Updated the meta.yml of subworkflows

subworkflows/nf-core/bam_subsampledepth_samtools/meta.yml

@@ -11,18 +11,14 @@ components:
   - samtools/view
   - gawk
 input:
-  - ch_bam:
-      type: file
-      description: |
-        The input channel containing the BAM/CRAM/SAM files and their indexes and the depth at which to subsample them.
-        Structure: [ val(meta), path(bam), path(bai), val(depth) ]
-      pattern: "*.{bam,cram,sam}"
   - ch_fasta:
       type: file
       description: |
         The reference genome channel containing the fasta files and its index
         Structure: [ val(meta), path(fasta), path(fai) ]
       pattern: "*.{fa(sta)?}"
+  - ch_bam_bai_depth:
+      description: ""
 output:
   - bam_subsampled:
       type: file

subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/meta.yml

@@ -19,51 +19,24 @@ components:
   - gatk4/calculatecontamination
   - gatk4/filtermutectcalls
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
-  - input:
-      type: list
-      description: list containing one BAM file, also able to take CRAM as an input
-      pattern: "[ *.{bam/cram} ]"
-  - input_index:
-      type: list
-      description: list containing one BAM file indexe, also able to take CRAM index as an input
-      pattern: "[ *.{bam.bai/cram.crai} ]"
-  - fasta:
-      type: file
-      description: The reference fasta file
-      pattern: "*.fasta"
-  - fai:
-      type: file
-      description: Index of reference fasta file
-      pattern: "*.fasta.fai"
-  - dict:
-      type: file
-      description: GATK sequence dictionary
-      pattern: "*.dict"
-  - germline_resource:
-      type: file
-      description: Population vcf of germline sequencing, containing allele fractions.
-      pattern: "*.vcf.gz"
-  - germline_resource_tbi:
-      type: file
-      description: Index file for the germline resource.
-      pattern: "*.vcf.gz.tbi"
-  - panel_of_normals:
-      type: file
-      description: vcf file to be used as a panel of normals.
-      pattern: "*.vcf.gz"
-  - panel_of_normals_tbi:
-      type: file
-      description: Index for the panel of normals.
-      pattern: "*.vcf.gz.tbi"
-  - interval_file:
-      type: file
-      description: File containing intervals.
-      pattern: "*.interval_list"
+  - ch_input:
+      description: ""
+  - ch_fasta:
+      description: ""
+  - ch_fai:
+      description: ""
+  - ch_dict:
+      description: ""
+  - ch_germline_resource:
+      description: ""
+  - ch_germline_resource_tbi:
+      description: ""
+  - ch_panel_of_normals:
+      description: ""
+  - ch_panel_of_normals_tbi:
+      description: ""
+  - ch_interval_file:
+      description: ""
 output:
   - versions:
       type: file
@@ -73,10 +46,6 @@ output:
       type: file
       description: Compressed vcf file to be used for variant_calling.
       pattern: "[ *.vcf.gz ]"
-  - mutect2_tbi:
-      type: file
-      description: Indexes of the mutect2_vcf file
-      pattern: "[ *vcf.gz.tbi ]"
   - mutect2_stats:
       type: file
       description: Stats files for the mutect2 vcf
@@ -97,14 +66,14 @@ output:
       type: file
       description: file containing filtered mutect2 calls.
       pattern: "*.vcf.gz"
-  - filtered_tbi:
-      type: file
-      description: tbi file that pairs with filtered vcf.
-      pattern: "*.vcf.gz.tbi"
   - filtered_stats:
       type: file
       description: file containing statistics of the filtermutectcalls run.
       pattern: "*.filteringStats.tsv"
+  - mutect2_index:
+      description: ""
+  - filtered_index:
+      description: ""
 authors:
   - "@GCJMackenzie"
 maintainers:

subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/meta.yml

@@ -13,66 +13,17 @@ components:
   - bcftools/sort
   - bcftools/index
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
-  - input1:
-      type: file
-      description: BAM/CRAM/SAM file;
-      pattern: "*.{bam,cram,sam}"
-  - index1:
-      type: file
-      description: Index BAI/CRAI/CSI file
-      pattern: "*.{bai,crai,csi}"
-  - input2:
-      type: file
-      description: BAM/CRAM/SAM file; used to run variant calling with pair (normal vs tumor)
-      pattern: "*.{bam,cram,sam}"
-  - index2:
-      type: file
-      description: Index BAI/CRAI/CSI file
-      pattern: "*.{bai,crai,csi}"
-  - bed:
-      type: file
-      description: Optional - Limit analysis to targets listed in this BED-format FILE.
-      pattern: "*.bed"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'test' ]
-  - fasta:
-      type: file
-      description: reference fasta file
-      pattern: ".{fa,fa.gz,fasta,fasta.gz}"
-  - fai:
-      type: file
-      description: reference fasta file index
-      pattern: "*.{fa,fasta}.fai"
-  - samples:
-      type: file
-      description: Optional - Limit analysis to samples listed (one per line) in the FILE.
-      pattern: "*.txt"
-  - populations:
-      type: file
-      description: Optional - Each line of FILE should list a sample and a population which it is part of.
-      pattern: "*.txt"
-  - cnv:
-      type: file
-      description: |
-        A copy number map BED file, which has either a sample-level ploidy:
-        sample_name copy_number
-        or a region-specific format:
-        seq_name start end sample_name copy_number
-      pattern: "*.bed"
+  - ch_input:
+      description: ""
+  - ch_fasta_fai:
+      description: ""
+  - ch_samples:
+      description: ""
+  - ch_populations:
+      description: ""
+  - ch_cnv:
+      description: ""
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
   - versions:
       type: file
       description: File containing software versions

subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml

@@ -1,6 +1,7 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "bam_variant_demix_boot_freyja"
-description: Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference)
+description: Recover relative lineage abundances from mixed SARS-CoV-2 samples from
+  a sequencing dataset (BAM aligned to the Hu-1 reference)
 keywords:
   - bam
   - variants
@@ -37,22 +38,14 @@ input:
       description: |
         Structure: path(lineages_meta)
         File containing lineage metadata that correspond to barcodes
+  - val_skip_boot:
+      description: ""
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
   - variants:
       type: file
       description: |
         Structure: [ val(meta), path(variants) ]
         File containing identified variants in a gff-like format
-  - depths:
-      type: file
-      description: |
-        Structure: [ val(meta), path(variants) ]
-        File containing depth of the variants
   - demix:
       type: file
       description: |
@@ -70,10 +63,12 @@ output:
         a csv file that includes the lineages present but summarized by constellation and their corresponding abundances
   - barcodes:
       type: file
-      description: path(barcodes) a csv file that includes the lineages present but summarized by constellation and their corresponding abundances
+      description: path(barcodes) a csv file that includes the lineages present but
+        summarized by constellation and their corresponding abundances
   - lineages_meta:
       type: file
-      description: path(lineages_meta) a csv file that includes the lineages present but summarized by constellation and their corresponding abundances
+      description: path(lineages_meta) a csv file that includes the lineages present
+        but summarized by constellation and their corresponding abundances
   - versions:
       type: file
       description: File containing software versions

subworkflows/nf-core/bcl_demultiplex/meta.yml

@@ -11,27 +11,12 @@ components:
   - bcl2fastq
   - bclconvert
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'string', lane: int ]
-  - samplesheet:
-      type: file
-      description: |
-        CSV file containing information about samples to be demultiplexed in Illumina SampleSheet format
-  - flowcell:
-      type: file
-      description: Directory or tar archive containing Illumina BCL data, sequencer output directory
   - demultiplexer:
       type: string
       description: Which demultiplexer to use, bcl2fastq or bclconvert
+  - ch_flowcell:
+      description: ""
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
   - fastq:
       type: file
       description: Demultiplexed fastq files
@@ -52,6 +37,8 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - empty_fastq:
+      description: ""
 authors:
   - "@matthdsm"
 maintainers:

subworkflows/nf-core/deepvariant/meta.yml

@@ -1,6 +1,7 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: deepvariant
-description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
+description: DeepVariant is an analysis pipeline that uses a deep neural network to
+  call genetic variants from next-generation DNA sequencing data
 keywords:
   - variant calling
   - machine learning

subworkflows/nf-core/fasta_binning_concoct/meta.yml

@@ -25,11 +25,6 @@ input:
         BAM and associated index files file representing reads mapped against each
         contig in ch_fasta. Meta must be identical between ch_fasta and ch_bam entries.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
   - coverage_table:
       type: file
       description: |
@@ -60,16 +55,12 @@ output:
       description: |
         Structure: [ val(meta), path(csv) ]
         CSV file containing final cluster assignments of original input contigs
-  - bin:
-      type: file
-      description: |
-        Structure: [ val(meta), path(fasta) ]
-        FASTA files containing CONCOCT predicted bin clusters, named numerically
-        by CONCOCT cluster ID
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - bins:
+      description: ""
 authors:
   - "@jfy133"
 maintainers:

subworkflows/nf-core/fasta_clean_fcs/meta.yml

@@ -1,6 +1,7 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "fasta_clean_fcs"
-description: Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies
+description: Foreign Contamination Screen (FCS) is a tool suite for identifying and
+  removing contaminant sequences in genome assemblies
 keywords:
   - contamination screening
   - cleaning
@@ -10,21 +11,11 @@ components:
   - fcs/fcsadaptor
   - fcs/fcsgx
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
-  - assembly:
-      type: file
-      description: assembly fasta file
-      pattern: "*.{fasta,fa}"
+  - ch_fasta:
+      description: ""
+  - database:
+      description: ""
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
   - versions:
       type: file
       description: File containing software versions
@@ -49,14 +40,12 @@ output:
       type: file
       description: Skipped trim information
       pattern: "*.{skipped_trims.jsonl}"
-  - fcs_gx_report:
-      type: file
-      description: Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)
-      pattern: "*.fcs_gx_report.txt"
   - fcsgx_taxonomy_report:
       type: file
       description: Report containing the contig identifier and mapped contaminant species
       pattern: "*.taxonomy.rpt"
+  - fcsgx_report:
+      description: ""
 authors:
   - "@scorreard"
 maintainers:

subworkflows/nf-core/fasta_explore_search_plot_tidk/meta.yml

@@ -31,6 +31,10 @@ input:
       description: |
         A priori sequence
         Structure: [ val(meta), val(sequence) ]
+  - //:
+      description: ""
+  - //:
+      description: ""
 output:
   - apriori_tsv:
       type: file