update tables

docs/assets/tables/all_inputs.tsv

@@ -94,6 +94,8 @@ mercury_prep_n_batch	sample_names	Array[String]	The samples you want to submit
 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	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	
@@ -732,14 +734,16 @@ fasta_utilities	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaV
 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	TheiaViral_Illumina_PE, TheiaViral_Panel	runtime	
-fastp	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	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:0.23.2	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	docker	
-fastp	fastp_args	String	Additional arguments to use with fastp		Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
-fastp	fastp_min_length	Int	Minimum read length	15	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
-fastp	fastp_quality_trim_score	Int	Minimum mean base quality relative to window size	20	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
-fastp	fastp_window_size	Int	Sliding window size for surveying read quality	4	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	general	
-fastp	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	TheiaViral_Illumina_PE, TheiaViral_Panel	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	
 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	
@@ -1589,15 +1593,21 @@ merlin_magic	virulencefinder_min_percent_coverage	Float	Internal component, do n
 merlin_magic	virulencefinder_min_percent_coverage	Float	The threshold for minimum coverage		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
 merlin_magic	virulencefinder_min_percent_identity	Float	Internal component, do not modify		Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
 merlin_magic	virulencefinder_min_percent_identity	Float	The threshold for minimum blast identity		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
-metabuli	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_ONT	runtime	
-metabuli	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
-metabuli	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/metabuli:1.1.0	Optional	TheiaViral_ONT	docker	
-metabuli	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaViral_ONT	runtime	
-metabuli	metabuli_db	File	Metabuli database file	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/refseq_virus-v223.tar.gz	Optional	TheiaViral_ONT	database	
-metabuli	min_percent_coverage	Float	Minimum query coverage threshold (0.0 - 1.0)	0	Optional	TheiaViral_ONT	general	
-metabuli	min_score	Float	Minimum sequenece similarity score (0.0 - 1.0)	0	Optional	TheiaViral_ONT	general	
-metabuli	min_sp_score	Float	Minimum score for species- or lower-level classification	0	Optional	TheiaViral_ONT	general	
-metabuli	taxonomy_path	File	Path to taxonomy file	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/new_taxdump.tar.gz	Optional	TheiaViral_ONT	general	
+metabuli	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Metabuli, TheiaViral_ONT	runtime	
+metabuli	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Metabuli, TheiaViral_ONT	runtime	
+metabuli	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/metabuli:1.1.1	Optional	Metabuli, TheiaViral_ONT	docker	
+metabuli	extract_unclassified	Boolean	True/False that determines if unclassified reads should be extracted and combined with the taxon specific extracted reads	False	Optional	Metabuli	general	
+metabuli	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Metabuli, TheiaViral_ONT	runtime	
+metabuli	metabuli_db	File	Metabuli database file	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/refseq_virus-v223.tar.gz	Optional	Metabuli, TheiaViral_ONT	database	
+metabuli	min_percent_coverage	Float	Minimum query coverage threshold (0.0 - 1.0)	0	Optional	Metabuli, TheiaViral_ONT	general	
+metabuli	min_score	Float	Minimum sequenece similarity score (0.0 - 1.0)	0	Optional	Metabuli, TheiaViral_ONT	general	
+metabuli	min_sp_score	Float	Minimum score for species- or lower-level classification	0	Optional	Metabuli, TheiaViral_ONT	general	
+metabuli	read2	File	Internal component, do not modify		Optional	TheiaViral_ONT	general	
+metabuli	taxdump_path	File	Path to compressed taxonomy dump	gs://theiagen-public-resources-rp/reference_data/databases/metabuli/ncbi_taxdump_20260211.tar.gz	Optional	Metabuli, TheiaViral_ONT	general	
+metabuli	taxon_id	String	NCBI taxon ID to enable read extraction, including descendant reads 		Optional	Metabuli	general	
+metabuli_wf	call_trim	Boolean	Call adapter and read trimming via Fastp (Illumina) or Porechop (ONT)	True	Optional	Metabuli	general	
+metabuli_wf	illumina	Boolean	Input reads are Illumina - automatically inferred if read2 is populated, ONT is assumed otherwise		Optional	Metabuli	general	
+metabuli_wf	read2	File	FASTQ file containing read2 sequences		Optional	Metabuli	general	
 metaspades_pe	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaMeta_Illumina_PE	runtime	
 metaspades_pe	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaMeta_Illumina_PE	runtime	
 metaspades_pe	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/spades:3.12.0--h9ee0642_3	Optional	TheiaMeta_Illumina_PE	docker	
@@ -1868,11 +1878,11 @@ plasmidfinder	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8
 plasmidfinder	method_path	String	Path to files for a user-specified method to use (blast or kma)		Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
 plasmidfinder	min_percent_coverage	Float	Threshold for minimum coverage, default threshold from PlasmidFinder CLI tool is used (0.60)	0.6	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
 plasmidfinder	min_percent_identity	Float	Threshold for mininum blast identity, default threshold from PlasmidFinder CLI tool is used (0.90). This default differs from the default of the PlasmidFinder webtool (0.95)	0.9	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
-porechop	cpu	Int	Number of CPUs to allocate to the task	4	Optional	TheiaViral_ONT	runtime	
-porechop	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	TheiaViral_ONT	runtime	
-porechop	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/porechop:0.2.4	Optional	TheiaViral_ONT	docker	
-porechop	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	TheiaViral_ONT	runtime	
-porechop	trimopts	String	Additional trimming options for Porechop		Optional	TheiaViral_ONT	general	
+porechop	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Metabuli, TheiaViral_ONT	runtime	
+porechop	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Metabuli, TheiaViral_ONT	runtime	
+porechop	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/porechop:0.2.4	Optional	Metabuli, TheiaViral_ONT	docker	
+porechop	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Metabuli, TheiaViral_ONT	runtime	
+porechop	trimopts	String	Additional trimming options for Porechop		Optional	Metabuli, TheiaViral_ONT	general	
 prep_augur_metadata	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Augur_Prep	runtime	
 prep_augur_metadata	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	Augur_Prep	runtime	
 prep_augur_metadata	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional	Augur_Prep	docker	
@@ -2741,8 +2751,8 @@ vadr_update	vadr_memory	Int	Amount of memory/RAM (in GB) to allocate to the task
 vadr_update	vadr_model_file	File	Path to the a tar + gzipped VADR model file	gs://theiagen-public-resources-rp/reference_data/databases/vadr_models/vadr-models-sarscov2-1.3-2.tar.gz	Optional	VADR_Update	database	True
 vadr_update	vadr_opts	String	Options for the v-annotate.pl VADR script	--noseqnamemax --glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn --out_allfasta	Optional	VADR_Update	general	True
 vadr_update	vadr_skip_length	Int	Minimum assembly length (unambiguous) to run VADR	10000	Optional	VADR_Update	general	True
-version_capture	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0	Optional	AMRFinderPlus, AMR_Search, Assembly_Fetch, Augur, Augur_Prep, BaseSpace_Fetch, CZGenEpi_Prep, Cauris_CladeTyper, Clair3_Variants_ONT, Concatenate_Column_Content, Concatenate_Illumina_Lanes, Core_Gene_SNP, Dorado_Basecalling, Fetch_SRR_Accession, Find_Shared_Variants, Freyja_Dashboard, Freyja_FASTQ, Freyja_Plot, Gambit_Query, Kraken_ONT, Kraken_PE, Kraken_SE, Lyve_SET, MashTree_FASTA, Mercury_Prep_N_Batch, NCBI_Scrub_PE, NCBI_Scrub_SE, Nextclade_Batch, Pangolin_Update, PhyloCompare, RASUSA, Rename_FASTQ, SRA_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree, Snippy_Variants, TBProfiler_tNGS, Terra_2_ENA, Terra_2_GISAID, Terra_2_NCBI, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaValidate, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel, Transfer_Column_Content, Usher, VADR_Update, Zip_Column_Content, kSNP3, kSNP4	docker	
-version_capture	timezone	String	Set the time zone to get an accurate date of analysis (uses UTC by default)		Optional	AMRFinderPlus, AMR_Search, Assembly_Fetch, Augur, Augur_Prep, BaseSpace_Fetch, CZGenEpi_Prep, Cauris_CladeTyper, Clair3_Variants_ONT, Concatenate_Column_Content, Concatenate_Illumina_Lanes, Core_Gene_SNP, Dorado_Basecalling, Fetch_SRR_Accession, Find_Shared_Variants, Freyja_Dashboard, Freyja_FASTQ, Freyja_Plot, Gambit_Query, Kraken_ONT, Kraken_PE, Kraken_SE, Lyve_SET, MashTree_FASTA, Mercury_Prep_N_Batch, NCBI_Scrub_PE, NCBI_Scrub_SE, Nextclade_Batch, Pangolin_Update, PhyloCompare, RASUSA, Rename_FASTQ, SRA_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree, Snippy_Variants, TBProfiler_tNGS, Terra_2_ENA, Terra_2_GISAID, Terra_2_NCBI, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaValidate, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel, Transfer_Column_Content, Usher, VADR_Update, Zip_Column_Content, kSNP3, kSNP4	general	
+version_capture	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0	Optional	AMRFinderPlus, AMR_Search, Assembly_Fetch, Augur, Augur_Prep, BaseSpace_Fetch, CZGenEpi_Prep, Cauris_CladeTyper, Clair3_Variants_ONT, Concatenate_Column_Content, Concatenate_Illumina_Lanes, Core_Gene_SNP, Dorado_Basecalling, Fetch_SRR_Accession, Find_Shared_Variants, Freyja_Dashboard, Freyja_FASTQ, Freyja_Plot, Gambit_Query, Kraken_ONT, Kraken_PE, Kraken_SE, Lyve_SET, MashTree_FASTA, Mercury_Prep_N_Batch, Metabuli, NCBI_Scrub_PE, NCBI_Scrub_SE, Nextclade_Batch, Pangolin_Update, PhyloCompare, RASUSA, Rename_FASTQ, SRA_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree, Snippy_Variants, TBProfiler_tNGS, Terra_2_ENA, Terra_2_GISAID, Terra_2_NCBI, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaValidate, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel, Transfer_Column_Content, Usher, VADR_Update, Zip_Column_Content, kSNP3, kSNP4	docker	
+version_capture	timezone	String	Set the time zone to get an accurate date of analysis (uses UTC by default)		Optional	AMRFinderPlus, AMR_Search, Assembly_Fetch, Augur, Augur_Prep, BaseSpace_Fetch, CZGenEpi_Prep, Cauris_CladeTyper, Clair3_Variants_ONT, Concatenate_Column_Content, Concatenate_Illumina_Lanes, Core_Gene_SNP, Dorado_Basecalling, Fetch_SRR_Accession, Find_Shared_Variants, Freyja_Dashboard, Freyja_FASTQ, Freyja_Plot, Gambit_Query, Kraken_ONT, Kraken_PE, Kraken_SE, Lyve_SET, MashTree_FASTA, Mercury_Prep_N_Batch, Metabuli, NCBI_Scrub_PE, NCBI_Scrub_SE, Nextclade_Batch, Pangolin_Update, PhyloCompare, RASUSA, Rename_FASTQ, SRA_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree, Snippy_Variants, TBProfiler_tNGS, Terra_2_ENA, Terra_2_GISAID, Terra_2_NCBI, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaValidate, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel, Transfer_Column_Content, Usher, VADR_Update, Zip_Column_Content, kSNP3, kSNP4	general	
 wg_reorder_matrix	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Snippy_Tree	runtime	
 wg_reorder_matrix	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Tree	runtime	
 wg_reorder_matrix	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1	Optional	Snippy_Tree	docker