	String	The name of the sample-level Terra data table that will be used for generating a data summary		Optional	MashTree_FASTA	general	
mashtree_fasta	data_summary_terra_workspace	String	The name of the Terra workspace you are in. This can be found at the top of the webpage, or in the URL after the billing project.		Optional	MashTree_FASTA	general	
mashtree_fasta	midpoint_root_tree	Boolean	If true, midpoint root the final tree	True	Optional	MashTree_FASTA	general	
mashtree_fasta	phandango_coloring	Boolean	Boolean variable that tells the data summary task and the reorder matrix task to include a suffix that enables consistent coloring on Phandango; by default, this suffix is not added. To add this suffix set this variable to true.	False	Optional	MashTree_FASTA	general	
mashtree_fasta	sample_names	Array[String]	The list of samples		Optional	MashTree_FASTA	general	
mashtree_task	cpu	Int	Number of CPUs to allocate to the task	16	Optional	MashTree_FASTA	runtime	
mashtree_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	MashTree_FASTA	runtime	
mashtree_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mashtree:1.2.0	Optional	MashTree_FASTA	docker	
mashtree_task	genomesize	Int	Genome size of the input samples	5000000	Optional	MashTree_FASTA	general	
mashtree_task	kmerlength	Int	Hashes will be based on strings of this many nucleotides	21	Optional	MashTree_FASTA	general	
mashtree_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	64	Optional	MashTree_FASTA	runtime	
mashtree_task	mindepth	Int	If set to zero, mashtree will run in "accurate" mode as it will chose a mindepth by itself in a slower method; this value otherwise indicates the minimum number of times a kmer must appear in order to be included	5	Optional	MashTree_FASTA	general	
mashtree_task	sketchsize	Int	Each sketch will have at most this many non-redundant min-hashes	10000	Optional	MashTree_FASTA	general	
mashtree_task	sort_order	String	For neighbor-joining, the sort order can make a difference. Options include: "ABC" (alphabetical), "random", "input-order"	ABC	Optional	MashTree_FASTA	general	
mashtree_task	truncLength	Int	How many characters to keep in a filename	250	Optional	MashTree_FASTA	general	
mask_low_coverage	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_ONT	runtime	
mask_low_coverage	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
mask_low_coverage	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/bedtools:2.31.0	Optional	TheiaViral_ONT	docker	
mask_low_coverage	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_ONT	runtime	
megahit	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_Illumina_PE	runtime	
megahit	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE	runtime	
megahit	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/megahit:1.2.9	Optional	TheiaViral_Illumina_PE	docker	
megahit	kmers	String	Comma-separated list of kmer sizes to use for assembly. All must be odd, in the range 15-255, increment <= 28	21,29,39,59,79,99,119,141	Optional	TheiaViral_Illumina_PE	general	
megahit	megahit_opts	String	Additional parameters for MEGAHIT assembler		Optional	TheiaViral_Illumina_PE	general	
megahit	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaViral_Illumina_PE	runtime	
megahit	min_contig_length	Int	Minimum contig length for MEGAHIT assembler	1	Optional	TheiaViral_Illumina_PE	general	
mercury	amplicon_primer_scheme	String	Populate to overwrite amplicon_primer_scheme column		Optional	Mercury_Prep_N_Batch	general	
mercury	amplicon_size	String	Populate to overwrite amplicon_size column		Optional	Mercury_Prep_N_Batch	general	
mercury	authors	String	Populate to overwrite authors column		Optional	Mercury_Prep_N_Batch	general	
mercury	bioproject_accession	String	Populate to overwrite bioproject_accession column		Optional	Mercury_Prep_N_Batch	general	
mercury	continent	String	Populate to overwrite continent column		Optional	Mercury_Prep_N_Batch	general	
mercury	country	String	Populate to overwrite country column		Optional	Mercury_Prep_N_Batch	general	
mercury	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Mercury_Prep_N_Batch	runtime	
mercury	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Mercury_Prep_N_Batch	runtime	
mercury	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.1.3	Optional	Mercury_Prep_N_Batch	docker	
mercury	gisaid_submitter	String	Populate to overwrite gisaid_submitter column		Optional	Mercury_Prep_N_Batch	general	
mercury	host_disease	String	Populate to overwrite host_disease column		Optional	Mercury_Prep_N_Batch	general	
mercury	instrument_model	String	Populate to overwrite instrument_model column		Optional	Mercury_Prep_N_Batch	general	
mercury	isolation_source	String	Populate to overwrite isolation_source column		Optional	Mercury_Prep_N_Batch	general	
mercury	library_layout	String	Populate to overwrite library_layout column		Optional	Mercury_Prep_N_Batch	general	
mercury	library_selection	String	Populate to overwrite library_selection column		Optional	Mercury_Prep_N_Batch	general	
mercury	library_source	String	Populate to overwrite library_source column		Optional	Mercury_Prep_N_Batch	general	
mercury	library_strategy	String	Populate to overwrite library_strategy column		Optional	Mercury_Prep_N_Batch	general	
mercury	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Mercury_Prep_N_Batch	runtime	
mercury	metadata_organism	String	Organism name for metadata population		Optional	Mercury_Prep_N_Batch	general	
mercury	number_N_threshold	Int	Only for "sars-cov-2" submissions; used to filter out any samples that contain more than the indicated number of Ns in the assembly file	5000	Optional	Mercury_Prep_N_Batch	general	
mercury	purpose_of_sequencing	String	Populate to overwrite purpose_of_sequencing column		Optional	Mercury_Prep_N_Batch	general	
mercury	seq_platform	String	Populate to overwrite seq_platform column		Optional	Mercury_Prep_N_Batch	general	
mercury	single_end	Boolean	Set to true if your data is single-end; this ensures that a read2 column is not included in the metadata	False	Optional	Mercury_Prep_N_Batch	general	
mercury	skip_county	Boolean	Use if your Terra table contains a county column that you do not want to include in your submission.	False	Optional	Mercury_Prep_N_Batch	general	
mercury	state	String	Populate to overwrite state column		Optional	Mercury_Prep_N_Batch	general	
mercury	submitter_email	String	Populate to overwrite submitter_email column		Optional	Mercury_Prep_N_Batch	general	
mercury	submitting_lab	String	Populate to overwrite submitting_lab column		Optional	Mercury_Prep_N_Batch	general	
mercury	submitting_lab_address	String	Populate to overwrite submitting_lab_address column		Optional	Mercury_Prep_N_Batch	general	
mercury	usa_territory	Boolean	If true, the "state" column will be used in place of the "country" column. For example, if "state" is Puerto Rico, then the GISAID virus name will be hCoV-19/Puerto Rico/<name>/<year>. The NCBI geo_loc_name will be "USA: Puerto Rico". This optional Boolean variable should only be used with clear understanding of what it does.	False	Optional	Mercury_Prep_N_Batch	general	
mercury	using_clearlabs_data	Boolean	When set to true will change read1_dehosted → clearlabs_fastq_gz; assembly_fasta → clearlabs_fasta; assembly_mean_coverage → clearlabs_sequencing_depth	False	Optional	Mercury_Prep_N_Batch	general	
mercury	using_reads_dehosted	Boolean	When set to true will only change read1_dehosted → reads_dehosted. Takes priority over the replacement for read1_dehosted made with the using_clearlabs_data Boolean input	False	Optional	Mercury_Prep_N_Batch	general	
mercury	vadr_alert_limit	Int	Only for "sars-cov-2" submissions; used to filter out any samples that contain more than the indicated number of vadr alerts	0	Optional	Mercury_Prep_N_Batch	general	
mercury_prep_n_batch	authors_sbt	File	Only for "mpox" submissions; a file that contains author information. This file can be created here: <https://submit.ncbi.nlm.nih.gov/genbank/template/submission/>		Optional	Mercury_Prep_N_Batch	general	
mercury_prep_n_batch	organism	String	The organism that you want submission prepare for — each organism requires different metadata fields so please ensure this field is accurate. Options: "flu", "mpox"" or "sars-cov-2"	sars-cov-2	Optional	Mercury_Prep_N_Batch	general	
mercury_prep_n_batch	output_name	String	Free text prefix for all output files	mercury	Optional	Mercury_Prep_N_Batch	general	
mercury_prep_n_batch	skip_ncbi	Boolean	Set to true if you only want to prepare GISAID submission files	False	Optional	Mercury_Prep_N_Batch	general	
merlin_magic	abricate_abaum_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-abaum-plasmid	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	abricate_abaum_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-abaum-plasmid	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	abricate_abaum_min_percent_coverage	Int	Internal component, do not modify	80	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	abricate_abaum_min_percent_coverage	Int	Minimum DNA percent coverage	80	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	abricate_abaum_min_percent_identity	Int	Internal component, do not modify	95	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	abricate_abaum_min_percent_identity	Int	Minimum DNA percent identity; set to 95 because there is a strict threshold of 95% identity for typing purposes	95	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	abricate_vibrio_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-vibrio-cholera	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	abricate_vibrio_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-vibrio-cholera	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	abricate_vibrio_min_percent_coverage	Int	Internal component, do not modify	80	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	abricate_vibrio_min_percent_coverage	Int	Minimum DNA percent coverage	80	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	abricate_vibrio_min_percent_identity	Int	Internal component, do not modify	80	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	abricate_vibrio_min_percent_identity	Int	Minimum DNA percent identity	80	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	agrvate_agr_typing_only	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	agrvate_agr_typing_only	Boolean	Set to true to skip agr operon extraction and frameshift detection	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	agrvate_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/biocontainers/agrvate:1.0.2--hdfd78af_0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	agrvate_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/agrvate:1.0.2--hdfd78af_0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	amr_search_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
merlin_magic	amr_search_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
merlin_magic	amr_search_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	amr_search_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
merlin_magic	assembly_only	Boolean	Set to true if only analyzing input assembly	False	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	call_poppunk	Boolean	Internal component, do not modify	True	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	call_poppunk	Boolean	If true, runs PopPUNK for GPSC cluster designation for S. pneumoniae	True	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	call_shigeifinder_reads_input	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	call_shigeifinder_reads_input	Boolean	If set to "true", the ShigEiFinder task will run again but using read files as input instead of the assembly file. Input is shown but not used for TheiaProk_FASTA.	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	call_stxtyper	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	call_stxtyper	Boolean	If set to "true", the StxTyper task will run on all samples regardless of the gambit_predicted_taxon output. Useful if you suspect a non-E.coli or non-Shigella sample contains stx genes.	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	call_tbp_parser	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	call_tbp_parser	Boolean	If set to "true", activates the tbp_parser module and results in more outputs, including tbp_parser_looker_report_csv, tbp_parser_laboratorian_report_csv,  tbp_parser_lims_report_csv, tbp_parser_coverage_report, and tbp_parser_genome_percent_coverage	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	cauris_cladetyper_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	docker	
merlin_magic	cauris_cladetyper_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/gambit:1.0.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	cladetyper_kmer_size	Int	Kmer size for cladetyper	11	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	cladetyper_kmer_size	Int	Internal component, do not modify	11	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	cladetyper_max_distance	Float	The maximum GAMBIT distance to report a *C. auris* clade hit	0.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	cladetyper_max_distance	Float	Internal component, do not modify	0.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	cladetyper_ref_clade1	File	Reference genome FASTA for *Candidozyma auris* clade1	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.3_Cand_auris_B8441_V3_genomic.fasta	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade1	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.3_Cand_auris_B8441_V3_genomic.fasta	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade1_annotated	File	Reference GBFF annotation for *C. auris* clade1	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.3_Cand_auris_B8441_V3_genomic.gbff	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade1_annotated	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.3_Cand_auris_B8441_V3_genomic.gbff	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade2	File	Reference genome FASTA for *C. auris* clade2	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.fasta	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade2	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.fasta	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade2_annotated	File	Reference GBFF annotation for *C. auris* clade2	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.gbff	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade2_annotated	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.gbff	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade3	File	Reference genome FASTA for *C. auris* clade3	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.fasta	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade3	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.fasta	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade3_annotated	File	Reference GBFF annotation for *C. auris* clade3	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.gbff	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade3_annotated	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.gbff	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade4	File	Reference genome FASTA for *C. auris* clade4	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.fasta	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade4	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.fasta	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade4_annotated	File	Reference GBFF annotation for *C. auris* clade4	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.gbff	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade4_annotated	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.gbff	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade5	File	Reference genome FASTA for *C. auris* clade5	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.fasta	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade5	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.fasta	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade5_annotated	File	Reference GBFF annotation for *C. auris* clade5	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.gbff	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade5_annotated	File	*Provide an empty file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.gbff	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade6	File	Reference genome FASTA for *C. auris* clade6	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade6_GCA_032714025.1_ASM3271402v1_genomic.fasta	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	cladetyper_ref_clade6	File	The reference assembly for clade 6	gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade6_GCA_032714025.1_ASM3271402v1_genomic.fasta	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	reference	
merlin_magic	cladetyper_ref_clade6_annotated	File	Reference GBFF annotation for *C. auris* clade6		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	cladetyper_ref_clade6_annotated	File	The path to the annotated reference for clade 6		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	clockwork_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/cdcgov/varpipe_wgs_with_refs:2bc7234074bd53d9e92a1048b0485763cd9bbf6f4d12d5a1cc82bfec8ca7d75e	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	clockwork_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/cdcgov/varpipe_wgs_with_refs:2bc7234074bd53d9e92a1048b0485763cd9bbf6f4d12d5a1cc82bfec8ca7d75e	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	ectyper_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/ectyper:2.0.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	ectyper_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ectyper:2.0.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	ectyper_h_min_percent_coverage	Int	Internal component, do not modify	50	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	ectyper_h_min_percent_coverage	Int	Minumum percent coverage required for an H antigen allele match	50	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	ectyper_h_min_percent_identity	Int	Internal component, do not modify	95	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	ectyper_h_min_percent_identity	Int	Percent identity required for an H antigen allele match	95	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	ectyper_o_min_percent_coverage	Int	Internal component, do not modify	90	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	ectyper_o_min_percent_coverage	Int	Minumum percent coverage required for an O antigen allele match	90	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	ectyper_o_min_percent_identity	Int	Internal component, do not modify	90	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	ectyper_o_min_percent_identity	Int	Percent identity required for an O antigen allele match	90	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	ectyper_print_alleles	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	ectyper_print_alleles	Boolean	Set to true to print the allele sequences as the final column	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	ectyper_verify	Boolean	Internal component, do not modify	True	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	ectyper_verify	Boolean	Set to true to enable E. coli species verification	True	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_align_diff	Int	Internal component, do not modify	5	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_align_diff	Int	Threshold for difference between alignment length and subject length in BLAST hit.	5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_cluster_distance	Int	Internal component, do not modify	500	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_cluster_distance	Int	Distance between cluster of matches to consider as different clusters.	500	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_culling_limit	Int	Internal component, do not modify	5	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_culling_limit	Int	Total hits to return in a position.	5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/biocontainers/emmtyper:0.2.0--py_0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/emmtyper:0.2.0--py_0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	emmtyper_gap	Int	Internal component, do not modify	2	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_gap	Int	Threshold gap to allow in BLAST hit.	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_max_size	Int	Internal component, do not modify	2000	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_max_size	Int	Maximum size of PCR product.	2000	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_min_good	Int	Internal component, do not modify	15	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_min_good	Int	Minimum size where there must be 2 matches for each mismatch.	15	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_min_percent_identity	Int	Internal component, do not modify	95	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_min_percent_identity	Int	Minimal percent identity of sequence.	95	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_min_perfect	Int	Internal component, do not modify	15	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_min_perfect	Int	Minimum size of perfect match at 3' primer end.	15	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_mismatch	Int	Internal component, do not modify	4	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_mismatch	Int	Threshold for number of mismatch to allow in BLAST hit.	4	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtyper_wf	String	Internal component, do not modify	blast	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtyper_wf	String	Choose workflow [blast|pcr]	blast	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	emmtypingtool_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/emmtypingtool:0.0.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	emmtypingtool_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/emmtypingtool:0.0.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	genotyphi_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.11.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	genotyphi_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.11.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	hicap_broken_gene_length	Int	Internal component, do not modify	60	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	hicap_broken_gene_length	Int	Minimum length to consider a broken gene	60	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	hicap_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/biocontainers/hicap:1.0.3--py_0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	hicap_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/hicap:1.0.3--py_0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	hicap_min_broken_gene_percent_identity	Float	Internal component, do not modify	0.8	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	hicap_min_broken_gene_percent_identity	Float	Minimum percentage identity to consider a broken gene	0.8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	hicap_min_gene_percent_coverage	Float	Internal component, do not modify	0.8	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	hicap_min_gene_percent_coverage	Float	Minimum percentage coverage to consider a single gene complete	0.8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	hicap_min_gene_percent_identity	Float	Internal component, do not modify	0.7	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	hicap_min_gene_percent_identity	Float	Minimum percentage identity to consider a single gene complete	0.7	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kaptive_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/kaptive:2.0.3	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kaptive_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/kaptive:2.0.3	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	kaptive_low_gene_percent_identity	Float	Internal component, do not modify	95.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kaptive_low_gene_percent_identity	Float	Percent identity threshold for what counts as a low identity match in the gene BLAST search	95.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kaptive_min_percent_coverage	Float	Internal component, do not modify	90.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kaptive_min_percent_coverage	Float	Minimum required percent coverage for the gene BLAST search via tBLASTn	90.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kaptive_min_percent_identity	Float	Internal component, do not modify	80.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kaptive_min_percent_identity	Float	Minimum required percent identity for the gene BLAST search via tBLASTn	80.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kaptive_start_end_margin	Int	Internal component, do not modify	10	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kaptive_start_end_margin	Int	Determines flexibility in identifying the start and end of a locus - if this value is 10, a locus match that is missing the first 8 base pairs will still count as capturing the start of the locus	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kleborate_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/kleborate:2.2.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kleborate_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/kleborate:2.2.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	kleborate_min_kaptive_confidence	String	Internal component, do not modify	Good	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kleborate_min_kaptive_confidence	String	{None,Low,Good,High,Very_high,Perfect} Minimum Kaptive confidence to call K/O loci - confidence levels below this will be reported as unknown	Good	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kleborate_min_percent_coverage	Float	Internal component, do not modify	80.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kleborate_min_percent_coverage	Float	Minimum alignment percent coverage for main results	80.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kleborate_min_percent_identity	Float	Internal component, do not modify	90.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kleborate_min_percent_identity	Float	Minimum alignment percent identity for main results	90.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kleborate_min_spurious_percent_coverage	Float	Internal component, do not modify	40.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kleborate_min_spurious_percent_coverage	Float	Minimum alignment percent coverage for spurious results	40.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kleborate_min_spurious_percent_identity	Float	Internal component, do not modify	80.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kleborate_min_spurious_percent_identity	Float	Minimum alignment percent identity for spurious results	80.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kleborate_skip_kaptive	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kleborate_skip_kaptive	Boolean	Equivalent to --kaptive_k --kaptive_	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	kleborate_skip_resistance	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	kleborate_skip_resistance	Boolean	Set to true to turn on resistance genes screening (default: no resistance gene screening)	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	legsta_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/legsta:0.5.1--hdfd78af_2	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	docker	
merlin_magic	legsta_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/biocontainers/legsta:0.5.1--hdfd78af_2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	lissero_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/biocontainers/lissero:0.4.9--py_0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	lissero_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/lissero:0.4.9--py_0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	lissero_min_percent_coverage	Float	Internal component, do not modify	95.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	lissero_min_percent_coverage	Float	Minimum percent coverage of the gene to accept a match	95.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	lissero_min_percent_identity	Float	Internal component, do not modify	95.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	lissero_min_percent_identity	Float	Minimum percent identity to accept a match	95.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	meningotype_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/biocontainers/meningotype:0.8.5--pyhdfd78af_0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	meningotype_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/meningotype:0.8.5--pyhdfd78af_0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	ngmaster_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/ngmaster:1.0.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	ngmaster_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ngmaster:1.0.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	ont_data	Boolean	Set to true if your data is ONT FASTQ files	False	Optional	TheiaEuk_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
merlin_magic	paired_end	Boolean	Set to true if your data is paired-end FASTQ files	True	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_ONT	general	
merlin_magic	pasty_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/pasty:1.0.3	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	pasty_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/pasty:1.0.3	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	pasty_min_percent_coverage	Int	Internal component, do not modify	95	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	pasty_min_percent_coverage	Int	Minimum coverage of a O-antigen to be considered for serogrouping by pasty	95	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	pasty_min_percent_identity	Int	Internal component, do not modify	95	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	pasty_min_percent_identity	Int	Minimum percent identity for a blast hit to be considered for serogrouping	95	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	pbptyper_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/pbptyper:1.0.4	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	pbptyper_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/pbptyper:1.0.4	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	pbptyper_min_percent_coverage	Int	Internal component, do not modify	95	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	pbptyper_min_percent_coverage	Int	Minimum percent coverage to count a hit	95	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	pbptyper_min_percent_identity	Int	Internal component, do not modify	95	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	pbptyper_min_percent_identity	Int	Minimum percent identity to count a hit	95	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	poppunk_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/poppunk:2.4.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/poppunk:2.4.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	poppunk_gps_clusters_csv	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_clusters.csv	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_clusters_csv	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_clusters.csv	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_dists_npy	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.dists.npy	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_dists_npy	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.dists.npy	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_dists_pkl	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.dists.pkl	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_dists_pkl	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.dists.pkl	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_external_clusters_csv	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_external_clusters.csv	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_external_clusters_csv	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_external_clusters.csv	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_fit_npz	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_fit.npz	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_fit_npz	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_fit.npz	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_fit_pkl	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_fit.pkl	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_fit_pkl	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_fit.pkl	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_graph_gt	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_graph.gt	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_graph_gt	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_graph.gt	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_h5	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.h5	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_h5	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.h5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_qcreport_txt	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_qcreport.txt	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_qcreport_txt	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_qcreport.txt	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_refs	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_refs	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_refs_dists_npy	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs.dists.npy	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_refs_dists_npy	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs.dists.npy	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_refs_dists_pkl	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs.dists.pkl	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_refs_dists_pkl	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs.dists.pkl	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_refs_graph_gt	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6refs_graph.gt	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_refs_graph_gt	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6refs_graph.gt	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_refs_h5	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs.h5	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_refs_h5	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6.refs.h5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	poppunk_gps_unword_clusters_csv	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_unword_clusters.csv	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	poppunk_gps_unword_clusters_csv	File	Poppunk database file *Provide an empty or local file if running TheiaProk on the command-line	gs://theiagen-public-resources-rp/reference_data/databases/poppunk/GPS_v6/GPS_v6_unword_clusters.csv	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	read1	File	Internal component, do not modify		Optional	TheiaEuk_ONT, TheiaProk_FASTA	general	
merlin_magic	read2	File	Internal component, do not modify		Optional	TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	run_amr_search	Boolean	If set to true AMR_Search workflow will be run if species is part of supported taxon, see AMR_Search docs.	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	seqsero2s_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/seqsero2s:1.1.4	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	seqsero2s_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/seqsero2s:1.1.4	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	seroba_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/seroba:1.0.2	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	seroba_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/seroba:1.0.2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	serotypefinder_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/serotypefinder:2.0.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	serotypefinder_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/serotypefinder:2.0.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	shigatyper_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/shigatyper:2.0.5	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	shigatyper_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/shigatyper:2.0.5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	shigeifinder_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/shigeifinder:1.3.5	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	shigeifinder_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/shigeifinder:1.3.5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	sistr_cpu	Int	Internal component, do not modify	2	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	sistr_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
merlin_magic	sistr_disk_size	Int	Internal component, do not modify	100	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	sistr_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
merlin_magic	sistr_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/sistr:1.1.3	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	sistr_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/sistr:1.1.3	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	sistr_memory	Int	Internal component, do not modify	8	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	sistr_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
merlin_magic	sistr_use_full_cgmlst_db	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	sistr_use_full_cgmlst_db	Boolean	Set to true to use the full set of cgMLST alleles which can include highly similar alleles. By default the smaller "centroid" alleles or representative alleles are used for each marker	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	
merlin_magic	snippy_base_quality	Int	Minimum quality for a nucleotide to be used in variant calling	13	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	snippy_base_quality	Int	Internal component, do not modify	13	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_gene_query_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	docker	
merlin_magic	snippy_gene_query_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_map_qual	Int	Minimum mapping quality to accept in variant calling	60	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	snippy_map_qual	Int	Internal component, do not modify	60	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_maxsoft	Int	Number of bases of alignment to soft-clip before discarding the alignment	10	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	snippy_maxsoft	Int	Internal component, do not modify	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_min_coverage	Int	Minimum read coverage of a position to identify a mutation	10	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	snippy_min_coverage	Int	Internal component, do not modify	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_min_frac	Float	Minimum fraction of bases at a given position to identify a mutation	0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	snippy_min_frac	Float	Internal component, do not modify	0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_min_quality	Int	Minimum VCF variant call "quality"	100	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	snippy_min_quality	Int	Internal component, do not modify	100	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_query_gene	String	Provide a gene to search for using Snippy	Default depends on detected organism	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	True
merlin_magic	snippy_query_gene	String	Internal component, do not modify		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_reference_afumigatus	File	Snippy reference for Aspergillus fumigatus	gs://theiagen-public-resources-rp/reference_data/eukaryotic/aspergillus/Aspergillus_fumigatus_GCF_000002655.1_ASM265v1_genomic.gbff	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	snippy_reference_afumigatus	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/eukaryotic/aspergillus/Aspergillus_fumigatus_GCF_000002655.1_ASM265v1_genomic.gbff	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_reference_cryptoneo	File	Snippy reference for Cryptococcus neoformans	gs://theiagen-public-resources-rp/reference_data/eukaryotic/cryptococcus/Cryptococcus_neoformans_GCF_000091045.1_ASM9104v1_genomic.gbff	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	reference	
merlin_magic	snippy_reference_cryptoneo	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/eukaryotic/cryptococcus/Cryptococcus_neoformans_GCF_000091045.1_ASM9104v1_genomic.gbff	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	snippy_variants_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snippy:4.6.0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	docker	
merlin_magic	snippy_variants_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/snippy:4.6.0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	sonneityping_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1-sonneityping	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	sonneityping_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1-sonneityping	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	sonneityping_mykrobe_opts	String	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	sonneityping_mykrobe_opts	String	Additional options for mykrobe in sonneityping		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	spatyper_do_enrich	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	spatyper_do_enrich	Boolean	Set to true to enable PCR product enrichment	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	spatyper_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/biocontainers/spatyper:0.3.3--pyhdfd78af_3	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	spatyper_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/spatyper:0.3.3--pyhdfd78af_3	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	srst2_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/srst2:0.2.0-vcholerae	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	srst2_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/srst2:0.2.0-vcholerae	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	srst2_gene_max_mismatch	Int	Internal component, do not modify	2000	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	srst2_gene_max_mismatch	Int	Maximum number of mismatches for SRST2 to call a gene as present	2000	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	srst2_max_divergence	Int	Internal component, do not modify	20	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	srst2_max_divergence	Int	Maximum divergence, in percentage, for SRST2 to call a gene as present	20	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	srst2_min_depth	Int	Internal component, do not modify	5	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	srst2_min_depth	Int	Minimum depth of coverage for SRST2 to call a gene as present	5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	srst2_min_edge_depth	Int	Internal component, do not modify	2	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	srst2_min_edge_depth	Int	Minimum edge depth for SRST2 to call a gene as present	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	srst2_min_percent_coverage	Int	Internal component, do not modify	80	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	srst2_min_percent_coverage	Int	Minimum breadth of coverage for SRST2 to call a gene as present	80	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	staphopia_sccmec_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	staphopia_sccmec_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	stxtyper_cpu	Int	Internal component, do not modify	1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	stxtyper_cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
merlin_magic	stxtyper_disk_size	Int	Internal component, do not modify	50	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	stxtyper_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
merlin_magic	stxtyper_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/stxtyper:1.0.45	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	stxtyper_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/stxtyper:1.0.45	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	stxtyper_enable_debug	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	stxtyper_enable_debug	Boolean	When enabled, additional messages are printed and files in $TMPDIR are not removed after running	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	stxtyper_memory	Int	Internal component, do not modify	4	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	stxtyper_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
merlin_magic	tbp_parser_add_cs_lims	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_add_cs_lims	Boolean	Set to true add cycloserine results to the LIMS report	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_config	File	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_config	File	The configuration file to use, in YAML format (overrides all other arguments except input_json and input_bam)		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_coverage_regions_bed	File	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_coverage_regions_bed	File	A bed file that lists the regions to be considered for QC		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_debug	Boolean	Internal component, do not modify	True	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_debug	Boolean	Activate the debug mode on tbp_parser; increases logging outputs	True	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.9.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.9.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	tbp_parser_etha237_frequency	Float	Internal component, do not modify	0.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_etha237_frequency	Float	Minimum frequency for a mutation in ethA at protein position 237 to pass QC in tbp-parser	0.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_expert_rule_regions_bed	File	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_expert_rule_regions_bed	File	A file that contains the regions where R mutations and expert rules are applied		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_min_depth	Int	Internal component, do not modify	10	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_min_depth	Int	Minimum depth for a variant to pass QC in tbp_parser	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_min_frequency	Float	Internal component, do not modify	0.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_min_frequency	Float	The minimum frequency for a mutation to pass QC	0.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_min_percent_coverage	Float	Internal component, do not modify	100	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_min_percent_coverage	Float	The minimum coverage for a region to pass QC in tbp_parser	100	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_min_read_support	Int	Internal component, do not modify	10	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_min_read_support	Int	The minimum read support for a mutation to pass QC	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_operator	String	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_operator	String	Fills the "operator" field in the tbp_parser output files	Operator not provided	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	True
merlin_magic	tbp_parser_output_seq_method_type	String	Internal component, do not modify	WGS	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_output_seq_method_type	String	Fills out the "seq_method" field in the tbp_parser output files	WGS	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_rpob449_frequency	Float	Internal component, do not modify	0.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_rpob449_frequency	Float	Minimum frequency for a mutation at protein position 449 to pass QC in tbp-parser	0.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_rrl_frequency	Float	Internal component, do not modify	0.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_rrl_frequency	Float	Minimum frequency for a mutation in rrl to pass QC in tbp-parser	0.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_rrl_read_support	Int	Internal component, do not modify	10	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_rrl_read_support	Int	Minimum read support for a mutation in rrl to pass QC in tbp-parser	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_rrs_frequency	Float	Internal component, do not modify	0.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_rrs_frequency	Float	Minimum frequency for a mutation in rrs to pass QC in tbp-parser	0.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_rrs_read_support	Int	Internal component, do not modify	10	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_rrs_read_support	Int	Minimum read support for a mutation in rrs to pass QC in tbp-parser	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbp_parser_tngs_data	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbp_parser_tngs_data	Boolean	Set to true to enable tNGS-specific parameters and runs in tbp-parser	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbprofiler_additional_parameters	String	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbprofiler_additional_parameters	String	Additional parameters for TBProfiler		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbprofiler_custom_db	File	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbprofiler_custom_db	File	TBProfiler uses by default the TBDB database; if you have a custom database you wish to use, you must provide a custom database in this field		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbprofiler_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:6.6.3	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbprofiler_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:6.6.3	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	tbprofiler_mapper	String	Internal component, do not modify	bwa	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbprofiler_mapper	String	The mapping tool used in TBProfiler to align the reads to the reference genome; see TBProfiler’s original documentation for available options.	bwa	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbprofiler_min_af	Float	Internal component, do not modify	0.1	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbprofiler_min_af	Float	The minimum allele frequency to call a variant	0.1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbprofiler_min_depth	Int	Internal component, do not modify	10	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbprofiler_min_depth	Int	The minimum depth for a variant to be called.	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbprofiler_tbdb_branch	String	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbprofiler_tbdb_branch	String	TBProfiler uses by default the TBDB database (a combination of the original library and the WHO v2 catalogue). You can opt to use a different mutation library by using this field to specify the name of the TBDB branch to use in TBProfiler; see [the TBProfiler documentation](https://jodyphelan.github.io/tb-profiler-docs/en/mutation-library/) for more information regarding available databases		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	True
merlin_magic	tbprofiler_variant_caller	String	Internal component, do not modify	gatk	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbprofiler_variant_caller	String	Select a different variant caller for TBProfiler to use by writing it in this block; see TBProfiler’s original documentation for available options.	gatk	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	tbprofiler_variant_calling_params	String	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	tbprofiler_variant_calling_params	String	Enter additional variant calling parameters in this free text input to customize how the variant caller works in TBProfiler		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	theiaeuk	Boolean	Internal component, do not modify	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	vibecheck_docker_image	String	Internal component, do not modify	watronfire/vibecheck:2025.06.26	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	vibecheck_docker_image	String	The Docker container to use for the task	watronfire/vibecheck:2025.06.26	Optional	TheiaProk_Illumina_PE	docker	
merlin_magic	vibecheck_lineage_barcodes	File	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	vibecheck_lineage_barcodes	File	Feather formatted lineage barcodes to use instead of default O1 barcodes		Optional	TheiaProk_Illumina_PE	general	
merlin_magic	vibecheck_skip_subsampling	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	vibecheck_skip_subsampling	Boolean	When enabled, will not subsample reads prior to classification. Will increase computation time	False	Optional	TheiaProk_Illumina_PE	general	
merlin_magic	vibecheck_subsampling_fraction	Float	Internal component, do not modify	0.2	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	vibecheck_subsampling_fraction	Float	Fraction of reads to use in classification.	0.2	Optional	TheiaProk_Illumina_PE	general	
merlin_magic	virulencefinder_database	String	Internal component, do not modify	virulence_ecoli	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	virulencefinder_database	String	The specific database to use	virulence_ecoli	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	database	
merlin_magic	virulencefinder_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/virulencefinder:2.0.4	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	virulencefinder_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/virulencefinder:2.0.4	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
merlin_magic	virulencefinder_min_percent_coverage	Float	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	virulencefinder_min_percent_coverage	Float	The threshold for minimum coverage		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
merlin_magic	virulencefinder_min_percent_identity	Float	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
merlin_magic	virulencefinder_min_percent_identity	Float	The threshold for minimum blast identity		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
metabuli	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Metabuli, TheiaViral_ONT	runtime	
metabuli	disk_size	Int	Amount of storage (in GB) to allocate to the task	250	Optional	TheiaViral_ONT	runtime	
metabuli	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/metabuli:1.1.1	Optional	Metabuli, TheiaViral_ONT	docker	
metabuli	extract_unclassified	Boolean	True/False that determines if unclassified reads should be extracted and combined with the taxon specific extracted reads	False	Optional	Metabuli	general	
metabuli	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaViral_ONT	runtime	
metabuli	metabuli_db	File	Metabuli database file	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/refseq_virus-v223.tar.gz	Optional	TheiaViral_ONT	database	
metabuli	min_percent_coverage	Float	Minimum query coverage threshold (0.0 - 1.0)	0	Optional	Metabuli, TheiaViral_ONT	general	
metabuli	min_score	Float	Minimum sequenece similarity score (0.0 - 1.0)	0	Optional	Metabuli, TheiaViral_ONT	general	
metabuli	min_sp_score	Float	Minimum score for species- or lower-level classification	0	Optional	Metabuli, TheiaViral_ONT	general	
metabuli	read2	File	Internal component, do not modify		Optional	TheiaViral_ONT	general	
metabuli	taxdump_path	File	Path to compressed taxonomy dump	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/ncbi_taxdump_20260211.tar.gz	Optional	TheiaViral_ONT	general	
metabuli_wf	call_trim	Boolean	Call adapter and read trimming via Fastp (Illumina) or Porechop (ONT)	True	Optional	Metabuli	general	
metabuli_wf	illumina	Boolean	Input reads are Illumina - automatically inferred if read2 is populated, ONT is assumed otherwise		Optional	Metabuli	general	
metabuli_wf	metabuli_disk_size	Int	Amount of storage (in GB) to allocate to the task	250	Optional	Metabuli	runtime	
metabuli_wf	metabuli_mem	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Metabuli	runtime	
metabuli_wf	read2	File	FASTQ file containing read2 sequences		Optional	Metabuli	general	
metabuli_wf	taxdump	File	Path to compressed taxonomy dump that corresponds with database	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/ncbi_taxdump_20260211.tar.gz	Optional	Metabuli	general	
metabuli_wf	taxon	String	NCBI taxonomy compatible taxon name/ID to enable read extraction		Optional	Metabuli	general	
metaspades_pe	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaMeta_Illumina_PE	runtime	
metaspades_pe	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
metaspades_pe	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/spades:3.12.0--h9ee0642_3	Optional	TheiaMeta_Illumina_PE	docker	
metaspades_pe	kmers	String	Kmers to use for the task		Optional	TheiaMeta_Illumina_PE	general	
metaspades_pe	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaMeta_Illumina_PE	runtime	
metaspades_pe	metaspades_opts	String	Metaspades optional parameters		Optional	TheiaMeta_Illumina_PE	general	
metaspades_pe	phred_offset	Int	Phred offset to use for the task	33	Optional	TheiaMeta_Illumina_PE	general	
minimap2	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaViral_ONT	runtime	
minimap2	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaViral_ONT	runtime	
minimap2	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22	Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaViral_ONT	docker	
minimap2	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaViral_ONT	runtime	
minimap2	query2	File	Internal component, do not modify		Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaViral_ONT	general	
minimap2_assembly	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
minimap2_assembly	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
minimap2_assembly	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22	Optional	TheiaMeta_Illumina_PE	docker	
minimap2_assembly	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
minimap2_assembly	query2	File	Internal component, do not modify		Optional	TheiaMeta_Illumina_PE	general	
minimap2_assembly_correction	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
minimap2_assembly_correction	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
minimap2_assembly_correction	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22	Optional	TheiaMeta_Illumina_PE	docker	
minimap2_assembly_correction	long_read_flags	Boolean	Use long read sequencing specific flags for alignment	False	Optional	TheiaMeta_Illumina_PE	general	
minimap2_assembly_correction	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
minimap2_reads	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
minimap2_reads	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
minimap2_reads	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22	Optional	TheiaMeta_Illumina_PE	docker	
minimap2_reads	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
morgana_magic	abricate_flu_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	abricate_flu_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	abricate_flu_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/abricate:1.0.1-insaflu-220727	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
morgana_magic	abricate_flu_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	abricate_flu_min_percent_coverage	Int	Minimum DNA percent coverage	60	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	abricate_flu_min_percent_identity	Int	Minimum DNA percent identity	70	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	assembly_metrics_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	assembly_metrics_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	assembly_metrics_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.23	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
morgana_magic	assembly_metrics_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	flu_track_antiviral_aa_subs	String	Additional list of antiviral resistance associated amino acid substitutions of interest to be searched against those called on the sample segments. They take the format of :, e.g. NA:A26V		Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	gene_coverage_bam	File	Bam file used for calculating gene coverage		Optional	TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	gene_coverage_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	gene_coverage_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	gene_coverage_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
morgana_magic	gene_coverage_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	gene_coverage_min_depth	Int	The minimum depth to determine if a position was covered.	10	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	genoflu_cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	genoflu_cross_reference	File	Internal component, do not modify		Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT	general	
morgana_magic	genoflu_cross_reference	File	An Excel file to cross-reference BLAST findings; probably useful if novel genotypes are not in the default file used by genoflu.py		Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	genoflu_disk_size	Int	Amount of storage (in GB) to allocate to the task	25	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	genoflu_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/genoflu:1.06	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
morgana_magic	genoflu_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	irma_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	irma_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	irma_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/irma:1.3.1	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
morgana_magic	irma_keep_ref_deletions	Boolean	True/False variable that determines if sites missed (i.e. 0 reads for a site in the reference genome) during read gathering should be deleted by ambiguation by inserting N's or deleting the sequence entirely. False sets this IRMA paramater to "DEL" and true sets it to "NNN"	True	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	reference	
morgana_magic	irma_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	nextclade_auspice_reference_tree_json	File	An Auspice JSON phylogenetic reference tree which serves as a target for phylogenetic placement.	Inherited from nextclade dataset	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	reference	True
morgana_magic	nextclade_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	nextclade_custom_input_dataset	File	Internal component, do not modify	Defaults are GenoFLU Genotype specific. Please find these default values here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT	general	True
morgana_magic	nextclade_custom_input_dataset	File	For H5N1 flu samples only. A custom Nextclade dataset in JSON format. If provided, this dataset will be used to process any H5N1 flu samples. If not provided, a custom dataset will be selected depending on the GenoFLU Genotype.	Defaults are GenoFLU Genotype specific. Please find these default values here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	True
morgana_magic	nextclade_dataset_name	String	NextClade organism dataset name	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, the default is "NA".	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	True
morgana_magic	nextclade_dataset_tag	String	NextClade organism dataset tag	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, the default is "NA".	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	True
morgana_magic	nextclade_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	nextclade_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.16.0	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
morgana_magic	nextclade_input_ref	File	A nucleotide sequence which serves as a reference for the pairwise alignment of all input sequences. This is also the sequence which defines the coordinate system of the genome annotation. See here for more info: <https://docs.nextstrain.org/projects/nextclade/en/latest/user/input-files/02-reference-sequence.html>	Inherited from nextclade dataset	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	reference	True
morgana_magic	nextclade_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	nextclade_output_parser_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	nextclade_output_parser_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	nextclade_output_parser_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/python/python:3.8.18-slim	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
morgana_magic	nextclade_output_parser_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	nextclade_pathogen_json	File	General dataset configuration file. See here for more info: <https://docs.nextstrain.org/projects/nextclade/en/latest/user/input-files/05-pathogen-config.html>	Inherited from nextclade dataset	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	True
morgana_magic	nextclade_reference_gff_file	File	A genome annotation to specify how to translate the nucleotide sequence to proteins (genome_annotation.gff3). specifying this enables codon-informed alignment and protein alignments. See here for more info: <https://docs.nextstrain.org/projects/nextclade/en/latest/user/input-files/03-genome-annotation.html>	Inherited from nextclade dataset	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	reference	True
morgana_magic	nextclade_verbosity	String	other options are: "off" , "error" , "info" , "debug" , and "trace" (highest level of verbosity)	warn	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	number_ATCG	Int	Internal component, do not modify		Optional	TheiaCoV_FASTA_Batch	general	
morgana_magic	pangolin_analysis_mode	String	Specify which inference engine to use. Options: accurate (UShER), fast (pangoLEARN), pangolearn, usher.		Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	pangolin_arguments	String	Optional arguments for pangolin e.g. ''--skip-scorpio''		Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	pangolin_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	pangolin_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	pangolin_docker_image	String	The Docker container to use for the task		Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	pangolin_expanded_lineage	Boolean	True/False that determines if a lineage should be expanded without aliases (e.g., BA.1 → B.1.1.529.1)	True	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	pangolin_max_ambig	Float	Maximum proportion of Ns allowed for pangolin to attempt assignment.	0.5	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	pangolin_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	pangolin_min_length	Int	Minimum query length allowed for pangolin to attempt an assignment	10000	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	pangolin_skip_designation_cache	Boolean	A True/False option that determines if the designation cache should be used	False	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	pangolin_skip_scorpio	Boolean	A True/False option that determines if scorpio should be skipped.	False	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	quasitools_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	quasitools_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	quasitools_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/quasitools:0.7.0--pyh864c0ab_1	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
morgana_magic	quasitools_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	read1	File	Internal component, do not modify		Optional	TheiaCoV_FASTA, TheiaCoV_FASTA_Batch	general	
morgana_magic	read2	File	Internal component, do not modify		Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_ONT	general	
morgana_magic	reference_gene_locations_bed	File	Use to provide locations of interest where average coverage will be calculated		Optional	TheiaCoV_FASTA, TheiaCoV_FASTA_Batch	general	
morgana_magic	sc2_s_gene_start	Int	Start position of S gene	21563	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	sc2_s_gene_stop	Int	End position of S gene	25384	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	vadr_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	vadr_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
morgana_magic	vadr_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/vadr:1.6.4	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
morgana_magic	vadr_max_length	Int	Maximum length for the fasta-trim-terminal-ambigs.pl VADR script		Optional	TheiaCoV_FASTA_Batch, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	vadr_memory	Int	Amount of memory/RAM (in GB) to allocate to the task		Optional	TheiaCoV_FASTA_Batch, TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	True
morgana_magic	vadr_min_length	Int	Minimum length for the fasta-trim-terminal-ambigs.pl VADR script	50	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	vadr_model_file	File	Path to the a tar + gzipped VADR model file		Optional	TheiaCoV_FASTA_Batch, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	vadr_options	String	Options to pass to the VADR script		Optional	TheiaCoV_FASTA_Batch, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
morgana_magic	vadr_skip_length	Int	Skip reads shorter than this length		Optional	TheiaCoV_FASTA_Batch, TheiaViral_Illumina_PE, TheiaViral_ONT	general	
mutation_context	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur	runtime	
mutation_context	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Augur	runtime	
mutation_context	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/nextstrain-mpox-mutation-context:2024-06-27	Optional	Augur	docker	
mutation_context	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Augur	runtime	
nanoplot_clean	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	runtime	
nanoplot_clean	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	runtime	
nanoplot_clean	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/nanoplot:1.40.0	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	docker	
nanoplot_clean	max_length	Int	The maximum length of clean reads, for which reads longer than the length specified will be hidden.	100000	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	general	
nanoplot_clean	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	runtime	
nanoplot_raw	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	runtime	
nanoplot_raw	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	runtime	
nanoplot_raw	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/nanoplot:1.40.0	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	docker	
nanoplot_raw	max_length	Int	The maximum length of clean reads, for which reads longer than the length specified will be hidden.	100000	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	general	
nanoplot_raw	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Freyja_FASTQ, TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT, TheiaViral_ONT	runtime	
nanoq	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_ONT	runtime	
nanoq	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
nanoq	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/nanoq:0.9.0--hec16e2b_1	Optional	TheiaViral_ONT	docker	
nanoq	max_read_length	Int	Maximum read length to keep	100000	Optional	TheiaViral_ONT	general	
nanoq	max_read_qual	Int	Maximum read quality to keep	100	Optional	TheiaViral_ONT	general	
nanoq	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaViral_ONT	runtime	
nanoq	min_read_length	Int	Minimum read length to keep	500	Optional	TheiaViral_ONT	general	
nanoq	min_read_qual	Int	Minimum read quality to keep	10	Optional	TheiaViral_ONT	general	
ncbi_datasets_download_genome_accession	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	runtime	
ncbi_datasets_download_genome_accession	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	runtime	
ncbi_datasets_download_genome_accession	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ncbi-datasets:16.38.1	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	docker	
ncbi_datasets_download_genome_accession	include_gbff	Boolean	Set to true if you would like the GenBank Flat File (GBFF) file included in the output. It contains nucleotide sequence, metadata, and annotations.	False	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	general	
ncbi_datasets_download_genome_accession	include_gff3	Boolean	Set to true if you would like the Genomic Feature File v3 (GFF3) file included in the output. It contains nucleotide sequence, metadata, and annotations	False	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	general	
ncbi_datasets_download_genome_accession	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	runtime	
ncbi_datasets_download_genome_accession	use_ncbi_virus	Boolean	Set to true to download from NCBI Virus Datasets	False	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	general	
ncbi_scrub_pe	cpu	Int	Number of CPUs to allocate to the task	4	Optional	NCBI_Scrub_PE, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
ncbi_scrub_pe	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	NCBI_Scrub_PE, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
ncbi_scrub_pe	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1	Optional	NCBI_Scrub_PE, TheiaViral_Illumina_PE, TheiaViral_Panel	docker	
ncbi_scrub_pe	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	NCBI_Scrub_PE, TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
ncbi_scrub_se	cpu	Int	Number of CPUs to allocate to the task	4	Optional	NCBI_Scrub_SE, TheiaCoV_ClearLabs, TheiaViral_ONT	runtime	
ncbi_scrub_se	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	NCBI_Scrub_SE, TheiaCoV_ClearLabs, TheiaViral_ONT	runtime	
ncbi_scrub_se	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1	Optional	NCBI_Scrub_SE, TheiaCoV_ClearLabs, TheiaViral_ONT	docker	
ncbi_scrub_se	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	NCBI_Scrub_SE, TheiaCoV_ClearLabs, TheiaViral_ONT	runtime	
ncbi_sftp_upload	additional_files	Array[File]	Internal component, do not modify	[]	Optional	Terra_2_NCBI	general	
ncbi_sftp_upload	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Terra_2_NCBI	runtime	
ncbi_sftp_upload	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Terra_2_NCBI	runtime	
ncbi_sftp_upload	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/broadinstitute/ncbi-tools:2.10.7.10	Optional	Terra_2_NCBI	docker	
ncbi_sftp_upload	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Terra_2_NCBI	runtime	
ncbi_sftp_upload	wait_for	String	Internal component, do not modify	1	Optional	Terra_2_NCBI	general	
nextclade_batch	dataset_tag	String	nextclade dataset tag	Uses the dataset tag associated with the nextclade docker image version	Optional	Nextclade_Batch	general	True
nextclade_batch	gene_annotations_gff	File	A genome annotations file for codon-aware alignment, gene translation and calling of amino acid mutations	Uses the genome annotation associated with the nextclade dataset name	Optional	Nextclade_Batch	general	True
nextclade_batch	input_ref	File	An optional FASTA file containing reference sequence. This file should contain exactly 1 sequence	Uses the reference fasta associated with the specified nextclade dataset name	Optional	Nextclade_Batch	reference	True
nextclade_batch	pathogen_json	File	An optional pathogen JSON file containing configuration and data specific to a pathogen	Uses the reference pathogen JSON file associated with the specified nextclade dataset name	Optional	Nextclade_Batch	general	True
nextclade_batch	reference_tree_json	File	An optional phylogenetic reference tree file which serves as a target for phylogenetic placement	Uses the reference tree associated with the specified nextclade dataset name	Optional	Nextclade_Batch	reference	True
nextclade_v3_set	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Nextclade_Batch	runtime	
nextclade_v3_set	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Nextclade_Batch	runtime	
nextclade_v3_set	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.14.5	Optional	Nextclade_Batch	docker	
nextclade_v3_set	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Nextclade_Batch	runtime	
nextclade_v3_set	verbosity	String	Set the nextclade output verbosity level. Options: off, error, warn, info, debug, trace	warn	Optional	Nextclade_Batch	general	
ont_barcode_concatenation	barcode_renaming_file	File	A tab-delimited file where the name of the barcode folders are mapped to the desired sample name in the Terra table (see above for examples)		Optional	ONT_Barcode_Concatenation	general	
ont_barcode_concatenation	file_extension	String	If your ONT data ends in a different extension, like ".fq.gz" or ".fastq", you can indicate that here.	.fastq.gz	Optional	ONT_Barcode_Concatenation	general	
organism_parameters	auspice_config	File	Auspice config file for customizing visualizations in the Augur_PHB workflow; takes priority over the other customization values available for augur_export. Defaults are set for various organisms & flu segments. A minimal auspice config file is set in cases where organism is not specified and user does not provide an optional input config file.		Optional	Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT	general	
organism_parameters	auspice_config	File	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	clades_tsv	File	Internal component, do not modify		Optional	Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, VADR_Update	general	
organism_parameters	flu_genoflu_genotype	String	Internal component, do not modify 	N/A	Optional	Augur, Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, VADR_Update	general	
organism_parameters	flu_segment	String	Influenza genome segment being analyzed. Options: "HA" or "NA". Automatically determined. This input is ignored if provided for TheiaCoV_Illumina_SE and TheiaCoV_ClearLabs	N/A	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT	general	
organism_parameters	flu_segment	String	Internal component, do not modify	N/A	Optional	VADR_Update	general	
organism_parameters	flu_subtype	String	The influenza subtype being analyzed. Options: "Yamagata", "Victoria", "H1N1", "H3N2", "H5N1". Automatically determined. This input is ignored if provided for TheiaCoV_Illumina_SE and TheiaCoV_ClearLabs	N/A	Optional	TheiaCoV_ClearLabs, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT	general	
organism_parameters	flu_subtype	String	Internal component, do not modify	N/A	Optional	VADR_Update	general	
organism_parameters	gene_locations_bed_file	File	Use to provide locations of interest where average coverage will be calculated	Default provided for SARS-CoV-2 ("gs://theiagen-public-resources-rp/reference_data/viral/sars-cov-2/sc2_gene_locations.bed") and mpox ("gs://theiagen-public-resources-rp/reference_data/viral/mpox/mpox_gene_locations.bed")	Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch	general	True
organism_parameters	gene_locations_bed_file	File	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	genome_length_input	Int	Use to specify the expected genome length; provided by default for all supported organisms	Default provided for SARS-CoV-2 (29903), mpox (197200), WNV (11000), flu (13000), RSV-A (16000), RSV-B (16000), HIV (primer versions 1 [9181] and 2 [9840])	Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA_Batch	general	True
organism_parameters	genome_length_input	Int	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	hiv_primer_version	String	The version of HIV primers used. Options are <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl#L156> and <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl#L164>. This input is ignored if provided for TheiaCoV_Illumina_SE and TheiaCoV_ClearLabs	v1	Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT	general	
organism_parameters	hiv_primer_version	String	Internal component, do not modify	v1	Optional	VADR_Update	general	
organism_parameters	kraken_target_organism_input	String	The organism whose abundance the user wants to check in their reads. This should be a proper taxonomic name recognized by the Kraken database.	Default provided for mpox (Monkeypox virus), WNV (West Nile virus), and HIV (Human immunodeficiency virus 1)	Optional	Augur, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_SE	general	True
organism_parameters	kraken_target_organism_input	String	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	lat_longs_tsv	File	Internal component, do not modify		Optional	Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, VADR_Update	general	
organism_parameters	min_date	Float	Internal component, do not modify		Optional	Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, VADR_Update	general	
organism_parameters	min_num_unambig	Int	Minimum number of called bases in genome to pass prefilter	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, the default value is 0	Optional	Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT	general	True
organism_parameters	min_num_unambig	Int	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	narrow_bandwidth	Float	Internal component, do not modify		Optional	Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, VADR_Update	general	
organism_parameters	nextclade_dataset_name_input	String	NextClade organism dataset name	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, the default is "NA".	Optional	Augur	general	True
organism_parameters	nextclade_dataset_name_input	String	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	nextclade_dataset_tag_input	String	NextClade organism dataset tag	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments and subtypes) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>. For an organism without set defaults, the default is "NA".	Optional	Augur	general	True
organism_parameters	nextclade_dataset_tag_input	String	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	pangolin_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34	Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA	docker	True
organism_parameters	pangolin_docker_image	String	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	pivot_interval	Int	Internal component, do not modify		Optional	Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, VADR_Update	general	
organism_parameters	primer_bed_file	File	The bed file containing the primers used when sequencing was performed	REQUIRED FOR SARS-CoV-2, MPOX, WNV, RSV-A & RSV-B. Provided by default only for HIV primer versions 1 ("gs://theiagen-public-resources-rp/reference_data/viral/hiv/HIV-1_v1.0.primer.hyphen.bed" and 2 ("gs://theiagen-public-resources-rp/reference_data/viral/hiv/HIV-1_v2.0.primer.hyphen400.1.bed")	Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch	general	True
organism_parameters	primer_bed_file	File	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	proportion_wide	Float	Internal component, do not modify		Optional	Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, VADR_Update	general	
organism_parameters	reference_genbank	File	Internal component, do not modify		Optional	Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, VADR_Update	general	
organism_parameters	reference_genome	File	An optional reference genome used for consensus assembly and QC		Optional	TheiaCoV_FASTA_Batch	general	
organism_parameters	reference_genome	File	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	reference_gff_file	File	Reference GFF file for the organism being analyzed	Default provided for mpox ("gs://theiagen-public-resources-rp/reference_data/viral/mpox/Mpox-MT903345.1.reference.gff3") and HIV (primer versions 1 ["gs://theiagen-public-resources-rp/reference_data/viral/hiv/NC_001802.1.gff3"] and 2 ["gs://theiagen-public-resources-rp/reference_data/viral/hiv/AY228557.1.gff3"])	Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_ONT	reference	True
organism_parameters	reference_gff_file	File	Internal component, do not modify		Optional	VADR_Update	general	
organism_parameters	vadr_max_length	Int	Maximum length for the fasta-trim-terminal-ambigs.pl VADR script	Default provided for SARS-CoV-2 (30000), mpox (210000), WNV (11000), flu (0), RSV-A (15500) and RSV-B (15500).	Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA_Batch	general	True
organism_parameters	vadr_mem	Int	Amount of memory/RAM (in GB) to allocate to the task	32 (RSV-A, RSV-B, WNV) and 16 (all other TheiaCoV organisms)	Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA_Batch	general	True
organism_parameters	vadr_model	File	Path to the a tar + gzipped VADR model file	gs://theiagen-public-resources-rp/reference_data/databases/vadr_models/vadr-models-sarscov2-1.3-2.tar.gz	Optional	Augur, Pangolin_Update, TheiaCoV_ClearLabs, TheiaCoV_FASTA_Batch	general	True
organism_parameters	vadr_options	String	Options for the v-annotate.pl VADR script	--mkey sarscov2 --glsearch -s -r --nomisc --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn --noseqnamemax --out_allfasta	Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA_Batch	general	True
organism_parameters	vadr_skip_length	Int	Minimum assembly length (unambiguous) to run VADR		Optional	Augur, TheiaCoV_ClearLabs, TheiaCoV_FASTA_Batch	general	
pan_iqtree	alrt	Int	Number of replicates to use for the SH-like approximate likelihood ratio test (Minimum recommended= 1000). Follows IQ-TREE "-alrt" option	1000	Optional	Core_Gene_SNP	general	
pan_iqtree	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Core_Gene_SNP	runtime	
pan_iqtree	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Core_Gene_SNP	runtime	
pan_iqtree	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/iqtree:1.6.7	Optional	Core_Gene_SNP	docker	
pan_iqtree	iqtree_model	String	Substitution model, frequency type (optional) and rate heterogeneity type (optional) used by IQ-TREE. This string follows the IQ-TREE "-m" option. For comparison to other tools use HKY for Bactopia, GTR+F+I for Grandeur, GTR+G4 for Nullarbor, GTR+G for Dryad	GTR+I+G	Optional	Core_Gene_SNP	general	
pan_iqtree	iqtree_opts	String	Additional options for IQ-TREE, see <http://www.iqtree.org/doc/Command-Reference>		Optional	Core_Gene_SNP	general	
pan_iqtree	iqtree_ultrafast_bootstraps	Int	Number of ultrafast bootstrap replicates. Follows IQ-TREE "-bb" option.	1000	Optional	Core_Gene_SNP	general	
pan_iqtree	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Core_Gene_SNP	runtime	
pan_reorder_matrix	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
pan_reorder_matrix	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
pan_reorder_matrix	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1	Optional	Core_Gene_SNP, kSNP3, kSNP4	docker	
pan_reorder_matrix	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
pan_reorder_matrix	outgroup_root	String	Tip name to root phylogenetic tree upon (overrides midpoint root)		Optional	Core_Gene_SNP, kSNP3, kSNP4	general	
pan_snp_dists	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
pan_snp_dists	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
pan_snp_dists	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2	Optional	Core_Gene_SNP, kSNP3, kSNP4	docker	
pan_snp_dists	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Core_Gene_SNP, kSNP3, kSNP4	runtime	
pangolin4	analysis_mode	String	Used to switch between usher and pangolearn analysis modes. Only use usher because pangolearn is no longer supported as of Pangolin v4.3 and higher versions.		Optional	Pangolin_Update	general	
pangolin4	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Pangolin_Update	runtime	
pangolin4	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Pangolin_Update	runtime	
pangolin4	expanded_lineage	Boolean	True/False that determines if a lineage should be expanded without aliases (e.g., BA.1 → B.1.1.529.1)	True	Optional	Pangolin_Update	general	
pangolin4	max_ambig	Float	The maximum proportion of Ns allowed for pangolin to attempt an assignment	0.5	Optional	Pangolin_Update	general	
pangolin4	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Pangolin_Update	runtime	
pangolin4	min_length	Int	Minimum query length allowed for pangolin to attempt an assignment	10000	Optional	Pangolin_Update	general	
pangolin4	pangolin_arguments	String	Optional arguments for pangolin e.g. ''--skip-scorpio''		Optional	Pangolin_Update	general	
pangolin4	skip_designation_cache	Boolean	A True/False option that determines if the designation cache should be used	False	Optional	Pangolin_Update	general	
pangolin4	skip_scorpio	Boolean	A True/False option that determines if scorpio should be skipped.	False	Optional	Pangolin_Update	general	
pangolin_update	lineage_log	File	TSV file detailing previous lineage assignments and software versions for this sample.		Optional	Pangolin_Update	general	
pangolin_update	new_pangolin_docker	String	The Pangolin docker image used to update the Pangolin lineage assignments.		Optional	Pangolin_Update	general	
pangolin_update	organism	String	The organism to be analyzed	sars-cov-2	Optional	Pangolin_Update	general	
pangolin_update_log	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Pangolin_Update	runtime	
pangolin_update_log	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Pangolin_Update	runtime	
pangolin_update_log	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	Pangolin_Update	docker	
pangolin_update_log	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Pangolin_Update	runtime	
pangolin_update_log	timezone	String	Set the time zone to get an accurate date of update (uses UTC by default)		Optional	Pangolin_Update	general	
parse_mapping	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_ONT	runtime	
parse_mapping	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
parse_mapping	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17	Optional	TheiaViral_ONT	docker	
parse_mapping	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_ONT	runtime	
phylocompare	midpoint	Boolean	Root phylogenies at their midpoint	False	Optional	PhyloCompare	general	
phylocompare	outgroup	String	Root phylogenies with an outgroup tip		Optional	PhyloCompare	general	
phylocompare	validate	Boolean	Run phylogenetic validation by calculating the distance between two phylogenies' tips and branching order	False	Optional	PhyloCompare	general	
phylovalidate_task	cpu	Int	Number of CPUs to allocate to the task	1	Optional	PhyloCompare	runtime	
phylovalidate_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	PhyloCompare	runtime	
phylovalidate_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/theiaphylo:0.2.0	Optional	PhyloCompare	docker	
phylovalidate_task	max_distance	Float	Maximum tolerable distance during validation		Optional	PhyloCompare	general	
phylovalidate_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	PhyloCompare	runtime	
phylovalidate_task	resolve_tip_discrepancies	Boolean	Remove tips that are discrepant between trees instead of failing	True	Optional	PhyloCompare	general	
pilon	cpu	Int	Number of CPUs to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
pilon	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
pilon	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/pilon:1.24--hdfd78af_0	Optional	TheiaMeta_Illumina_PE	docker	
pilon	fix	String	Additional options for fixing assembly errors (all, snps, indels, gaps)		Optional	TheiaMeta_Illumina_PE	general	
pilon	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaMeta_Illumina_PE	runtime	
pilon	min_base_quality	Int	Minimum base quality to consider a base for assembly		Optional	TheiaMeta_Illumina_PE	general	
pilon	min_depth	Float	Minimum depth to consider a region for assembly		Optional	TheiaMeta_Illumina_PE	general	
pilon	min_mapping_quality	Int	Minimum mapping quality to consider a read for assembly		Optional	TheiaMeta_Illumina_PE	general	
pirate	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Core_Gene_SNP	runtime	
pirate	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Core_Gene_SNP	runtime	
pirate	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/pirate:1.0.5--hdfd78af_0	Optional	Core_Gene_SNP	docker	
pirate	features	String	Features to use for pangenome construction [default: CDS]	CDS	Optional	Core_Gene_SNP	general	
pirate	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Core_Gene_SNP	runtime	
pirate	nucl	Boolean	Boolean variable that instructs pirate to create a pangenome on CDS features using nucleotide identity, rather than amino acid identity, if true.	False	Optional	Core_Gene_SNP	general	
pirate	panopt	String	Additional arguments for Pirate		Optional	Core_Gene_SNP	general	
pirate	steps	String	Identity thresholds to use for pangenome construction	50,60,70,80,90,95,98	Optional	Core_Gene_SNP	general	
plasmidfinder	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
plasmidfinder	database	String	User-specified database		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
plasmidfinder	database_path	String	Path to user-specified database		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
plasmidfinder	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
plasmidfinder	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/plasmidfinder:2.1.6	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
plasmidfinder	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
plasmidfinder	method_path	String	Path to files for a user-specified method to use (blast or kma)		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
plasmidfinder	min_percent_coverage	Float	Threshold for minimum coverage, default threshold from PlasmidFinder CLI tool is used (0.60)	0.6	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
plasmidfinder	min_percent_identity	Float	Threshold for mininum blast identity, default threshold from PlasmidFinder CLI tool is used (0.90). This default differs from the default of the PlasmidFinder webtool (0.95)	0.9	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
porechop	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_ONT	runtime	
porechop	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
porechop	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/porechop:0.2.4	Optional	TheiaViral_ONT	docker	
porechop	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaViral_ONT	runtime	
porechop	trimopts	String	Additional trimming options for Porechop		Optional	TheiaViral_ONT	general	
prep_augur_metadata	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur_Prep	runtime	
prep_augur_metadata	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	Augur_Prep	runtime	
prep_augur_metadata	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	Augur_Prep	docker	
prep_augur_metadata	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	3	Optional	Augur_Prep	runtime	
prep_augur_metadata	organism	String	The organism to be analyzed in Augur; options: "sars-cov-2", "flu", "MPXV", "rsv-a", "rsv-b"	sars-cov-2	Optional	Augur_Prep	general	
primer_trim	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Freyja_FASTQ	runtime	
primer_trim	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ	runtime	
primer_trim	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ivar:1.3.1-titan	Optional	Freyja_FASTQ	docker	
primer_trim	keep_noprimer_reads	Boolean	Include reads with no primers	True	Optional	Freyja_FASTQ	general	
primer_trim	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Freyja_FASTQ	runtime	
prokka	compliant	Boolean	If true (default), forces Genbank/ENA/DDJB compliant headers in Prokka output files	True	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
prokka	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
prokka	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
prokka	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/prokka:1.14.5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
prokka	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
prokka	prodigal_tf	File	<https://github.com/tseemann/prokka#option---prodigaltf>		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
prokka	prokka_arguments	String	Any additional <https://github.com/tseemann/prokka#command-line-options>		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
prokka	proteins	Boolean	FASTA file of trusted proteins for Prokka to first use for annotations	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
prune_table	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Terra_2_NCBI	runtime	
prune_table	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Terra_2_NCBI	runtime	
prune_table	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16	Optional	Terra_2_NCBI	docker	
prune_table	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Terra_2_NCBI	runtime	
prune_table	read1_column_name	String	The column header of the read1 column	read1	Optional	Terra_2_NCBI	general	
prune_table	read2_column_name	String	The column header of the read2 column	read2	Optional	Terra_2_NCBI	general	
qc_check_task	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
qc_check_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
qc_check_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2024-08-27	Optional	Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
qc_check_task	gambit_predicted_taxon	String	Internal component, do not modify		Optional	Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT	general	
qc_check_task	irma_qc_table	File	Internal component, do not modify		Optional	Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
qc_check_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
qualimap	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Freyja_FASTQ	runtime	
qualimap	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Freyja_FASTQ	runtime	
qualimap	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/qualimap-custom-html:2.3	Optional	Freyja_FASTQ	docker	
qualimap	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Freyja_FASTQ	runtime	
quast	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
quast	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
quast	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/quast:5.0.2	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
quast	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
quast	min_contig_length	Int	Minimum length of contig for QUAST	500	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
quast_denovo	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
quast_denovo	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
quast_denovo	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/quast:5.0.2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
quast_denovo	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
quast_denovo	min_contig_length	Int	Minimum length of contig for QUAST	500	Optional	TheiaViral_ONT	general	
rasusa	bases	String	Explicitly set the number of bases required e.g., 4.3kb, 7Tb, 9000, 4.1MB. If this option is given, --coverage and --genome-size are ignored		Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
rasusa	coverage	Float	The desired coverage to sub-sample the reads to. If --bases is not provided, this option and --genome-size are required	250	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
rasusa	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
rasusa	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
rasusa	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
rasusa	frac	Float	Subsample to a fraction of the reads - e.g., 0.5 samples half the reads		Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
rasusa	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
rasusa	num	Int	Subsample to a specific number of reads		Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
rasusa	read2	File	Internal component, do not modify		Optional	TheiaViral_ONT	general	
rasusa	seed	Int	Random seed for reproducibility		Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
rasusa_task	bases	String	Explicitly set the number of bases required e.g., 4.3kb, 7Tb, 9000, 4.1MB. If this option is given, --coverage and --genome-size are ignored		Optional	RASUSA, TheiaEuk_Illumina_PE	general	
rasusa_task	cpu	Int	Number of CPUs to allocate to the task	4	Optional	RASUSA, TheiaEuk_Illumina_PE	runtime	
rasusa_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	RASUSA, TheiaEuk_Illumina_PE	runtime	
rasusa_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0	Optional	RASUSA, TheiaEuk_Illumina_PE	docker	
rasusa_task	frac	Float	Explicitly define the fraction of reads to keep in the subsample; when used, genome size and coverage are ignored; acceptable inputs include whole numbers and decimals, e.g. 50.0 will leave 50% of the reads in the subsample		Optional	RASUSA, TheiaEuk_Illumina_PE	general	
rasusa_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	RASUSA, TheiaEuk_Illumina_PE	runtime	
rasusa_task	num	Int	Optional: explicitly define the number of reads in the subsample; when used, genome size and coverage are ignored; acceptable metric suffixes include: b, k, m, g, and t for base, kilo, mega, giga, and tera, respectively		Optional	RASUSA, TheiaEuk_Illumina_PE	general	
rasusa_task	seed	Int	Use to assign a name to the "random seed" that is used by the subsampler; i.e. this allows the exact same subsample to be produced from the same input file/s in subsequent runs when providing the seed identifier; do not input values for random downsampling		Optional	RASUSA, TheiaEuk_Illumina_PE	general	
rasusa_workflow	read2	File	FASTQ file containing read2 sequences		Optional	RASUSA	general	
raven	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_ONT	runtime	
raven	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
raven	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/raven:1.8.3	Optional	TheiaViral_ONT	docker	
raven	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaViral_ONT	runtime	
raven	raven_identity	Float	Threshold for overlap between two reads in order to construct an edge between them	0	Optional	TheiaViral_ONT	general	
raven	raven_opts	String	Additional parameters for Raven assembler		Optional	TheiaViral_ONT	general	
raven	raven_polishing_iterations	Int	Number of polishing iterations	2	Optional	TheiaViral_ONT	general	
raw_check_reads	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
raw_check_reads	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
raw_check_reads	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/bactopia/gather_samples:2.0.2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
raw_check_reads	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
raw_check_reads	workflow_series	String	Internal component, do not modify	theiaviral	Optional	TheiaEuk_ONT	general	
read_mapping_stats	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
read_mapping_stats	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
read_mapping_stats	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.23	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
read_mapping_stats	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
read_mapping_stats	read2	File	Internal component, do not modify		Optional	TheiaViral_ONT	general	
read_QC_trim	adapters	File	File with adapter sequences to be removed		Optional	TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	artic_guppyplex_cpu	Int	Number of CPUs to allocate to the task	8	Optional	TheiaCoV_ONT	runtime	
read_QC_trim	artic_guppyplex_cpu	Int	Internal component, do not modify	8	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	artic_guppyplex_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ONT	runtime	
read_QC_trim	artic_guppyplex_disk_size	Int	Internal component, do not modify	100	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	artic_guppyplex_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019:1.3.0-medaka-1.4.3	Optional	TheiaCoV_ONT	docker	
read_QC_trim	artic_guppyplex_docker	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019:1.3.0-medaka-1.4.3	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	artic_guppyplex_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaCoV_ONT	runtime	
read_QC_trim	artic_guppyplex_memory	Int	Internal component, do not modify	16	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	bbduk_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
read_QC_trim	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database		Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	call_kraken	Boolean	Internal component, do not modify	False	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	general	
read_QC_trim	call_kraken	Boolean	True/False variable that determines if the Kraken2 task should be called; for non-TheiaCoV workflows, the `kraken_db` variable must be provided.	False	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	call_midas	Boolean	True/False variable that determines if the MIDAS task should be called.	False	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	call_midas	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE	general	
read_QC_trim	downsampling_coverage	Float	The desired coverage to sub-sample the reads to with RASUSA	150	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	fastp_args	String	Additional arguments to use with fastp	--detect_adapter_for_pe -g -5 20 -3 20	Optional	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE	general	
read_QC_trim	fastp_args	String	Additional arguments to use with fastp	-g -5 20 -3 20	Optional	TheiaCoV_Illumina_SE, TheiaProk_Illumina_SE	general	
read_QC_trim	kraken_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
read_QC_trim	kraken_db	File	A kraken2 database to use with the kraken2 optional task. The file must be a .tar.gz kraken2 database. Must contain human and viral sequences	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE	database	
read_QC_trim	kraken_db	File	A kraken2 database to use with the kraken2 optional task. The file must be a .tar.gz kraken2 database.	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz	Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	database	
read_QC_trim	kraken_disk_size	Int	Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database)	100	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
read_QC_trim	kraken_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	runtime	
read_QC_trim	max_length	Int	Internal component, do not modify	700	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	metabuli_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	runtime	
read_QC_trim	metabuli_db	File	Metabuli database for read taxonomy classification, compressed in .tar.gz format	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/refseq_virus-v223.tar.gz	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	database	
read_QC_trim	metabuli_disk_size	Int	Amount of storage (in GB) to allocate to the task	250	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	runtime	
read_QC_trim	metabuli_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/metabuli:1.1.1	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	docker	
read_QC_trim	metabuli_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	runtime	
read_QC_trim	metabuli_taxdump_path	File	Path to taxonkit-generated taxdump for Metabuli taxonomy parsing	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/ncbi_taxdump_20260211.tar.gz	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	midas_db	File	Internal component, do not modify	gs://theiagen-public-resources-rp/reference_data/databases/midas/midas_db_v1.2.tar.gz	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE	general	
read_QC_trim	midas_db	File	The database used by the MIDAS task in .tar.gz format	gs://theiagen-public-resources-rp/reference_data/databases/midas/midas_db_v1.2.tar.gz	Optional	TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	database	
read_QC_trim	min_length	Int	Internal component, do not modify	400	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	nanoq_cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	runtime	
read_QC_trim	nanoq_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	runtime	
read_QC_trim	nanoq_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/nanoq:0.9.0--hec16e2b_1	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	docker	
read_QC_trim	nanoq_max_read_length	Int	The maximum read length to keep after trimming	100000	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	nanoq_max_read_qual	Int	The maximum read quality to keep after trimming	100	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	nanoq_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	runtime	
read_QC_trim	nanoq_min_read_length	Int	The minimum read length to keep after trimming	500	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	nanoq_min_read_qual	Int	The minimum read quality to keep after trimming	10	Optional	TheiaCoV_ONT, TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	ncbi_scrub_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaCoV_ONT	runtime	
read_QC_trim	ncbi_scrub_cpu	Int	Internal component, do not modify	4	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	ncbi_scrub_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ONT	runtime	
read_QC_trim	ncbi_scrub_disk_size	Int	Internal component, do not modify	100	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	ncbi_scrub_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1	Optional	TheiaCoV_ONT	docker	
read_QC_trim	ncbi_scrub_docker	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	ncbi_scrub_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_ONT	runtime	
read_QC_trim	ncbi_scrub_memory	Int	Internal component, do not modify	8	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	phix	File	A file containing the phix used during Illumina sequencing; used in the BBDuk task		Optional	TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	rasusa_bases	String	Internal component, do not modify		Optional	TheiaCoV_ONT	general	
read_QC_trim	rasusa_bases	String	Explicitly set the number of bases required e.g., 4.3kb, 7Tb, 9000, 4.1MB. If this option is given, --coverage and --genome-size are ignored		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	rasusa_cpu	Int	Internal component, do not modify	4	Optional	TheiaCoV_ONT	general	
read_QC_trim	rasusa_cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
read_QC_trim	rasusa_disk_size	Int	Internal component, do not modify	100	Optional	TheiaCoV_ONT	general	
read_QC_trim	rasusa_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
read_QC_trim	rasusa_docker	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0	Optional	TheiaCoV_ONT, TheiaEuk_ONT	general	
read_QC_trim	rasusa_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0	Optional	TheiaProk_ONT	docker	
read_QC_trim	rasusa_fraction_of_reads	Float	Internal component, do not modify		Optional	TheiaCoV_ONT	general	
read_QC_trim	rasusa_fraction_of_reads	Float	Subsample to a fraction of the reads - e.g., 0.5 samples half the reads		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	rasusa_memory	Int	Internal component, do not modify	8	Optional	TheiaCoV_ONT	general	
read_QC_trim	rasusa_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaEuk_ONT, TheiaProk_ONT	runtime	
read_QC_trim	rasusa_number_of_reads	Int	Internal component, do not modify		Optional	TheiaCoV_ONT	general	
read_QC_trim	rasusa_number_of_reads	Int	Subsample to a specific number of reads		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	rasusa_seed	Int	Internal component, do not modify		Optional	TheiaCoV_ONT	general	
read_QC_trim	rasusa_seed	Int	Random seed to use		Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	read_processing	String	The name of the tool to perform basic read processing; options: "trimmomatic" or "fastp"	trimmomatic	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	read_qc	String	The tool used for quality control (QC) of reads. Options are "fastq_scan" (default) and "fastqc"	fastq_scan	Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	run_prefix	String	Internal component, do not modify	artic_ncov2019	Optional	TheiaEuk_ONT, TheiaProk_ONT	general	
read_QC_trim	target_organism	String	This string is searched for in the kraken2 outputs to extract the read percentage		Optional	TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	target_organism	String	Internal component, do not modify		Optional	TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_ONT	general	
read_QC_trim	trim_min_length	Int	Specifies minimum length of each read after trimming to be kept	75	Optional	TheiaMeta_Illumina_PE	general	
read_QC_trim	trim_quality_min_score	Int	Specifies the average quality of bases in a sliding window to be kept	30	Optional	TheiaMeta_Illumina_PE	general	
read_QC_trim	trim_window_size	Int	Specifies window size for trimming (the number of bases to average the quality across)	4	Optional	TheiaMeta_Illumina_PE	general	
read_QC_trim	trimmomatic_override_args	String	Additional arguments to pass to trimmomatic. Can be used to override all trimming parameters		Optional	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE	general	
read_QC_trim	workflow_series	String	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE	general	
read_QC_trim_ont	artic_guppyplex_cpu	Int	Number of CPUs to allocate to the task	8	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	artic_guppyplex_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	artic_guppyplex_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019:1.3.0-medaka-1.4.3	Optional	Freyja_FASTQ	docker	
read_QC_trim_ont	artic_guppyplex_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	downsampling_coverage	Float	Internal component, do not modify	150	Optional	Freyja_FASTQ	general	
read_QC_trim_ont	genome_length	Int	Length of the genome	5000000	Optional	Freyja_FASTQ	general	
read_QC_trim_ont	max_length	Int	Internal component, do not modify	700	Optional	Freyja_FASTQ	general	
read_QC_trim_ont	metabuli_cpu	Int	Number of CPUs to allocate to the task	4	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	metabuli_db	File	Metabuli database for read taxonomy classification, compressed in .tar.gz format	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/refseq_virus-v223.tar.gz	Optional	Freyja_FASTQ	database	
read_QC_trim_ont	metabuli_disk_size	Int	Amount of storage (in GB) to allocate to the task	250	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	metabuli_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/metabuli:1.1.1	Optional	Freyja_FASTQ	docker	
read_QC_trim_ont	metabuli_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	metabuli_taxdump_path	File	Path to taxonkit-generated taxdump for Metabuli taxonomy parsing	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/ncbi_taxdump_20260211.tar.gz	Optional	Freyja_FASTQ	general	
read_QC_trim_ont	min_length	Int	Internal component, do not modify	400	Optional	Freyja_FASTQ	general	
read_QC_trim_ont	nanoq_cpu	Int	Number of CPUs to allocate to the task	2	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	nanoq_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	nanoq_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/nanoq:0.9.0--hec16e2b_1	Optional	Freyja_FASTQ	docker	
read_QC_trim_ont	nanoq_max_read_length	Int	Maximum read length to use for filtering	100000	Optional	Freyja_FASTQ	general	
read_QC_trim_ont	nanoq_max_read_qual	Int	Maximum read quality to use for filtering	100	Optional	Freyja_FASTQ	general	
read_QC_trim_ont	nanoq_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	nanoq_min_read_length	Int	Minimum read length to use for filtering	500	Optional	Freyja_FASTQ	general	
read_QC_trim_ont	nanoq_min_read_qual	Int	Minimum read quality to use for filtering	10	Optional	Freyja_FASTQ	general	
read_QC_trim_ont	ncbi_scrub_cpu	Int	Number of CPUs to allocate to the task	4	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	ncbi_scrub_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	ncbi_scrub_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1	Optional	Freyja_FASTQ	docker	
read_QC_trim_ont	ncbi_scrub_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	rasusa_bases	String	Explicitly set the number of bases required e.g., 4.3kb, 7Tb, 9000, 4.1MB. If this option is given, --coverage and --genome-size are ignored		Optional	Freyja_FASTQ	general	
read_QC_trim_ont	rasusa_cpu	Int	Number of CPUs to allocate to the task	4	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	rasusa_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	rasusa_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0	Optional	Freyja_FASTQ	docker	
read_QC_trim_ont	rasusa_fraction_of_reads	Float	Subsample to a fraction of the reads - e.g., 0.5 samples half the reads		Optional	Freyja_FASTQ	general	
read_QC_trim_ont	rasusa_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Freyja_FASTQ	runtime	
read_QC_trim_ont	rasusa_number_of_reads	Int	Subsample to a specific number of reads		Optional	Freyja_FASTQ	general	
read_QC_trim_ont	rasusa_seed	Int	Random seed to use		Optional	Freyja_FASTQ	general	
read_QC_trim_ont	run_prefix	String	Internal component, do not modify	artic_ncov2019	Optional	Freyja_FASTQ	general	
read_QC_trim_pe	adapters	File	A FASTA file containing adapter sequences		Optional	Freyja_FASTQ	general	
read_QC_trim_pe	bbduk_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Freyja_FASTQ	runtime	
read_QC_trim_pe	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database		Optional	Freyja_FASTQ	general	
read_QC_trim_pe	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	Freyja_FASTQ	general	
read_QC_trim_pe	call_midas	Boolean	True/False variable that determines if the MIDAS task should be called.	False	Optional	Freyja_FASTQ	general	
read_QC_trim_pe	fastp_args	String	Additional arguments to use with fastp	--detect_adapter_for_pe -g -5 20 -3 20	Optional	Freyja_FASTQ	general	
read_QC_trim_pe	kraken_cpu	Int	Number of CPUs to allocate to the task	4	Optional	Freyja_FASTQ	runtime	
read_QC_trim_pe	kraken_db	File	A kraken2 database to use with the kraken2 optional task. The file must be a .tar.gz kraken2 database.	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz	Optional	Freyja_FASTQ	database	
read_QC_trim_pe	kraken_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ	runtime	
read_QC_trim_pe	kraken_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Freyja_FASTQ	runtime	
read_QC_trim_pe	midas_db	File	Database to use with MIDAS. Not required as one will be auto-selected when running the MIDAS task.	gs://theiagen-public-resources-rp/reference_data/databases/midas/midas_db_v1.2.tar.gz	Optional	Freyja_FASTQ	database	
read_QC_trim_pe	phix	File	The file containing the phix sequence to be used during bbduk task		Optional	Freyja_FASTQ	general	
read_QC_trim_pe	read_processing	String	Options: "trimmomatic" or "fastp" to indicate which read trimming module to use	trimmomatic	Optional	Freyja_FASTQ	general	
read_QC_trim_pe	read_qc	String	Allows the user to decide between fastq_scan (default) and fastqc for the evaluation of read quality.	fastq_scan	Optional	Freyja_FASTQ	general	
read_QC_trim_pe	trim_quality_min_score	Int	The minimum quality score to keep during trimming	30	Optional	Freyja_FASTQ	general	
read_QC_trim_pe	trim_window_size	Int	The window size to use during trimming	4	Optional	Freyja_FASTQ	general	
read_QC_trim_pe	trimmomatic_override_args	String	Additional arguments to pass to trimmomatic. Can be used to override all trimming parameters		Optional	Freyja_FASTQ	general	
read_QC_trim_se	adapters	File	A FASTA file containing adapter sequences		Optional	Freyja_FASTQ	general	
read_QC_trim_se	bbduk_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Freyja_FASTQ	runtime	
read_QC_trim_se	bracken_kmer_length	Int	Kmer length for Bracken to use instead of auto-detection - must be present in database		Optional	Freyja_FASTQ	general	
read_QC_trim_se	call_bracken	Boolean	Call Bracken kraken2 report refinement	True	Optional	Freyja_FASTQ	general	
read_QC_trim_se	call_midas	Boolean	True/False variable that determines if the MIDAS task should be called.	False	Optional	Freyja_FASTQ	general	
read_QC_trim_se	fastp_args	String	Additional arguments to use with fastp	-g -5 20 -3 20	Optional	Freyja_FASTQ	general	
read_QC_trim_se	kraken_cpu	Int	Number of CPUs to allocate to the task	4	Optional	Freyja_FASTQ	runtime	
read_QC_trim_se	kraken_db	File	A kraken2 database to use with the kraken2 optional task. The file must be a .tar.gz kraken2 database.	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz	Optional	Freyja_FASTQ	database	
read_QC_trim_se	kraken_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Freyja_FASTQ	runtime	
read_QC_trim_se	kraken_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Freyja_FASTQ	runtime	
read_QC_trim_se	midas_db	File	Database to use with MIDAS. Not required as one will be auto-selected when running the MIDAS task.	gs://theiagen-public-resources-rp/reference_data/databases/midas/midas_db_v1.2.tar.gz	Optional	Freyja_FASTQ	database	
read_QC_trim_se	phix	File	The file containing the phix sequence to be used during bbduk task		Optional	Freyja_FASTQ	general	
read_QC_trim_se	read_processing	String	Options: "trimmomatic" or "fastp" to indicate which read trimming module to use	trimmomatic	Optional	Freyja_FASTQ	general	
read_QC_trim_se	read_qc	String	Allows the user to decide between fastq_scan (default) and fastqc for the evaluation of read quality.	fastq_scan	Optional	Freyja_FASTQ	general	
read_QC_trim_se	trim_quality_min_score	Int	The minimum quality score to keep during trimming	30	Optional	Freyja_FASTQ	general	
read_QC_trim_se	trim_window_size	Int	The window size to use during trimming	4	Optional	Freyja_FASTQ	general	
read_QC_trim_se	trimmomatic_override_args	String	Additional arguments to pass to trimmomatic. Can be used to override all trimming parameters		Optional	Freyja_FASTQ	general	
referenceseeker	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	runtime	
referenceseeker	disk_size	Int	Amount of storage (in GB) to allocate to the task	200	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	runtime	
referenceseeker	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/referenceseeker:1.8.0--pyhdfd78af_0	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	docker	
referenceseeker	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	runtime	
referenceseeker	referenceseeker_ani_threshold	Float	Bidirectional average nucleotide identity to use as a cut off for identifying reference assemblies with ReferenceSeeker; default value set according to <https://github.com/oschwengers/referenceseeker#description>	0.95	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	general	True
referenceseeker	referenceseeker_conserved_dna_threshold	Float	Conserved DNA % to use as a cut off for identifying reference assemblies with ReferenceSeeker; default value set according to <https://github.com/oschwengers/referenceseeker#description>	0.69	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	general	True
referenceseeker	referenceseeker_db	File	Database used by the referenceseeker tool that contains bacterial genomes from RefSeq release 205. Downloaded from the referenceseeker GitHub repository.	gs://theiagen-public-resources-rp/reference_data/databases/referenceseeker/referenceseeker-bacteria-refseq-205.v20210406.tar.gz	Optional	Assembly_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA	database	
register_ena_samples	batch_size	Int	Number of samples to process in each batch	100	Optional	Terra_2_ENA	general	
register_ena_samples	center	String	Name of submitting center		Optional	Terra_2_ENA	general	
register_ena_samples	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Terra_2_ENA	runtime	
register_ena_samples	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Terra_2_ENA	runtime	
register_ena_samples	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra_to_ena:0.6	Optional	Terra_2_ENA	docker	
register_ena_samples	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Terra_2_ENA	runtime	
rename_fastq_files	read2	File	FASTQ file containing read2 sequences		Optional	Rename_FASTQ	general	
rename_PE_files	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Rename_FASTQ	runtime	
rename_PE_files	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Rename_FASTQ	runtime	
rename_PE_files	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ubuntu/ubuntu:jammy-20230816	Optional	Rename_FASTQ	docker	
rename_PE_files	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Rename_FASTQ	runtime	
rename_SE_files	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Rename_FASTQ	runtime	
rename_SE_files	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Rename_FASTQ	runtime	
rename_SE_files	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ubuntu/ubuntu:jammy-20230816	Optional	Rename_FASTQ	docker	
rename_SE_files	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Rename_FASTQ	runtime	
reorder_matrix	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur, MashTree_FASTA	runtime	
reorder_matrix	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Augur, MashTree_FASTA	runtime	
reorder_matrix	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1	Optional	Augur, MashTree_FASTA	docker	
reorder_matrix	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Augur, MashTree_FASTA	runtime	
reorder_matrix	outgroup_root	String	Tip name to root phylogenetic tree upon (overrides midpoint root)		Optional	MashTree_FASTA	general	
reorder_matrix	phandango_coloring	Boolean	Whether or not Phandango coloring will color all items from the same column the same	False	Optional	Augur	general	
resfinder_task	acquired	Boolean	Set to true to tell ResFinder to identify acquired resistance genes	True	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
resfinder_task	call_pointfinder	Boolean	Set to true to enable detection of point mutations.	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
resfinder_task	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
resfinder_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
resfinder_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/resfinder:4.1.11	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
resfinder_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
resfinder_task	min_percent_coverage	Float	Minimum coverage breadth of a gene for it to be identified	0.5	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
resfinder_task	min_percent_identity	Float	Minimum identity for ResFinder to identify a gene	0.9	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
retrieve_aligned_contig_paf	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
retrieve_aligned_contig_paf	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
retrieve_aligned_contig_paf	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/seqkit:2.4.0--h9ee0642_0	Optional	TheiaMeta_Illumina_PE	docker	
retrieve_aligned_contig_paf	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
retrieve_aligned_pe_reads_sam	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
retrieve_aligned_pe_reads_sam	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
retrieve_aligned_pe_reads_sam	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17	Optional	TheiaMeta_Illumina_PE	docker	
retrieve_aligned_pe_reads_sam	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
retrieve_unaligned_pe_reads_sam	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
retrieve_unaligned_pe_reads_sam	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
retrieve_unaligned_pe_reads_sam	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17	Optional	TheiaMeta_Illumina_PE	docker	
retrieve_unaligned_pe_reads_sam	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
root_tree1_task	cpu	Int	Number of CPUs to allocate to the task	1	Optional	PhyloCompare	runtime	
root_tree1_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	PhyloCompare	runtime	
root_tree1_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/theiaphylo:0.1.8	Optional	PhyloCompare	docker	
root_tree1_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	PhyloCompare	runtime	
root_tree2_task	cpu	Int	Number of CPUs to allocate to the task	1	Optional	PhyloCompare	runtime	
root_tree2_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	PhyloCompare	runtime	
root_tree2_task	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/theiaphylo:0.1.8	Optional	PhyloCompare	docker	
root_tree2_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	PhyloCompare	runtime	
sam_to_sorted_bam	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaMeta_Illumina_PE	runtime	
sam_to_sorted_bam	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaMeta_Illumina_PE	runtime	
sam_to_sorted_bam	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17	Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaMeta_Illumina_PE	docker	
sam_to_sorted_bam	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaMeta_Illumina_PE	runtime	
sam_to_sorted_bam	min_qual	Int	Minimum quality score for reads to be included in the analysis		Optional	Clair3_Variants_ONT, Freyja_FASTQ, TheiaMeta_Illumina_PE	general	
samtools_faidx	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Clair3_Variants_ONT	runtime	
samtools_faidx	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Clair3_Variants_ONT	runtime	
samtools_faidx	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17	Optional	Clair3_Variants_ONT	docker	
samtools_faidx	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Clair3_Variants_ONT	runtime	
semibin	cpu	Int	Number of CPUs to allocate to the task	6	Optional	TheiaMeta_Illumina_PE	runtime	
semibin	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
semibin	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/semibin:2.0.2--pyhdfd78af_0	Optional	TheiaMeta_Illumina_PE	docker	
semibin	environment	String	Environment model to use. Options:• human_gut• dog_gut• ocean• soil• cat_gut• human_oral• mouse_gut• pig_gut• built_environment• wastewater• chicken_caecum• global	global	Optional	TheiaMeta_Illumina_PE	general	
semibin	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
semibin	min_length	Int	Minimum contig length for binning	1000	Optional	TheiaMeta_Illumina_PE	general	
semibin	ratio	Float	If the ratio of the number of base pairs of contigs between 1000-2500 bp smaller than this value, the minimal length will be set as 1000bp, otherwise 2500bp.	0.05	Optional	TheiaMeta_Illumina_PE	general	
shared_variants	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Find_Shared_Variants, Snippy_Tree	runtime	
shared_variants	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Find_Shared_Variants, Snippy_Tree	runtime	
shared_variants	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16	Optional	Find_Shared_Variants, Snippy_Tree	docker	
shared_variants	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Find_Shared_Variants, Snippy_Tree	runtime	
skani	acc2taxon_map	File	Tab-delimited map between reference genome accessions and their affiliated taxon	gs://theiagen-public-resources-rp/reference_data/databases/skani/viral_fna_20251107/viral_accession2taxon_20251107.tsv	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
skani	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
skani	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
skani	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/skani:0.2.2	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
skani	fasta_dir	String	Reference genome database base directory	gs://theiagen-public-resources-rp/reference_data/databases/skani/viral_fna_20251107/fna/	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	general	
skani	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
skani	skani_db	File	Skani database file	gs://theiagen-public-resources-rp/reference_data/databases/skani/skani_db_20251107.tar	Optional	TheiaViral_ONT	database	
sm_theiacov_fasta_wrangling	cpu	Int	Number of CPUs to allocate to the task	8	Optional	TheiaCoV_FASTA_Batch	runtime	
sm_theiacov_fasta_wrangling	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_FASTA_Batch	runtime	
sm_theiacov_fasta_wrangling	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-08-28-v4	Optional	TheiaCoV_FASTA_Batch	docker	
sm_theiacov_fasta_wrangling	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TheiaCoV_FASTA_Batch	runtime	
snippy_gene_query	cpu	Int	Number of CPUs to allocate to the task	8	Optional	Snippy_Variants	runtime	
snippy_gene_query	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Variants	runtime	
snippy_gene_query	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	Snippy_Variants	docker	
snippy_gene_query	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Snippy_Variants	runtime	
snippy_streamline	assembly_fasta	Array[File]	The assembly files for your samples (Required if a reference genome is not provided)		Optional	Snippy_Streamline	general	
snippy_streamline	reference_genome_file	File	Reference genome in FASTA or GENBANK format (must be the same reference used in Snippy_Variants workflow); provide this if you want to skip the detection of a suitable reference		Optional	Snippy_Streamline	general	
snippy_streamline	use_centroid_as_reference	Boolean	Set to true if you want to use the centroid sample as the reference sample instead of using the centroid to detect a suitable one	False	Optional	Snippy_Streamline	general	True
snippy_streamline_fasta	reference_genome_file	File	Reference genome in FASTA or GENBANK format (must be the same reference used in Snippy_Variants workflow); provide this if you want to skip the detection of a suitable reference		Optional	Snippy_Streamline_FASTA	general	
snippy_streamline_fasta	use_centroid_as_reference	Boolean	Set to true if you want to use the centroid sample as the reference sample instead of using the centroid to detect a suitable one	False	Optional	Snippy_Streamline_FASTA	general	True
snippy_tree_wf	call_shared_variants	Boolean	When true, workflow generates table that combines variants across all samples and a table showing variants shared across samples	True	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	core_genome	Boolean	When true, workflow generates core genome phylogeny; when false, whole genome is used	True	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	data_summary_column_names	String	A comma-separated list of the column names from the sample-level data table for generating a data summary (presence/absence .csv matrix)		Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	data_summary_terra_project	String	The billing project for your current workspace. This can be found after the "#workspaces/" section in the workspace's URL		Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	data_summary_terra_table	String	The name of the sample-level Terra data table that will be used for generating a data summary		Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	data_summary_terra_workspace	String	The name of the Terra workspace you are in. This can be found at the top of the webpage, or in the URL after the billing project.		Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	gubbins_cpu	Int	Number of CPUs to allocate to the task	4	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	gubbins_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	gubbins_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/gubbins:3.3--py310pl5321h8472f5a_0	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	docker	
snippy_tree_wf	gubbins_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	iqtree2_cpu	Int	Number of CPUs to allocate to the task	4	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	iqtree2_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	iqtree2_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/iqtree2:2.1.2	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	docker	
snippy_tree_wf	iqtree2_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	iqtree2_model	String	Nucelotide substitution model to use when generating the final tree with IQTree2. By default, IQtree runs its ModelFinder algorithm to identify the model it thinks best fits your dataset		Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	iqtree2_opts	String	Additional options to pass to IQTree2		Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	iqtree2_ultrafast_bootstraps	Int	Number of replicates for <http://www.iqtree.org/doc/Tutorial#assessing-branch-supports-with-ultrafast-bootstrap-approximation> (Minimum recommended= 1000)	1000	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	midpoint_root_tree	Boolean	A True/False option that determines whether the tree used in the SNP matrix re-ordering task should be re-rooted or not. Options: true or false	True	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	phandango_coloring	Boolean	Boolean variable that tells the data summary task and the reorder matrix task to include a suffix that enables consistent coloring on Phandango; by default, this suffix is not added. To add this suffix set this variable to true.	False	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	snippy_core_bed	File	User-provided bed file to mask out regions of the genome when creating multiple sequence alignments		Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_tree_wf	snippy_core_cpu	Int	Number of CPUs to allocate to the task	8	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	snippy_core_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	snippy_core_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snippy:4.6.0	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	docker	
snippy_tree_wf	snippy_core_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	snippy_variants_qc_metrics	Array[File]	Files produced by the Snippy_Variants workflow used to concatenate the reports for each sample in the tree		Optional	Snippy_Tree	general	
snippy_tree_wf	snp_dists_cpu	Int	Number of CPUs to allocate to the task	1	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	snp_dists_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	snp_dists_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	docker	
snippy_tree_wf	snp_dists_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	snp_sites_cpu	Int	Number of CPUs to allocate to the task	1	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	snp_sites_disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	snp_sites_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snp-sites:2.5.1	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	docker	
snippy_tree_wf	snp_sites_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	runtime	
snippy_tree_wf	use_gubbins	Boolean	When "true", workflow removes recombination with gubbins tasks; when "false", gubbins is not used	True	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree	general	
snippy_variants	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Variants	runtime	
snippy_variants_wf	assembly_fasta	File	The assembly file for your sample in FASTA format		Optional	Snippy_Streamline, Snippy_Variants	general	
snippy_variants_wf	base_quality	Int	Minimum quality for a nucleotide to be used in variant calling	13	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	general	
snippy_variants_wf	cpu	Int	Number of CPUs to allocate to the task	8	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	runtime	
snippy_variants_wf	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snippy:4.6.0	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	docker	
snippy_variants_wf	map_qual	Int	Minimum mapping quality to accept in variant calling	60	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	general	
snippy_variants_wf	maxsoft	Int	Number of bases of alignment to soft-clip before discarding the alignment	10	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	general	
snippy_variants_wf	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	runtime	
snippy_variants_wf	min_coverage	Int	Minimum read coverage of a position to identify a mutation	10	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	general	
snippy_variants_wf	min_frac	Float	Minimum fraction of bases at a given position to identify a mutation	0	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	general	
snippy_variants_wf	min_quality	Int	Minimum VCF variant call "quality"	100	Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	general	
snippy_variants_wf	query_gene	String	Comma-separated strings (e.g. gene names) in which to search for mutations to output to data table		Optional	Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Variants	general	
snippy_variants_wf	read1	File	Internal component, do not modify		Optional	Snippy_Streamline_FASTA	general	
snippy_variants_wf	read1	File	FASTQ file containing read1 sequences		Optional	Snippy_Variants	general	
snippy_variants_wf	read2	File	Internal component, do not modify		Optional	Snippy_Streamline_FASTA	general	
snippy_variants_wf	read2	File	FASTQ file containing read2 sequences		Optional	Snippy_Variants	general	
snp_dists	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur	runtime	
snp_dists	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	Augur	runtime	
snp_dists	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snp-dists:0.8.2	Optional	Augur	docker	
snp_dists	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Augur	runtime	
sort_bam_assembly_correction	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaMeta_Illumina_PE	runtime	
sort_bam_assembly_correction	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
sort_bam_assembly_correction	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17	Optional	TheiaMeta_Illumina_PE	docker	
sort_bam_assembly_correction	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaMeta_Illumina_PE	runtime	
sort_bam_assembly_correction	min_qual	Int	Minimum quality score for reads to be included in the analysis		Optional	TheiaMeta_Illumina_PE	general	
spades	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_Illumina_PE	runtime	
spades	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_Illumina_PE	runtime	
spades	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/spades:4.1.0	Optional	TheiaViral_Illumina_PE	docker	
spades	kmers	String	list of k-mer sizes (must be odd and less than 128)	auto	Optional	TheiaViral_Illumina_PE	general	True
spades	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaViral_Illumina_PE	runtime	
spades	phred_offset	Int	PHRED quality offset in the input reads (33 or 64)	33	Optional	TheiaViral_Illumina_PE	general	
spades	spades_opts	String	Additional parameters for Spades assembler		Optional	TheiaViral_Illumina_PE	general	
sra_tsv_to_xml	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Terra_2_NCBI	runtime	
sra_tsv_to_xml	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Terra_2_NCBI	runtime	
sra_tsv_to_xml	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/broadinstitute/ncbi-tools:2.10.7.10	Optional	Terra_2_NCBI	docker	
sra_tsv_to_xml	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Terra_2_NCBI	runtime	
stats_n_coverage	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	runtime	
stats_n_coverage	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	runtime	
stats_n_coverage	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.23	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	docker	
stats_n_coverage	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	runtime	
stats_n_coverage	read2	File	Internal component, do not modify		Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	general	
stats_n_coverage_primtrim	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	runtime	
stats_n_coverage_primtrim	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	runtime	
stats_n_coverage_primtrim	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/samtools:1.23	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	docker	
stats_n_coverage_primtrim	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	runtime	
stats_n_coverage_primtrim	read2	File	Internal component, do not modify		Optional	TheiaCoV_ClearLabs, TheiaCoV_ONT	general	
submit_ena_data	bam_column	String	Column name containing BAM file paths	bam_file	Optional	Terra_2_ENA	general	
submit_ena_data	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Terra_2_ENA	runtime	
submit_ena_data	cram_column	String	Column name containing CRAM file paths	cram_file	Optional	Terra_2_ENA	general	
submit_ena_data	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Terra_2_ENA	runtime	
submit_ena_data	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra_to_ena:0.6	Optional	Terra_2_ENA	docker	
submit_ena_data	experiment_name	String	Internal component, do not modify		Optional	Terra_2_ENA	general	
submit_ena_data	instrument	String	Internal component, do not modify		Optional	Terra_2_ENA	general	
submit_ena_data	library_selection	String	Internal component, do not modify	RANDOM	Optional	Terra_2_ENA	general	
submit_ena_data	library_source	String	Internal component, do not modify	GENOMIC	Optional	Terra_2_ENA	general	
submit_ena_data	library_strategy	String	Internal component, do not modify	WGS	Optional	Terra_2_ENA	general	
submit_ena_data	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Terra_2_ENA	runtime	
submit_ena_data	platform	String	Internal component, do not modify	ILLUMINA	Optional	Terra_2_ENA	general	
submit_ena_data	read1_column	String	Column name containing read1 file paths	read1	Optional	Terra_2_ENA	general	
submit_ena_data	read2_column	String	Column name containing read2 file paths	read2	Optional	Terra_2_ENA	general	
submit_ena_data	submit_to_production	Boolean	If false, performs a test submission of metadata	False	Optional	Terra_2_ENA	general	
summarize_data	cpu	Int	Number of CPUs to allocate to the task	8	Optional	Core_Gene_SNP, MashTree_FASTA, Snippy_Tree, kSNP3, kSNP4	runtime	
summarize_data	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Core_Gene_SNP, MashTree_FASTA, Snippy_Tree, kSNP3, kSNP4	runtime	
summarize_data	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16	Optional	Core_Gene_SNP, MashTree_FASTA, Snippy_Tree, kSNP3, kSNP4	docker	
summarize_data	id_column_name	String	If the sample IDs are in a different column to samplenames, it can be passed here and it will be used instead.		Optional	Core_Gene_SNP, MashTree_FASTA, Snippy_Tree, kSNP3, kSNP4	general	
summarize_data	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	1	Optional	Core_Gene_SNP, MashTree_FASTA, Snippy_Tree, kSNP3, kSNP4	runtime	
table2asn	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Mercury_Prep_N_Batch	runtime	
table2asn	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Mercury_Prep_N_Batch	runtime	
table2asn	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ncbi-table2asn:1.26.678	Optional	Mercury_Prep_N_Batch	docker	
table2asn	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	1	Optional	Mercury_Prep_N_Batch	runtime	
tbp_parser	add_cycloserine_lims	Boolean	Set to true add cycloserine results to the LIMS report	False	Optional	TBProfiler_tNGS	general	
tbp_parser	config	File	The configuration file to use, in YAML format (overrides all other arguments except input_json and input_bam)		Optional	TBProfiler_tNGS	general	
tbp_parser	coverage_regions_bed	File	A file that contains the regions to perform coverage analysis on		Optional	TBProfiler_tNGS	general	
tbp_parser	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TBProfiler_tNGS	runtime	
tbp_parser	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TBProfiler_tNGS	runtime	
tbp_parser	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.9.1	Optional	TBProfiler_tNGS	docker	
tbp_parser	etha237_frequency	Float	Minimum frequency for a mutation in ethA at protein position 237 to pass QC in tbp-parser	0.1	Optional	TBProfiler_tNGS	general	
tbp_parser	expert_rule_regions_bed	File	A file that contains the regions where R mutations and expert rules are applied		Optional	TBProfiler_tNGS	general	
tbp_parser	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	TBProfiler_tNGS	runtime	
tbp_parser	min_depth	Int	Minimum depth for a variant to pass QC in tbp_parser	10	Optional	TBProfiler_tNGS	general	
tbp_parser	min_frequency	Float	Minimum allele frequency for a variant to pass QC in tbp-parser	0.1	Optional	TBProfiler_tNGS	general	
tbp_parser	min_percent_coverage	Float	The minimum percentage of a region to exceed the minimum depth for a region to pass QC in tbp_parser	100	Optional	TBProfiler_tNGS	general	
tbp_parser	min_read_support	Int	Minimum read support for a variant to pass QC in tbp-parser	10	Optional	TBProfiler_tNGS	general	
tbp_parser	operator	String	Fills the "operator" field in the tbp_parser output files		Optional	TBProfiler_tNGS	general	
tbp_parser	rpob449_frequency	Float	Minimum frequency for a mutation at protein position 449 to pass QC in tbp-parser	0.1	Optional	TBProfiler_tNGS	general	
tbp_parser	rrl_frequency	Float	Minimum frequency for a mutation in rrl to pass QC in tbp-parser	0.1	Optional	TBProfiler_tNGS	general	
tbp_parser	rrl_read_support	Int	Minimum read support for a mutation in rrl to pass QC in tbp-parser	10	Optional	TBProfiler_tNGS	general	
tbp_parser	rrs_frequency	Float	Minimum frequency for a mutation in rrs to pass QC in tbp-parser	0.1	Optional	TBProfiler_tNGS	general	
tbp_parser	rrs_read_support	Int	Minimum read support for a mutation in rrs to pass QC in tbp-parser	10	Optional	TBProfiler_tNGS	general	
tbp_parser	sequencing_method	String	Fills out the "seq_method" field in the tbp_parser output files		Optional	TBProfiler_tNGS	general	
tbp_parser	tbp_parser_debug	Boolean	Activate the debug mode on tbp_parser; increases logging outputs	True	Optional	TBProfiler_tNGS	general	
tbprofiler	additional_parameters	String	Additional parameters for TBProfiler		Optional	TBProfiler_tNGS	general	
tbprofiler	cpu	Int	Number of CPUs to allocate to the task	8	Optional	TBProfiler_tNGS	runtime	
tbprofiler	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TBProfiler_tNGS	runtime	
tbprofiler	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/tbprofiler:6.6.3	Optional	TBProfiler_tNGS	docker	
tbprofiler	mapper	String	The mapping tool used in TBProfiler to align the reads to the reference genome; see TBProfiler's original documentation for available options.	bwa	Optional	TBProfiler_tNGS	general	
tbprofiler	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TBProfiler_tNGS	runtime	
tbprofiler	min_af	Float	The minimum allele frequency to call a variant	0.1	Optional	TBProfiler_tNGS	general	
tbprofiler	min_depth	Int	The minimum depth for a variant to be called.	10	Optional	TBProfiler_tNGS	general	
tbprofiler	ont_data	Boolean	Specifies nanopore specific tbprofiler parameters	False	Optional	TBProfiler_tNGS	general	
tbprofiler	tbprofiler_custom_db	File	TBProfiler uses by default the TBDB database; if you have a custom database you wish to use, you must provide a custom database in this field		Optional	TBProfiler_tNGS	general	
tbprofiler	variant_caller	String	Select a different variant caller for TBProfiler to use by writing it in this block; see TBProfiler's original documentation for available options.	gatk	Optional	TBProfiler_tNGS	general	
tbprofiler	variant_calling_params	String	Enter additional variant calling parameters in this free text input to customize how the variant caller works in TBProfiler		Optional	TBProfiler_tNGS	general	
tbprofiler_tngs	run_clockwork	Boolean	Set to True to run Clockwork read decontamination	False	Optional	TBProfiler_tNGS	general	
tbprofiler_tngs	run_trimmomatic	Boolean	Set to False to skip trimmomatic read trimming	True	Optional	TBProfiler_tNGS	general	
tbprofiler_tngs	tbdb_branch	String	TBProfiler uses by default the TBDB database (a combination of the original library and the WHO v2 catalogue). You can opt to use a different mutation library by using this field to specify the name of the TBDB branch to use in TBProfiler; see [the TBProfiler documentation](https://jodyphelan.github.io/tb-profiler-docs/en/mutation-library/) for more information regarding available databases		Optional	TBProfiler_tNGS	database	True
Terra_2_ENA	allow_missing	Boolean	Whether to allow missing values in metadata	False	Optional	Terra_2_ENA	general	
Terra_2_ENA	column_mappings	File	TSV file mapping Terra table columns to ENA submission fields		Optional	Terra_2_ENA	general	
Terra_2_NCBI	column_mapping_file	File	TSV file mapping Terra table columns to NCBI submission fields		Optional	Terra_2_NCBI	general	
Terra_2_NCBI	input_table	File	Internal component, do not modify		Optional	Terra_2_NCBI	general	
Terra_2_NCBI	skip_biosample	Boolean	Boolean switch to turn on actual production level submission	False	Optional	Terra_2_NCBI	general	
Terra_2_NCBI	submit_to_production	Boolean	Used to indicate whether or not the workflow should submit to NCBI's production environment. If set to true, then a Production submission will occur. Otherwise, by default (false), it will perform a Test submission.	False	Optional, Required	Terra_2_NCBI	general	True
theiacov_clearlabs	medaka_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019:1.3.0-medaka-1.4.3	Optional	TheiaCoV_ClearLabs	docker	
theiacov_clearlabs	nextclade_dataset_name	String	Nextclade organism dataset names. However, if organism input is set correctly, this input will be automatically assigned the corresponding dataset name. See organism defaults for more information	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_ClearLabs	general	True
theiacov_clearlabs	nextclade_dataset_tag	String	Nextclade dataset tag. Used for pulling up-to-date reference genomes and associated information specific to nextclade datasets (QC thresholds, organism-specific information like SARS-CoV-2 clade & lineage information, etc.) that is required for running the Nextclade tool.	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_ClearLabs	general	True
theiacov_clearlabs	normalise	Int	Used to normalize the amount of reads to the indicated level before variant calling	20000	Optional	TheiaCoV_ClearLabs	general	
theiacov_clearlabs	organism	String	The organism that is being analyzed. Options: "sars-cov-2", "MPXV", "WNV", "HIV", "flu", "rsv_a", "rsv_b". However, "flu" is not available for TheiaCoV_Illumina_SE	sars-cov-2	Optional	TheiaCoV_ClearLabs	general	
theiacov_clearlabs	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaCoV_ClearLabs	general	
theiacov_clearlabs	reference_genome	File	An optional reference genome used for consensus assembly and QC		Optional	TheiaCoV_ClearLabs	general	
theiacov_clearlabs	seq_method	String	The sequencing methodology used to generate the input read data; for TheiaProk workflows, this input will be used in the "seq_id" column in any taxon-specific tables created in the Export Taxon Tables task	OXFORD_NANOPORE	Optional	TheiaCoV_ClearLabs	general	
theiacov_clearlabs	target_organism	String	The organism whose abundance the user wants to check in their reads. This should be a proper taxonomic name recognized by the Kraken database.		Optional	TheiaCoV_ClearLabs	general	
theiacov_fasta	flu_segment	String	Influenza genome segment being analyzed. Options: "HA" or "NA". Only required if input assembly is a singular flu segment.		Optional, Required	TheiaCoV_FASTA	general	True
theiacov_fasta	flu_subtype	String	The influenza subtype being analyzed. Options: "Yamagata", "Victoria", "H1N1", "H3N2", "H5N1". Automatically determined.		Optional	TheiaCoV_FASTA	general	
theiacov_fasta	genome_length	Int	User-specified expected genome length to be used in genome statistics calculations		Optional	TheiaCoV_FASTA	general	
theiacov_fasta	nextclade_dataset_name	String	Nextclade organism dataset names. However, if organism input is set correctly, this input will be automatically assigned the corresponding dataset name. See organism defaults for more information	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_FASTA	general	True
theiacov_fasta	nextclade_dataset_tag	String	Nextclade dataset tag. Used for pulling up-to-date reference genomes and associated information specific to nextclade datasets (QC thresholds, organism-specific information like SARS-CoV-2 clade & lineage information, etc.) that is required for running the Nextclade tool.	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_FASTA	general	True
theiacov_fasta	organism	String	The organism that is being analyzed. Options: "sars-cov-2", "MPXV", "WNV", "HIV", "flu", "rsv_a", "rsv_b". However, "flu" is not available for TheiaCoV_Illumina_SE	sars-cov-2	Optional	TheiaCoV_FASTA	general	
theiacov_fasta	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaCoV_FASTA	general	
theiacov_fasta	reference_genome	File	An optional reference genome used for consensus assembly and QC		Optional	TheiaCoV_FASTA	general	
theiacov_fasta	vadr_max_length	Int	Maximum length of contig allowed to run VADR		Optional	TheiaCoV_FASTA	general	
theiacov_fasta	vadr_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32 (RSV-A and RSV-B) and 8 (all other TheiaCoV organisms)	Optional	TheiaCoV_FASTA	runtime	True
theiacov_fasta	vadr_model_file	File	Path to the a tar + gzipped VADR model file	Defaults are organism-specific. Please find default values for all organisms here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>.	Optional	TheiaCoV_FASTA	general	True
theiacov_fasta	vadr_opts	String	Additional options to provide to VADR		Optional	TheiaCoV_FASTA	general	
theiacov_fasta	vadr_skip_length	Int	Minimum assembly length (unambiguous) to run VADR	10000	Optional	TheiaCoV_FASTA	general	True
theiacov_fasta_batch	nextclade_dataset_name	String	Nextclade organism dataset name. Options: "nextstrain/sars-cov-2/wuhan-hu-1/orfs" However, if organism input is set correctly, this input will be automatically assigned the corresponding dataset name.	sars-cov-2	Optional	TheiaCoV_FASTA_Batch	general	True
theiacov_fasta_batch	nextclade_dataset_tag	String	Nextclade dataset tag. Used for pulling up-to-date reference genomes and associated information specific to nextclade datasets (QC thresholds, organism-specific information like SARS-CoV-2 clade & lineage information, etc.) that is required for running the Nextclade tool.	2024-06-13--23-42-47Z	Optional	TheiaCoV_FASTA_Batch	general	True
theiacov_fasta_batch	organism	String	The organism that is being analyzed. Options: "sars-cov-2"	sars-cov-2	Optional	TheiaCoV_FASTA_Batch	general	
theiacov_fasta_batch	pangolin_docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34	Optional	TheiaCoV_FASTA_Batch	docker	True
theiacov_illumina_pe	adapters	File	A FASTA file containing adapter sequences	/bbmap/resources/adapters.fa	Optional	TheiaCoV_Illumina_PE	general	True
theiacov_illumina_pe	consensus_min_freq	Float	The minimum frequency for a variant to be called a SNP in consensus genome	0.6	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	genome_length	Int	User-specified expected genome length to be used in genome statistics calculations		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	max_genome_length	Int	Maximum genome length able to pass read screening	2673870	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	min_basepairs	Int	Minimum number of base pairs able to pass read screening	17000	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	min_coverage	Int	Minimum genome coverage able to pass read screening	10	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	min_depth	Int	Minimum depth of reads required to call variants and generate a consensus genome. This value is passed to the iVar software.	100	Optional	TheiaCoV_Illumina_PE	general	True
theiacov_illumina_pe	min_genome_length	Int	Minimum genome length to pass read screening	1700	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	min_proportion	Int	Minimum proportion of total reads in each read file to pass read screening	40	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	min_reads	Int	Minimum number of reads to pass read screening	57	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	nextclade_dataset_name	String	Nextclade organism dataset names. However, if organism input is set correctly, this input will be automatically assigned the corresponding dataset name. See organism defaults for more information	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_Illumina_PE	general	True
theiacov_illumina_pe	nextclade_dataset_tag	String	Nextclade dataset tag. Used for pulling up-to-date reference genomes and associated information specific to nextclade datasets (QC thresholds, organism-specific information like SARS-CoV-2 clade & lineage information, etc.) that is required for running the Nextclade tool.	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_Illumina_PE	general	True
theiacov_illumina_pe	organism	String	The organism that is being analyzed. Options: "sars-cov-2", "MPXV", "WNV", "HIV", "flu", "rsv_a", "rsv_b". However, "flu" is not available for TheiaCoV_Illumina_SE	sars-cov-2	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	pangolin_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34	Optional	TheiaCoV_Illumina_PE	docker	True
theiacov_illumina_pe	phix	File	File that contains the phix used	/bbmap/resources/phix174_ill.ref.fa.gz	Optional	TheiaCoV_Illumina_PE	general	True
theiacov_illumina_pe	primer_bed	File	The bed file containing the primers used when sequencing was performed		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	reference_gene_locations_bed	File	Use to provide locations of interest where average coverage will be calculated		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	reference_genome	File	An optional reference genome used for consensus assembly and QC		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	reference_gff	File	The general feature format (gff) of the reference genome.		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	seq_method	String	The sequencing methodology used to generate the input read data; for TheiaProk workflows, this input will be used in the "seq_id" column in any taxon-specific tables created in the Export Taxon Tables task	ILLUMINA	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	skip_screen	Boolean	Set to True to skip the read screening prior to analysis	False	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	target_organism	String	The organism whose abundance the user wants to check in their reads. This should be a proper taxonomic name recognized by the Kraken database.		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	trim_min_length	Int	Specifies minimum length of each read after trimming to be kept	75	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	trim_primers	Boolean	A True/False option that determines if primers should be trimmed.	True	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	trim_quality_min_score	Int	Specifies the minimum average quality of bases in a sliding window to be kept	30	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	trim_window_size	Int	Specifies window size for trimming (the number of bases to average the quality across)	4	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	vadr_max_length	Int	Maximum length of contig allowed to run VADR		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	vadr_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32 (RSV-A and RSV-B) and 8 (all other TheiaCoV organisms)	Optional	TheiaCoV_Illumina_PE	runtime	True
theiacov_illumina_pe	vadr_model_file	File	Path to the a tar + gzipped VADR model file	Defaults are organism-specific. Please find default values for all organisms here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>.	Optional	TheiaCoV_Illumina_PE	general	True
theiacov_illumina_pe	vadr_options	String	Additional options to provide to VADR		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	vadr_skip_length	Int	Minimum assembly length (unambiguous) to run VADR		Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_pe	variant_min_freq	Float	Minimum frequency for a variant to be reported in ivar outputs	0.6	Optional	TheiaCoV_Illumina_PE	general	
theiacov_illumina_se	adapters	File	A FASTA file containing adapter sequences	/bbmap/resources/adapters.fa	Optional	TheiaCoV_Illumina_SE	general	True
theiacov_illumina_se	consensus_min_freq	Float	The minimum frequency for a variant to be called a SNP in consensus genome	0.6	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	genome_length	Int	User-specified expected genome length to be used in genome statistics calculations		Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	max_genome_length	Int	Maximum genome length able to pass read screening	2673870	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	min_basepairs	Int	Minimum number of base pairs able to pass read screening	17000	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	min_coverage	Int	Minimum genome coverage able to pass read screening	10	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	min_depth	Int	Minimum depth of reads required to call variants and generate a consensus genome. This value is passed to the iVar software.	100	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	min_genome_length	Int	Minimum genome length to pass read screening	1700	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	min_reads	Int	Minimum number of reads to pass read screening	57	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	nextclade_dataset_name	String	Nextclade organism dataset names. However, if organism input is set correctly, this input will be automatically assigned the corresponding dataset name. See organism defaults for more information	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_Illumina_SE	general	True
theiacov_illumina_se	nextclade_dataset_tag	String	Nextclade dataset tag. Used for pulling up-to-date reference genomes and associated information specific to nextclade datasets (QC thresholds, organism-specific information like SARS-CoV-2 clade & lineage information, etc.) that is required for running the Nextclade tool.	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_Illumina_SE	general	True
theiacov_illumina_se	organism	String	The organism that is being analyzed. Options: "sars-cov-2", "MPXV", "WNV", "HIV", "flu", "rsv_a", "rsv_b". However, "flu" is not available for TheiaCoV_Illumina_SE	sars-cov-2	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	pangolin_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34	Optional	TheiaCoV_Illumina_SE	docker	True
theiacov_illumina_se	phix	File	File that contains the phix used	/bbmap/resources/phix174_ill.ref.fa.gz	Optional	TheiaCoV_Illumina_SE	general	True
theiacov_illumina_se	primer_bed	File	The bed file containing the primers used when sequencing was performed		Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	reference_gene_locations_bed	File	Use to provide locations of interest where average coverage will be calculated		Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	reference_genome	File	An optional reference genome used for consensus assembly and QC		Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	reference_gff	File	The general feature format (gff) of the reference genome.		Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	seq_method	String	The sequencing methodology used to generate the input read data; for TheiaProk workflows, this input will be used in the "seq_id" column in any taxon-specific tables created in the Export Taxon Tables task	ILLUMINA	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	skip_mash	Boolean	If true, skips estimation of genome size and coverage using mash in read screening steps. As a result, providing true also prevents screening using these parameters.	False	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	skip_screen	Boolean	Set to True to skip the read screening prior to analysis	False	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	trim_min_length	Int	Specifies minimum length of each read after trimming to be kept	25	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	trim_primers	Boolean	A True/False option that determines if primers should be trimmed.	True	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	trim_quality_min_score	Int	Specifies the minimum average quality of bases in a sliding window to be kept	30	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	trim_window_size	Int	Specifies window size for trimming (the number of bases to average the quality across)	4	Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	vadr_max_length	Int	Maximum length of contig allowed to run VADR		Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	vadr_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32 (RSV-A and RSV-B) and 8 (all other TheiaCoV organisms)	Optional	TheiaCoV_Illumina_SE	runtime	True
theiacov_illumina_se	vadr_model_file	File	Path to the a tar + gzipped VADR model file	Defaults are organism-specific. Please find default values for all organisms here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>.	Optional	TheiaCoV_Illumina_SE	general	True
theiacov_illumina_se	vadr_options	String	Additional options to provide to VADR		Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	vadr_skip_length	Int	Minimum assembly length (unambiguous) to run VADR		Optional	TheiaCoV_Illumina_SE	general	
theiacov_illumina_se	variant_min_freq	Float	Minimum frequency for a variant to be reported in ivar outputs	0.6	Optional	TheiaCoV_Illumina_SE	general	
theiacov_ont	genome_length	Int	User-specified expected genome length to be used in genome statistics calculations		Optional	TheiaCoV_ONT	general	
theiacov_ont	irma_min_consensus_support	Int	Minimum consensus support threshold used by IRMA with ONT data.	50	Optional	TheiaCoV_ONT	general	
theiacov_ont	max_genome_length	Int	Maximum genome length able to pass read screening	2673870	Optional	TheiaCoV_ONT	general	
theiacov_ont	max_length	Int	Maximum length for a read based on the SARS-CoV-2 primer scheme	700	Optional	TheiaCoV_ONT	general	
theiacov_ont	min_basepairs	Int	Minimum number of base pairs able to pass read screening	17000	Optional	TheiaCoV_ONT	general	
theiacov_ont	min_coverage	Int	Minimum genome coverage able to pass read screening	10	Optional	TheiaCoV_ONT	general	
theiacov_ont	min_genome_length	Int	Minimum genome length to pass read screening	1700	Optional	TheiaCoV_ONT	general	
theiacov_ont	min_length	Int	Minimum length of a read based on the SARS-CoV-2 primer scheme	400	Optional	TheiaCoV_ONT	general	
theiacov_ont	min_reads	Int	Minimum number of reads to pass read screening	57	Optional	TheiaCoV_ONT	general	
theiacov_ont	nextclade_dataset_name	String	Nextclade organism dataset names. However, if organism input is set correctly, this input will be automatically assigned the corresponding dataset name. See organism defaults for more information	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_ONT	general	True
theiacov_ont	nextclade_dataset_tag	String	Nextclade dataset tag. Used for pulling up-to-date reference genomes and associated information specific to nextclade datasets (QC thresholds, organism-specific information like SARS-CoV-2 clade & lineage information, etc.) that is required for running the Nextclade tool.	Defaults are organism-specific. Please find default values for all organisms (and for Flu - their respective genome segments) here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>	Optional	TheiaCoV_ONT	general	True
theiacov_ont	normalise	Int	Used to normalize the amount of reads to the indicated level before variant calling	200	Optional	TheiaCoV_ONT	general	
theiacov_ont	organism	String	The organism that is being analyzed. Options: "sars-cov-2", "MPXV", "WNV", "HIV", "flu", "rsv_a", "rsv_b". However, "flu" is not available for TheiaCoV_Illumina_SE	sars-cov-2	Optional	TheiaCoV_ONT	general	
theiacov_ont	pangolin_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.34	Optional	TheiaCoV_ONT	docker	True
theiacov_ont	primer_bed	File	The bed file containing the primers used when sequencing was performed		Optional	TheiaCoV_ONT	general	
theiacov_ont	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaCoV_ONT	general	
theiacov_ont	reference_gene_locations_bed	File	Use to provide locations of interest where average coverage will be calculated		Optional	TheiaCoV_ONT	general	
theiacov_ont	reference_genome	File	An optional reference genome used for consensus assembly and QC		Optional	TheiaCoV_ONT	general	
theiacov_ont	seq_method	String	The sequencing methodology used to generate the input read data; for TheiaProk workflows, this input will be used in the "seq_id" column in any taxon-specific tables created in the Export Taxon Tables task	OXFORD_NANOPORE	Optional	TheiaCoV_ONT	general	
theiacov_ont	skip_mash	Boolean	If true, skips estimation of genome size and coverage using mash in read screening steps. As a result, providing true also prevents screening using these parameters.	False	Optional	TheiaCoV_ONT	general	
theiacov_ont	skip_screen	Boolean	Set to True to skip the read screening prior to analysis	False	Optional	TheiaCoV_ONT	general	
theiacov_ont	target_organism	String	The organism whose abundance the user wants to check in their reads. This should be a proper taxonomic name recognized by the Kraken database.		Optional	TheiaCoV_ONT	general	
theiacov_ont	vadr_max_length	Int	Maximum length of contig allowed to run VADR		Optional	TheiaCoV_ONT	general	
theiacov_ont	vadr_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	32 (RSV-A and RSV-B) and 8 (all other TheiaCoV organisms)	Optional	TheiaCoV_ONT	runtime	True
theiacov_ont	vadr_model_file	File	Path to the a tar + gzipped VADR model file	Defaults are organism-specific. Please find default values for all organisms here: <https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_organism_parameters.wdl>.	Optional	TheiaCoV_ONT	general	True
theiacov_ont	vadr_options	String	Additional options to provide to VADR		Optional	TheiaCoV_ONT	general	
theiacov_ont	vadr_skip_length	Int	Minimum assembly length (unambiguous) to run VADR		Optional	TheiaCoV_ONT	general	
theiaeuk_illumina_pe	busco_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.3.2_cv1	Optional	TheiaEuk_Illumina_PE	docker	
theiaeuk_illumina_pe	busco_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	24	Optional	TheiaEuk_Illumina_PE	runtime	
theiaeuk_illumina_pe	call_rasusa	Boolean	If true, RASUSA will subsample raw reads to  a specified read depth (150X by default)	True	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	cpu	Int	Number of CPUs to allocate to the task	8	Optional	TheiaEuk_Illumina_PE	runtime	
theiaeuk_illumina_pe	expected_taxon	String	If provided, this input will override the taxonomic assignment made by GAMBIT and launch the relevant taxon-specific submodules. It will also modify the organism flag used by AMRFinderPlus. Example format: "Salmonella enterica"		Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	gambit_db_genomes	File	User-provided database of assembled query genomes; requires complementary signatures file. If not provided, uses default database, "/gambit-db"	gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-metadata-1.0.0-20241213.gdb	Optional	TheiaEuk_Illumina_PE	database	
theiaeuk_illumina_pe	gambit_db_signatures	File	User-provided signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used.	gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-signatures-1.0.0-20241213.gs	Optional	TheiaEuk_Illumina_PE	database	
theiaeuk_illumina_pe	genome_length	Int	User-specified expected genome length to be used in genome statistics calculations		Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	max_genome_length	Int	Maximum genome size able to pass read screening	178000000	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaEuk_Illumina_PE	runtime	
theiaeuk_illumina_pe	min_basepairs	Int	Minimum number of base pairs able to pass read screening	45000000	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	min_contig_length	Int	Minimum contig length for assembler	1000	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	min_coverage	Int	Minimum genome coverage able to pass read screening	10	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	min_genome_length	Int	Minimum genome size able to pass read screening	9000000	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	min_proportion	Int	Minimum proportion of total reads in each read file to pass read screening	40	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	min_reads	Int	Minimum number of reads to pass read screening	30000	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	seq_method	String	Sequencing method used for the samples	ILLUMINA	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	skip_screen	Boolean	Option to skip the read screening prior to analysis; if setting to true, please provide a value for the theiaeuk_pe genome_length optional input, OR set call_rasusa to false. Otherwise RASUSA will attempt to downsample to an expected genome size of 0 bp, and the workflow will fail.	False	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	subsample_coverage	Float	Read depth for RASUSA task to subsample reads to	150	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	trim_min_length	Int	Specifies minimum length of each read after trimming to be kept	75	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	trim_quality_min_score	Int	Specifies the minimum average quality of bases in a sliding window to be kept	20	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_illumina_pe	trim_window_size	Int	Size of the trimming window to use	10	Optional	TheiaEuk_Illumina_PE	general	
theiaeuk_ont	busco_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ezlabgva/busco:v5.3.2_cv1	Optional	TheiaEuk_ONT	docker	
theiaeuk_ont	busco_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	24	Optional	TheiaEuk_ONT	runtime	
theiaeuk_ont	gambit_db_genomes	File	User-provided database of assembled query genomes; requires complementary signatures file. If not provided, uses default database, "/gambit-db"	gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-metadata-1.0.0-20241213.gdb	Optional	TheiaEuk_ONT	database	
theiaeuk_ont	gambit_db_signatures	File	User-provided signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used.	gs://gambit-databases-rp/fungal-version/1.0.0/gambit-fungal-signatures-1.0.0-20241213.gs	Optional	TheiaEuk_ONT	database	
theiaeuk_ont	genome_length	Int	User-specified expected genome length to be used in genome statistics calculations	50000000	Optional	TheiaEuk_ONT	general	
theiaeuk_ont	max_genome_length	Int	Maximum genome size able to pass read screening	178000000	Optional	TheiaEuk_ONT	general	
theiaeuk_ont	min_basepairs	Int	Minimum number of base pairs able to pass read screening	45000000	Optional	TheiaEuk_ONT	general	
theiaeuk_ont	min_coverage	Int	Minimum genome coverage able to pass read screening	5	Optional	TheiaEuk_ONT	general	
theiaeuk_ont	min_genome_length	Int	Minimum genome size able to pass read screening	9000000	Optional	TheiaEuk_ONT	general	
theiaeuk_ont	min_reads	Int	Minimum number of reads to pass read screening	5000	Optional	TheiaEuk_ONT	general	
theiaeuk_ont	skip_mash	Boolean	If true, skips estimation of genome size and coverage using mash in read screening steps. As a result, providing true also prevents screening using these parameters.	True	Optional	TheiaEuk_ONT	general	
theiaeuk_ont	skip_screen	Boolean	Option to skip the read screening prior to analysis; if setting to true, please provide a value for the theiaeuk_pe genome_length optional input, OR set call_rasusa to false. Otherwise RASUSA will attempt to downsample to an expected genome size of 0 bp, and the workflow will fail.	False	Optional	TheiaEuk_ONT	general	
theiaeuk_ont	workflow_series	String	Internal component, do not modify	theiaeuk	Optional	TheiaEuk_ONT	general	
theiameta_illumina_pe	call_bracken	Boolean	Call Bracken kraken2 report refinement	False	Optional	TheiaMeta_Illumina_PE	general	
theiameta_illumina_pe	kraken2_db	File	A Kraken2 database in .tar.gz format	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_standard_08gb_20230605.tar.gz	Optional	TheiaMeta_Illumina_PE	database	
theiameta_illumina_pe	output_additional_files	Boolean	Output additional files such as aligned and unaligned reads to reference	False	Optional	TheiaMeta_Illumina_PE	general	
theiameta_illumina_pe	reference	File	Reference file for consensus calling, in FASTA format		Optional	TheiaMeta_Illumina_PE	general	
theiaprok_fasta	abricate_db	String	Database to use with the Abricate tool. Options: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB	vfdb	Optional	TheiaProk_FASTA	database	
theiaprok_fasta	amrfinder_use_gff	Boolean	Whether or not to use the GFF and protein FASTA files for AMRFinderPlus	False	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	bakta_db	String	Database selection for Bakta annotation. Options: light (smaller, faster), full (more comprehensive), or a Google Storage URI (gs://...) pointing to a custom Bakta database archive (.tar.gz). The selected database will be extracted before annotation.	full	Optional	TheiaProk_FASTA	database	
theiaprok_fasta	call_abricate	Boolean	Set to true to enable the Abricate task	False	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	call_ani	Boolean	Set to true to enable the ANI task	False	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	call_arln_stats	Boolean	Set to true to enable the return of ARLN required Auto PASS/FAIL outputs	False	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	call_gamma	Boolean	Set to true in order to enable GAMMA task	False	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	call_kmerfinder	Boolean	Set to true to enable the kmerfinder task	False	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	call_plasmidfinder	Boolean	Set to true to enable the plasmidfinder task	True	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	call_resfinder	Boolean	Set to true to enable the ResFinder task	False	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	city	String	Will be used in the "city" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_FASTA	general	
theiaprok_fasta	collection_date	String	Will be used in the "collection_date" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_FASTA	general	
theiaprok_fasta	county	String	Will be used in the "county" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_FASTA	general	
theiaprok_fasta	expected_taxon	String	If provided, this input will override the taxonomic assignment made by GAMBIT and launch the relevant taxon-specific submodules. It will also modify the organism flag used by AMRFinderPlus. Example format: "Salmonella enterica"		Optional	TheiaProk_FASTA	general	
theiaprok_fasta	genome_annotation	String	If set to "bakta", TheiaProk will use Bakta rather than Prokka to annotate the genome	prokka	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	mlst_run_secondary_scheme	Boolean	If true, will run secondary scheme if primary scheme is of ecoli or abaumannii, these two have multiple schemes that are relevant.	False	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	mlst_scheme_override	Boolean	If true, will force E. coli scheme to be used when Gambit predicts Escherichia coli, otherwise will return scheme MLST predicts.	False	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	originating_lab	String	Will be used in the "originating_lab" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_FASTA	general	
theiaprok_fasta	perform_characterization	Boolean	Set to "false" if you want to only generate an assembly and relevant QC metrics and skip all characterization tasks	True	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaProk_FASTA	general	
theiaprok_fasta	run_id	String	Will be used in the "run_id" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_FASTA	general	
theiaprok_fasta	seq_method	String	The sequencing methodology used to generate the input read data; for TheiaProk workflows, this input will be used in the "seq_id" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_FASTA	general	
theiaprok_fasta	taxon_tables	File	File indicating data table names to copy samples of a particular taxon to		Optional	TheiaProk_FASTA	general	
theiaprok_fasta	terra_project	String	The name of the Terra Project where you want the taxon tables written to	NA	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	terra_workspace	String	The name of the Terra Workspace where you want the taxon tables written to	NA	Optional	TheiaProk_FASTA	general	
theiaprok_fasta	zip	String	Will be used in the "zip" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_FASTA	general	
theiaprok_illumina_pe	abricate_db	String	Database to use with the Abricate tool. Options: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB	vfdb	Optional	TheiaProk_Illumina_PE	database	
theiaprok_illumina_pe	amrfinder_use_gff	Boolean	Whether or not to use the GFF and protein FASTA files for AMRFinderPlus	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	bakta_db	String	Database selection for Bakta annotation. Options: light (smaller, faster), full (more comprehensive), or a Google Storage URI (gs://...) pointing to a custom Bakta database archive (.tar.gz). The selected database will be extracted before annotation.	full	Optional	TheiaProk_Illumina_PE	database	
theiaprok_illumina_pe	call_abricate	Boolean	Set to true to enable the Abricate task	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	call_ani	Boolean	Set to true to enable the ANI task	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	call_arln_stats	Boolean	Set to true to enable the return of ARLN required Auto PASS/FAIL outputs	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	call_gamma	Boolean	Set to true in order to enable GAMMA task	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	call_kmerfinder	Boolean	Set to true to enable the kmerfinder task	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	call_plasmidfinder	Boolean	Set to true to enable the plasmidfinder task	True	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	call_resfinder	Boolean	Set to true to enable the ResFinder task	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	city	String	Will be used in the "city" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	collection_date	String	Will be used in the "collection_date" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	county	String	Will be used in the "county" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	expected_taxon	String	If provided, this input will override the taxonomic assignment made by GAMBIT and launch the relevant taxon-specific submodules. It will also modify the organism flag used by AMRFinderPlus. Example format: "Salmonella enterica"		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	genome_annotation	String	If set to "bakta", TheiaProk will use Bakta rather than Prokka to annotate the genome	prokka	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	genome_length	Int	User-specified expected genome length to be used in genome statistics calculations		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	max_genome_length	Int	Maximum genome length able to pass read screening.	18040666	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	min_basepairs	Int	Minimum number of base pairs able to pass read screening	2241820	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	min_coverage	Int	Minimum genome coverage able to pass read screening	10	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	min_genome_length	Int	Minimum genome length able to pass read screening.	100000	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	min_proportion	Int	Minimum proportion of total reads in each read file to pass read screening	40	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	min_reads	Int	Minimum number of reads to pass read screening	7472	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	mlst_run_secondary_scheme	Boolean	If true, will run secondary scheme if primary scheme is of ecoli or abaumannii, these two have multiple schemes that are relevant.	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	mlst_scheme_override	Boolean	If true, will force E. coli scheme to be used when Gambit predicts Escherichia coli, otherwise will return scheme MLST predicts.	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	originating_lab	String	Will be used in the "originating_lab" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	perform_characterization	Boolean	Set to "false" if you want to only generate an assembly and relevant QC metrics and skip all characterization tasks	True	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	read1_lane2	File	If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	read1_lane3	File	If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	read1_lane4	File	If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	read2_lane2	File	If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	read2_lane3	File	If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	read2_lane4	File	If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	run_id	String	Will be used in the "run_id" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	seq_method	String	The sequencing methodology used to generate the input read data; for TheiaProk workflows, this input will be used in the "seq_id" column in any taxon-specific tables created in the Export Taxon Tables task	ILLUMINA	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	skip_screen	Boolean	Set to True to skip the read screening prior to analysis	False	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	taxon_tables	File	File indicating data table names to copy samples of a particular taxon to		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	terra_project	String	The name of the Terra Project where you want the taxon tables written to	NA	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	terra_workspace	String	The name of the Terra Workspace where you want the taxon tables written to	NA	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	trim_min_length	Int	Specifies minimum length of each read after trimming to be kept	75	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	trim_quality_min_score	Int	Specifies the minimum average quality of bases in a sliding window to be kept	20	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	trim_window_size	Int	Specifies window size for trimming (the number of bases to average the quality across)	10	Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_pe	zip	String	Will be used in the "zip" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_PE	general	
theiaprok_illumina_se	abricate_db	String	Database to use with the Abricate tool. Options: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB	vfdb	Optional	TheiaProk_Illumina_SE	database	
theiaprok_illumina_se	amrfinder_use_gff	Boolean	Whether or not to use the GFF and protein FASTA files for AMRFinderPlus	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	bakta_db	String	Database selection for Bakta annotation. Options: light (smaller, faster), full (more comprehensive), or a Google Storage URI (gs://...) pointing to a custom Bakta database archive (.tar.gz). The selected database will be extracted before annotation.	full	Optional	TheiaProk_Illumina_SE	database	
theiaprok_illumina_se	call_abricate	Boolean	Set to true to enable the Abricate task	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	call_ani	Boolean	Set to true to enable the ANI task	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	call_arln_stats	Boolean	Set to true to enable the return of ARLN required Auto PASS/FAIL outputs	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	call_gamma	Boolean	Set to true in order to enable GAMMA task	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	call_kmerfinder	Boolean	Set to true to enable the kmerfinder task	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	call_plasmidfinder	Boolean	Set to true to enable the plasmidfinder task	True	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	call_resfinder	Boolean	Set to true to enable the ResFinder task	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	city	String	Will be used in the "city" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	collection_date	String	Will be used in the "collection_date" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	county	String	Will be used in the "county" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	expected_taxon	String	If provided, this input will override the taxonomic assignment made by GAMBIT and launch the relevant taxon-specific submodules. It will also modify the organism flag used by AMRFinderPlus. Example format: "Salmonella enterica"		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	genome_annotation	String	If set to "bakta", TheiaProk will use Bakta rather than Prokka to annotate the genome	prokka	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	genome_length	Int	User-specified expected genome length to be used in genome statistics calculations		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	max_genome_length	Int	Maximum genome length able to pass read screening.	18040666	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	min_basepairs	Int	Minimum number of base pairs able to pass read screening	2241820	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	min_coverage	Int	Minimum genome coverage able to pass read screening	10	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	min_genome_length	Int	Minimum genome length able to pass read screening.	100000	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	min_reads	Int	Minimum number of reads to pass read screening	7472	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	mlst_run_secondary_scheme	Boolean	If true, will run secondary scheme if primary scheme is of ecoli or abaumannii, these two have multiple schemes that are relevant.	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	mlst_scheme_override	Boolean	If true, will force E. coli scheme to be used when Gambit predicts Escherichia coli, otherwise will return scheme MLST predicts.	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	originating_lab	String	Will be used in the "originating_lab" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	perform_characterization	Boolean	Set to "false" if you want to only generate an assembly and relevant QC metrics and skip all characterization tasks	True	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	read1_lane2	File	If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	read1_lane3	File	If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	read1_lane4	File	If provided, the Concatenate_Illumina_Lanes subworkflow will concatenate all files from the same lane before doing any subsequent analysis		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	run_id	String	Will be used in the "run_id" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	seq_method	String	The sequencing methodology used to generate the input read data; for TheiaProk workflows, this input will be used in the "seq_id" column in any taxon-specific tables created in the Export Taxon Tables task	ILLUMINA	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	skip_mash	Boolean	If true, skips estimation of genome size and coverage using mash in read screening steps. As a result, providing true also prevents screening using these parameters.	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	skip_screen	Boolean	Set to True to skip the read screening prior to analysis	False	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	taxon_tables	File	File indicating data table names to copy samples of a particular taxon to		Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	terra_project	String	The name of the Terra Project where you want the taxon tables written to	NA	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	terra_workspace	String	The name of the Terra Workspace where you want the taxon tables written to	NA	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	trim_min_length	Int	Specifies minimum length of each read after trimming to be kept	25	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	trim_quality_min_score	Int	Specifies the average quality of bases in a sliding window to be kept	30	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	trim_window_size	Int	Specifies window size for trimming (the number of bases to average the quality across)	4	Optional	TheiaProk_Illumina_SE	general	
theiaprok_illumina_se	zip	String	Will be used in the "zip" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_Illumina_SE	general	
theiaprok_ont	abricate_db	String	Database to use with the Abricate tool. Options: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB	vfdb	Optional	TheiaProk_ONT	database	
theiaprok_ont	amrfinder_use_gff	Boolean	Whether or not to use the GFF and protein FASTA files for AMRFinderPlus	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	bakta_db	String	Database selection for Bakta annotation. Options: light (smaller, faster), full (more comprehensive), or a Google Storage URI (gs://...) pointing to a custom Bakta database archive (.tar.gz). The selected database will be extracted before annotation.	full	Optional	TheiaProk_ONT	database	
theiaprok_ont	call_abricate	Boolean	Set to true to enable the Abricate task	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	call_ani	Boolean	Set to true to enable the ANI task	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	call_arln_stats	Boolean	Set to true to enable the return of ARLN required Auto PASS/FAIL outputs	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	call_gamma	Boolean	Set to true in order to enable GAMMA task	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	call_kmerfinder	Boolean	Set to true to enable the kmerfinder task	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	call_plasmidfinder	Boolean	Set to true to enable the plasmidfinder task	True	Optional	TheiaProk_ONT	general	
theiaprok_ont	call_resfinder	Boolean	Set to true to enable the ResFinder task	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	city	String	Will be used in the "city" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_ONT	general	
theiaprok_ont	collection_date	String	Will be used in the "collection_date" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_ONT	general	
theiaprok_ont	county	String	Will be used in the "county" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_ONT	general	
theiaprok_ont	expected_taxon	String	If provided, this input will override the taxonomic assignment made by GAMBIT and launch the relevant taxon-specific submodules. It will also modify the organism flag used by AMRFinderPlus. Example format: "Salmonella enterica"		Optional	TheiaProk_ONT	general	
theiaprok_ont	genome_annotation	String	If set to "bakta", TheiaProk will use Bakta rather than Prokka to annotate the genome	prokka	Optional	TheiaProk_ONT	general	
theiaprok_ont	genome_length	Int	User-specified expected genome length to be used in genome statistics calculations	5000000	Optional	TheiaProk_ONT	general	
theiaprok_ont	max_genome_length	Int	Maximum genome length able to pass read screening. For TheiaProk_ONT, screening using max_genome_length is skipped by default.	18040666	Optional	TheiaProk_ONT	general	
theiaprok_ont	min_basepairs	Int	Minimum number of base pairs able to pass read screening	2241820	Optional	TheiaProk_ONT	general	
theiaprok_ont	min_coverage	Int	Minimum genome coverage able to pass read screening. Screening using min_coverage is skipped by default.	5	Optional	TheiaProk_ONT	general	
theiaprok_ont	min_genome_length	Int	Minimum genome length able to pass read screening. For TheiaProk_ONT, screening using min_genome_length is skipped by default.	100000	Optional	TheiaProk_ONT	general	
theiaprok_ont	min_reads	Int	Minimum number of reads to pass read screening	5000	Optional	TheiaProk_ONT	general	
theiaprok_ont	mlst_run_secondary_scheme	Boolean	If true, will run secondary scheme if primary scheme is of ecoli or abaumannii, these two have multiple schemes that are relevant.	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	mlst_scheme_override	Boolean	If true, will force E. coli scheme to be used when Gambit predicts Escherichia coli, otherwise will return scheme MLST predicts.	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	originating_lab	String	Will be used in the "originating_lab" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_ONT	general	
theiaprok_ont	perform_characterization	Boolean	Set to "false" if you want to only generate an assembly and relevant QC metrics and skip all characterization tasks	True	Optional	TheiaProk_ONT	general	
theiaprok_ont	qc_check_table	File	TSV value with taxons for rows and QC values for columns; internal cells represent user-determined QC thresholds; if provided, turns on the QC Check task. See below for an example QC Check table.		Optional	TheiaProk_ONT	general	
theiaprok_ont	run_id	String	Will be used in the "run_id" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_ONT	general	
theiaprok_ont	seq_method	String	The sequencing methodology used to generate the input read data; for TheiaProk workflows, this input will be used in the "seq_id" column in any taxon-specific tables created in the Export Taxon Tables task	ONT	Optional	TheiaProk_ONT	general	
theiaprok_ont	skip_mash	Boolean	If true, skips estimation of genome size and coverage using mash in read screening steps. As a result, providing true also prevents screening using these parameters.	True	Optional	TheiaProk_ONT	general	
theiaprok_ont	skip_screen	Boolean	Set to True to skip the read screening prior to analysis	False	Optional	TheiaProk_ONT	general	
theiaprok_ont	taxon_tables	File	File indicating data table names to copy samples of a particular taxon to		Optional	TheiaProk_ONT	general	
theiaprok_ont	terra_project	String	The name of the Terra Project where you want the taxon tables written to	NA	Optional	TheiaProk_ONT	general	
theiaprok_ont	terra_workspace	String	The name of the Terra Workspace where you want the taxon tables written to	NA	Optional	TheiaProk_ONT	general	
theiaprok_ont	zip	String	Will be used in the "zip" column in any taxon-specific tables created in the Export Taxon Tables task		Optional	TheiaProk_ONT	general	
theiavalidate	column_translation_tsv	File	If the user wants to link two columns of different names, they may supply a TSV file that provides a "column translation" between the two files (see the section below this table).		Optional	TheiaValidate	general	
theiavalidate	terra_project2_name	String	If the table2_name is located in a different Terra project, indicate it here. Otherwise, the workflow will look for table2_name in the Terra project indicated in terra_project1_name.	value for terra_project1_name	Optional	TheiaValidate	general	True
theiavalidate	terra_workspace2_name	String	If the table2_name is located in a different Terra workspace, indicate it here. Otherwise, the workflow will look for table2_name in the Terra workspace indicated in terra_workspace1_name.	value for terra_workspace1_name	Optional	TheiaValidate	general	True
theiavalidate	validation_criteria_tsv	File	If the user wants to specify a different comparison than the default exact string match, they may supply a TSV file that indicates the different options (see the section below this table).		Optional	TheiaValidate	general	
theiaviral_illumina_pe	call_metaviralspades	Boolean	True/False to call assembly with MetaviralSPAdes and use Megahit as fallback	True	Optional	TheiaViral_Illumina_PE	general	
theiaviral_illumina_pe	checkv_db	File	Database used for CheckV	gs://theiagen-public-resources-rp/reference_data/databases/checkv/checkv-db-v1.5.tar.gz	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	database	
theiaviral_illumina_pe	extract_unclassified	Boolean	True/False that determines if unclassified reads should be extracted and combined with the taxon specific extracted reads	True	Optional	TheiaViral_Illumina_PE	general	
theiaviral_illumina_pe	extract_unclassified	Boolean	Internal component, do not modify	True	Optional	TheiaViral_Panel	general	
theiaviral_illumina_pe	genome_length	Int	Expected genome length of taxon of interest		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
theiaviral_illumina_pe	host	String	Host taxon/accession to dehost reads, if provided		Optional	TheiaViral_Illumina_PE	general	
theiaviral_illumina_pe	host	String	Internal component, do not modify		Optional	TheiaViral_Panel	general	
theiaviral_illumina_pe	kraken2_db	File	Kraken2 database file	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz	Optional	TheiaViral_Illumina_PE	database	
theiaviral_illumina_pe	min_allele_freq	Float	Minimum allele frequency required for a variant to populate the consensus sequence	0.6	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
theiaviral_illumina_pe	min_depth	Int	Minimum read depth required for a variant to populate the consensus sequence	10	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
theiaviral_illumina_pe	min_map_quality	Int	Minimum mapping quality required for read alignments	20	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
theiaviral_illumina_pe	read_extraction_rank	String	Taxonomic rank to use for read extraction - limits taxons to only those within the specified ranks.	family	Optional	TheiaViral_Illumina_PE	general	
theiaviral_illumina_pe	read_extraction_rank	String	Internal component, do not modify	family	Optional	TheiaViral_Panel	general	
theiaviral_illumina_pe	reference_fasta	File	Reference genome in FASTA format		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
theiaviral_illumina_pe	reference_gene_locations_bed	File	Use to provide locations of interest where average coverage will be calculated		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
theiaviral_illumina_pe	skani_db	File	Skani database file	gs://theiagen-public-resources-rp/reference_data/databases/skani/skani_db_20251107.tar	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	database	
theiaviral_illumina_pe	skip_qc	Boolean	Internal component, do not modify	False	Optional	TheiaViral_Illumina_PE	general	
theiaviral_illumina_pe	skip_rasusa	Boolean	True/False to skip read subsampling with Rasusa	True	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
theiaviral_illumina_pe	skip_screen	Boolean	True/False to skip read screening check prior to analysis	False	Optional	TheiaViral_Illumina_PE	general	
theiaviral_ont	call_porechop	Boolean	True/False to trim adapters with porechop	False	Optional	TheiaViral_ONT	general	
theiaviral_ont	call_raven	Boolean	True/False to call assembly with Raven and use Flye as fallback	True	Optional	TheiaViral_ONT	general	
theiaviral_ont	extract_unclassified	Boolean	True/False that determines if unclassified reads should be extracted and combined with the taxon specific extracted reads	True	Optional	TheiaViral_ONT	general	
theiaviral_ont	genome_length	Int	Expected genome length of taxon of interest		Optional	TheiaViral_ONT	general	
theiaviral_ont	host	String	Host taxon/accession to dehost reads, if provided		Optional	TheiaViral_ONT	general	
theiaviral_ont	min_allele_freq	Float	Minimum allele frequency required for a variant to populate the consensus sequence	0.6	Optional	TheiaViral_ONT	general	
theiaviral_ont	min_depth	Int	Minimum read depth required for a variant to populate the consensus sequence	10	Optional	TheiaViral_ONT	general	
theiaviral_ont	min_map_quality	Int	Minimum mapping quality required for read alignments	20	Optional	TheiaViral_ONT	general	
theiaviral_ont	read_extraction_rank	String	Taxonomic rank to use for read extraction - limits taxons to only those within the specified ranks.	family	Optional	TheiaViral_ONT	general	
theiaviral_ont	reference_fasta	File	Reference genome in FASTA format		Optional	TheiaViral_ONT	general	
theiaviral_ont	reference_gene_locations_bed	File	Use to provide locations of interest where average coverage will be calculated		Optional	TheiaViral_ONT	general	
theiaviral_ont	skip_rasusa	Boolean	True/False to skip read subsampling with Rasusa	True	Optional	TheiaViral_ONT	general	
theiaviral_ont	skip_screen	Boolean	True/False to skip read screening check prior to analysis	False	Optional	TheiaViral_ONT	general	
theiaviral_panel	call_metaviralspades	Boolean	Whether to run metaviralspades for assembly	True	Optional	TheiaViral_Panel	general	
theiaviral_panel	extract_unclassified	Boolean	True/False that determines if unclassified reads should be extracted and combined with the taxon specific extracted reads	False	Optional	TheiaViral_Panel	general	
theiaviral_panel	host	String	Host taxon/accession to dehost reads, if provided		Optional	TheiaViral_Panel	general	
theiaviral_panel	kraken2_db	File	Kraken2 database file in .tar.gz format.	gs://theiagen-public-resources-rp/reference_data/databases/kraken2/k2_viral-refseq_human-GRCh38_20260220.tar.gz	Optional	TheiaViral_Panel	database	
theiaviral_panel	min_read_count	Int	Minimum number of reads required to consider a taxon for assembly	1000	Optional	TheiaViral_Panel	general	
theiaviral_panel	output_taxon_table	File	A TSV file containing organism names and their corresponding output table names.	gs://theiagen-public-resources-rp/reference_data/family_agnostic/theiaviral_panel_taxon_table_20251111.tsv	Optional	TheiaViral_Panel	general	
theiaviral_panel	taxon_ids	Array[String]	An array of taxon IDs user wishes to analyze.	["1618189", "37124", "46839", "12637", "1216928", "59301", "2169701", "118655", "11587", "11029", "11033", "11034", "1608084", "64286", "11082", "11089", "64320", "10804", "12092", "3052230", "12475", "11676", "11709", "68887", "1980456", "3052470", "3052490", "169173", "3052489", "238817", "1980442", "3052496", "3052499", "90961", "80935", "35305", "1221391", "38767", "11021", "38768", "2847089", "3052223", "260964", "35511", "11072", "11577", "38766", "1474807", "12538", "11079", "3052225", "11083", "11292", "11580", "11080", "45270", "11084", "11036", "11039", "1313215", "138948", "138949", "138950", "138951", "1239565", "1239570", "1239573", "142786", "28875", "28876", "36427", "1348384", "1330524", "95341", "2849717", "1424613", "2010960", "565995", "3052302", "3052518", "3052477", "3052307", "3052480", "2169991", "33743", "3052310", "3052148", "3052314", "3052303", "3052317", "33727", "12542", "3052493", "186539", "11588", "2907957", "3052498", "1003835", "1452514", "186540", "186541", "3052503", "1891762", "10376", "10359", "333760", "333761", "337044", "337050", "1671798", "333754", "333767", "746830", "746831", "943908", "10632", "1891764", "1965344", "493803", "1203539", "1497391", "1891767", "1277649", "862909", "862909", "440266", "11234", "152219", "10244", "2560602", "11041", "10335", "10255", "129875", "108098", "129951", "130310", "130308", "130309", "536079", "329641", "11137", "290028", "277944", "31631", "162145", "12730", "2560525", "11216", "2560526", "1803956", "10798", "11250", "11320", "11520", "11552", "1335626", "147711", "147712", "463676", "2901879", "2697049", "10404", "3052505", "337041", "337042", "333757", "337048", "333754", "333766", "337049"]	Optional	TheiaViral_Panel	general	
transfer_files	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Transfer_Column_Content	runtime	
transfer_files	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Transfer_Column_Content	runtime	
transfer_files	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/cloudsdktool/google-cloud-cli:427.0.0-alpine	Optional	Transfer_Column_Content	docker	
transfer_files	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Transfer_Column_Content	runtime	
trim_genbank_fastas	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Mercury_Prep_N_Batch	runtime	
trim_genbank_fastas	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Mercury_Prep_N_Batch	runtime	
trim_genbank_fastas	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/vadr:1.3	Optional	Mercury_Prep_N_Batch	docker	
trim_genbank_fastas	max_length	Int	Only for "sars-cov-2" submissions; the maximum genome length for trimming terminal ambiguous nucleotides. If your sample's genome is higher than this value, the workflow will error/fail.	30000	Optional	Mercury_Prep_N_Batch	general	
trim_genbank_fastas	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Mercury_Prep_N_Batch	runtime	
trim_genbank_fastas	min_length	Int	Only for "sars-cov-2" submissions; the minimum genome length for trimming terminal ambiguous nucleotides. If your sample's genome is lower than this value, the workflow will error/fail.	50	Optional	Mercury_Prep_N_Batch	general	
trimmomatic	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TBProfiler_tNGS	runtime	
trimmomatic	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TBProfiler_tNGS	runtime	
trimmomatic	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/trimmomatic:0.40	Optional	TBProfiler_tNGS	docker	
trimmomatic	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TBProfiler_tNGS	runtime	
trimmomatic	trimmomatic_adapter_fasta	File	A FASTA file containing adapter sequences	TruSeq3-PE-2.fa	Optional	TBProfiler_tNGS	general	True
trimmomatic	trimmomatic_adapter_trim_args	String	Colon-delimited adapter trimming parameters representing [seed mismatches: palindrome clip threshold: simple clip threshold]	2:30:10	Optional	TBProfiler_tNGS	general	True
trimmomatic	trimmomatic_min_length	Int	Specifies minimum length of each read after trimming to be kept	75	Optional	TBProfiler_tNGS	general	
trimmomatic	trimmomatic_override_args	String	Additional arguments to pass to trimmomatic. Can be used to override all trimming parameters		Optional	TBProfiler_tNGS	general	
trimmomatic	trimmomatic_trim_adapters	Boolean	A True/False option that determines if adapters should be trimmed	False	Optional	TBProfiler_tNGS	general	
trimmomatic	trimmomatic_window_quality	Int	The trimming window quality score	30	Optional	TBProfiler_tNGS	general	
trimmomatic	trimmomatic_window_size	Int	The window size for trimming	4	Optional	TBProfiler_tNGS	general	
ts_mlst	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
ts_mlst	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
ts_mlst	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mlst:2.23.0-2024-12-31	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
ts_mlst	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
ts_mlst	min_percent_coverage	Float	Minimum % breadth of coverage to report an MLST allele	10	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
ts_mlst	min_percent_identity	Float	Minimum % identity to known MLST gene to report an MLST allele	95	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
ts_mlst	minscore	Float	Minimum score <https://github.com/tseemann/mlst#scoring-system> to assign an MLST profile	50	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
ts_mlst	nopath	Boolean	true = use mlst --nopath. If set to false, filename paths are not stripped from FILE column in output TSV	True	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
ts_mlst	scheme	String	Don’t autodetect the MLST scheme; force this scheme on all inputs (see <https://github.com/tseemann/mlst/blob/master/db/scheme_species_map.tab> for accepted strings)	none	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	True
tsv_join	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Augur	runtime	
tsv_join	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Augur	runtime	
tsv_join	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/broadinstitute/viral-core:2.1.33	Optional	Augur	docker	
tsv_join	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	7	Optional	Augur	runtime	
tsv_join	out_suffix	String	Suffix of merged tsv files	.tsv	Optional	Augur	general	
usher	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Usher	runtime	
usher	disk_size	Int	Amount of storage (in GB) to allocate to the task	200	Optional	Usher	runtime	
usher	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/pathogengenomics/usher:0.6.2	Optional	Usher	docker	
usher	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Usher	runtime	
usher	mutation_annotated_tree_pb	File	Required for organisms other than sars-cov-2, mpox, RSV-A or RSV-B. This is the mutation-annotated global phylogeny upon which your samples will be placed		Optional, Required	Usher	general	True
usher	reference_genome	File	Required for organisms other than sars-cov-2, mpox, RSV-A or RSV-B. This is the reference genome used to determine your sequence's mutations to accurately place the sample on the phylogeny.		Optional, Required	Usher	general	True
usher	subtree_size	Int	Indicates how many of the closest-related samples you want to show in a subtree; more subtrees are made if there is more sequence diversity in the set of input samples (multiple subtrees are only generated if this workflow is run on the set level).	20	Optional	Usher	general	
vadr	cpu	Int	Number of CPUs to allocate to the task	4	Optional	VADR_Update	runtime	
vadr	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	VADR_Update	runtime	
vadr	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/vadr:1.6.4	Optional	VADR_Update	docker	
vadr	min_length	Int	Minimum length subsequence to possibly replace Ns for the fasta-trim-terminal-ambigs.pl VADR script	50	Optional	VADR_Update	general	
vadr_update	organism	String	Target organism for VADR	sars-cov-2	Optional	VADR_Update	general	
vadr_update	vadr_max_length	Int	Maximum length for the fasta-trim-terminal-ambigs.pl VADR script	30000	Optional	VADR_Update	general	True
vadr_update	vadr_memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	VADR_Update	runtime	True
vadr_update	vadr_model_file	File	Path to the a tar + gzipped VADR model file	gs://theiagen-public-resources-rp/reference_data/databases/vadr_models/vadr-models-sarscov2-1.3-2.tar.gz	Optional	VADR_Update	database	True
vadr_update	vadr_opts	String	Options for the v-annotate.pl VADR script	--noseqnamemax --glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn --out_allfasta	Optional	VADR_Update	general	True
vadr_update	vadr_skip_length	Int	Minimum assembly length (unambiguous) to run VADR	10000	Optional	VADR_Update	general	True
version_capture	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0	Optional	AMRFinderPlus, AMR_Search, Assembly_Fetch, Augur, Augur_Prep, BaseSpace_Fetch, CZGenEpi_Prep, Cauris_CladeTyper, Clair3_Variants_ONT, Concatenate_Column_Content, Concatenate_Illumina_Lanes, Core_Gene_SNP, Dorado_Basecalling, Fetch_SRR_Accession, Find_Shared_Variants, Freyja_Dashboard, Freyja_FASTQ, Freyja_Plot, Gambit_Query, Kraken_PE, Kraken_SE, Lyve_SET, MashTree_FASTA, Mercury_Prep_N_Batch, Metabuli, NCBI_Scrub_PE, NCBI_Scrub_SE, Nextclade_Batch, Pangolin_Update, PhyloCompare, RASUSA, Rename_FASTQ, SRA_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree, Snippy_Variants, TBProfiler_tNGS, Terra_2_ENA, Terra_2_GISAID, Terra_2_NCBI, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaValidate, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel, Transfer_Column_Content, Usher, VADR_Update, Zip_Column_Content, kSNP3, kSNP4	docker	
version_capture	timezone	String	Set the time zone to get an accurate date of analysis (uses UTC by default)		Optional	AMRFinderPlus, AMR_Search, Assembly_Fetch, Augur, Augur_Prep, BaseSpace_Fetch, CZGenEpi_Prep, Cauris_CladeTyper, Clair3_Variants_ONT, Concatenate_Column_Content, Concatenate_Illumina_Lanes, Core_Gene_SNP, Dorado_Basecalling, Fetch_SRR_Accession, Find_Shared_Variants, Freyja_Dashboard, Freyja_FASTQ, Freyja_Plot, Gambit_Query, Kraken_PE, Kraken_SE, Lyve_SET, MashTree_FASTA, Mercury_Prep_N_Batch, Metabuli, NCBI_Scrub_PE, NCBI_Scrub_SE, Nextclade_Batch, Pangolin_Update, PhyloCompare, RASUSA, Rename_FASTQ, SRA_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree, Snippy_Variants, TBProfiler_tNGS, Terra_2_ENA, Terra_2_GISAID, Terra_2_NCBI, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaValidate, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel, Transfer_Column_Content, Usher, VADR_Update, Zip_Column_Content, kSNP3, kSNP4	general	
wf_microreact_export	access_token	String	Users token used to upload projects to their Microreact account		Optional	Microreact_Export	general	
wf_microreact_export	date_column	String	Column within the input Terra table to be used as the date designation		Optional	Microreact_Export	general	
wf_microreact_export	download_table	Boolean	When true, will download th specified Terra table	True	Optional	Microreact_Export	general	
wf_microreact_export	matrix_files	Array[File]	A list of matrix files a user would like to upload to the Microreact project. Can be written as [this.matrix1, this.matrix2, etc].		Optional	Microreact_Export	general	
wf_microreact_export	metadata_columns	Array[String]	A list of column names from the input Terra table that the user would like to be included in their Microreact metadata table		Optional	Microreact_Export	general	
wf_microreact_export	metadata_file	File	To be used if a separate metadata TSV is required other than downloading a Terra table		Optional	Microreact_Export	general	
wf_microreact_export	project_url	String	URL used to update a microreact project. Can be found as the code within the webpage URL. "microreact.org/project/<project_url>-<title>""		Optional	Microreact_Export	general	
wf_microreact_export	remove_file_columns	Boolean	When true, this will remove all columns that contain file opjects to prevent the pushing of Google cloud addresses to the metadata table	True	Optional	Microreact_Export	general	
wf_microreact_export	restricted_access	Boolean	Sets the access level of the project to restricted when true. Only those specifically added will be able to access.	True	Optional	Microreact_Export	general	
wf_microreact_export	tree_files	Array[File]	A list of tree files a user would like to upload to the Microreact project. Can be written as [this.tree1, this.tree2, etc].		Optional	Microreact_Export	general	
wg_reorder_matrix	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Snippy_Tree	runtime	
wg_reorder_matrix	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Tree	runtime	
wg_reorder_matrix	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1	Optional	Snippy_Tree	docker	
wg_reorder_matrix	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	Snippy_Tree	runtime	
wg_reorder_matrix	outgroup_root	String	Tip name to root phylogenetic tree upon (overrides midpoint root)		Optional	Snippy_Tree	general	
zip_files	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Zip_Column_Content	runtime	
zip_files	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Zip_Column_Content	runtime	
zip_files	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	Zip_Column_Content	docker	
zip_files	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	Zip_Column_Content	runtime