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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_ont_wf kraken2_db File A Kraken2 database in .tar.gz format Required Kraken_ONT general
kraken2_ont_wf read1 File Forward read in FASTQ file format (compression optional) Required Kraken_ONT general
kraken2_ont_wf samplename String The name of the sample being analyzed Required Kraken_ONT 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
cg_snp_dists cpu Int Number of CPUs to allocate to the task 1 Optional Snippy_Tree runtime
cg_snp_dists disk_size Int Amount of storage (in GB) to allocate to the task 50 Optional Snippy_Tree runtime
cg_snp_dists memory Int Amount of memory/RAM (in GB) to allocate to the task 2 Optional Snippy_Tree runtime
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 2 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