nf-core · mirpedrol · Aug 7, 2023 · Jul 26, 2023 · Jul 27, 2023 · Jul 27, 2023
@@ -90,8 +90,8 @@ jobs:
       - name: Install pip
         run: python -m pip install --upgrade pip
 
-      - name: Install nf-core tools
-        run: python -m pip install nf-core
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
 
       - name: Install Nextflow
         env:

diff --git a/subworkflows/nf-core/bam_create_som_pon_gatk/meta.yml b/subworkflows/nf-core/bam_create_som_pon_gatk/meta.yml
@@ -9,7 +9,7 @@ keywords:
   - variant_calling
   - genomicsdb_workspace
   - panel_of_normals
-modules:
+components:
   - gatk4/mutect2
   - gatk4/genomicsdbimport
   - gatk4/createsomaticpanelofnormals

diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml
@@ -8,12 +8,13 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - umitools/dedup
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_stats_samtools
 input:
   - ch_bam_bai:
       description: |

diff --git a/subworkflows/nf-core/bam_docounts_contamination_angsd/meta.yml b/subworkflows/nf-core/bam_docounts_contamination_angsd/meta.yml
@@ -6,7 +6,7 @@ keywords:
   - bam
   - contamination
   - docounts
-modules:
+components:
   - angsd/docounts
   - angsd/contamination
 input:

diff --git a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml
@@ -7,12 +7,13 @@ keywords:
   - sam
   - cram
 
-modules:
+components:
   - picard/markduplicates
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_stats_samtools
 
 input:
   - ch_bam:

diff --git a/subworkflows/nf-core/bam_markduplicates_samtools/meta.yml b/subworkflows/nf-core/bam_markduplicates_samtools/meta.yml
@@ -6,7 +6,7 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - samtools/collate
   - samtools/fixmate
   - samtools/sort

diff --git a/subworkflows/nf-core/bam_ngscheckmate/meta.yml b/subworkflows/nf-core/bam_ngscheckmate/meta.yml
@@ -6,7 +6,7 @@ keywords:
   - qc
   - bam
   - snp
-modules:
+components:
   - bcftools/mpileup
   - ngscheckmate/ncm
 input:

diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml
@@ -1,5 +1,5 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: bam_qc
+name: bam_qc_picard
 description: Produces comprehensive statistics from BAM file
 keywords:
   - statistics
@@ -9,7 +9,7 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - picard/collectmultiplemetrics
   - picard/collectwgsmetrics
   - picard/collecthsmetrics

diff --git a/subworkflows/nf-core/bam_rseqc/meta.yml b/subworkflows/nf-core/bam_rseqc/meta.yml
@@ -12,8 +12,16 @@ keywords:
   - readdistribution
   - readduplication
   - tin
-modules:
+components:
   - rseqc
+  - rseqc/tin
+  - rseqc/readduplication
+  - rseqc/readdistribution
+  - rseqc/junctionsaturation
+  - rseqc/junctionannotation
+  - rseqc/innerdistance
+  - rseqc/inferexperiment
+  - rseqc/bamstat
 input:
   - meta:
       type: map

diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
@@ -6,12 +6,13 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - samtools/sort
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_stats_samtools
 input:
   - meta:
       type: map

diff --git a/subworkflows/nf-core/bam_split_by_region/meta.yml b/subworkflows/nf-core/bam_split_by_region/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - sam
   - cram
   - index
-modules:
+components:
   - samtools/view
   - samtools/index
 input:

diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat

diff --git a/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/meta.yml b/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/meta.yml
@@ -15,7 +15,7 @@ keywords:
   - variant_calling
   - tumor_only
   - filtered_vcf
-modules:
+components:
   - gatk4/mutect2
   - gatk4/learnreadorientationmodel
   - gatk4/getpileupsummaries

diff --git a/subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/meta.yml b/subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/meta.yml
@@ -1,5 +1,5 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: gatk_tumor_only_somatic_variant_calling
+name: bam_tumor_only_somatic_variant_calling_gatk
 description: |
   Perform variant calling on a single tumor sample using mutect2 tumor only mode.
   Run the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables.
@@ -13,7 +13,7 @@ keywords:
   - variant_calling
   - tumor_only
   - filtered_vcf
-modules:
+components:
   - gatk4/mutect2
   - gatk4/getpileupsummaries
   - gatk4/calculatecontamination

diff --git a/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/meta.yml b/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/meta.yml
@@ -8,7 +8,7 @@ keywords:
   - bam
   - cram
   - vcf
-modules:
+components:
   - freebayes
   - bcftools/sort
   - bcftools/index

diff --git a/subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml b/subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml
@@ -6,7 +6,7 @@ keywords:
   - variants
   - cram
 
-modules:
+components:
   - freyja/variants
   - freyja/demix
   - freyja/update

diff --git a/subworkflows/nf-core/bcl_demultiplex/meta.yml b/subworkflows/nf-core/bcl_demultiplex/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - bcl2fastq
   - demultiplex
   - fastq
-modules:
+components:
   - bcl2fastq
   - bclconvert
 input:

diff --git a/subworkflows/nf-core/bed_scatter_bedtools/meta.yml b/subworkflows/nf-core/bed_scatter_bedtools/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - bed
   - scatter
   - bedtools
-modules:
+components:
   - bedtools/split
 input:
   - ch_bed:

diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml
@@ -6,7 +6,7 @@ keywords:
   - bigwig
   - clip
   - conversion
-modules:
+components:
   - ucsc/bedclip
   - ucsc/bedgraphtobigwig
 input:

diff --git a/subworkflows/nf-core/fasta_binning_concoct/meta.yml b/subworkflows/nf-core/fasta_binning_concoct/meta.yml
@@ -6,7 +6,7 @@ keywords:
   - binning
   - metagenomics
   - contigs
-modules:
+components:
   - concoct/cutupfasta
   - concoct/concoctcoveragetable
   - concoct/concoct

diff --git a/subworkflows/nf-core/fasta_clean_fcs/meta.yml b/subworkflows/nf-core/fasta_clean_fcs/meta.yml
@@ -6,7 +6,7 @@ keywords:
   - cleaning
   - assemblies
   - fasta
-modules:
+components:
   - fcs/fcsadaptor
   - fcs/fcsgx
 input:

diff --git a/subworkflows/nf-core/fasta_index_dna/meta.yml b/subworkflows/nf-core/fasta_index_dna/meta.yml
@@ -11,7 +11,7 @@ keywords:
   - bwamem2
   - dragmap
   - snapaligner
-modules:
+components:
   - bowtie2/build
   - bwa/index
   - bwamem2/index

diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml b/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - alignment
   - fasta
   - newick
-modules:
+components:
   - hmmer/hmmbuild
   - hmmer/hmmalign
   - hmmer/eslalimask

diff --git a/subworkflows/nf-core/fastq_align_bowtie2/meta.yml b/subworkflows/nf-core/fastq_align_bowtie2/meta.yml
@@ -6,13 +6,14 @@ keywords:
   - fasta
   - genome
   - reference
-modules:
+components:
   - bowtie2/align
   - samtools/sort
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_sort_stats_samtools
 input:
   - meta:
       type: map

diff --git a/subworkflows/nf-core/fastq_align_bwa/meta.yml b/subworkflows/nf-core/fastq_align_bwa/meta.yml
@@ -6,13 +6,15 @@ keywords:
   - fasta
   - genome
   - reference
-modules:
+components:
+  - bwa/mem
   - bwa/align
   - samtools/sort
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_sort_stats_samtools
 input:
   - ch_reads:
       description: |

diff --git a/subworkflows/nf-core/fastq_align_bwaaln/meta.yml b/subworkflows/nf-core/fastq_align_bwaaln/meta.yml
@@ -1,5 +1,5 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "fastq_align_bwaaln_samtools"
+name: "fastq_align_bwaaln"
 description: Align FASTQ files against reference genome with the bwa aln short-read aligner producing a sorted and indexed BAM files
 keywords:
   - bwa
@@ -8,7 +8,7 @@ keywords:
   - bwa
   - align
   - map
-modules:
+components:
   - bwa/aln
   - bwa/sampe
   - bwa/samse

diff --git a/subworkflows/nf-core/fastq_align_chromap/meta.yml b/subworkflows/nf-core/fastq_align_chromap/meta.yml
@@ -10,13 +10,14 @@ keywords:
   - chip-seq
   - atac-seq
   - hic
-modules:
+components:
   - chromap/chromap
   - samtools/sort
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_sort_stats_samtools
 input:
   - meta:
       type: map

diff --git a/subworkflows/nf-core/fastq_align_dna/meta.yml b/subworkflows/nf-core/fastq_align_dna/meta.yml
@@ -9,7 +9,7 @@ keywords:
   - bwamem2
   - dragmap
   - snapaligner
-modules:
+components:
   - bowtie2/align
   - bwa/mem
   - bwamem2/mem

diff --git a/subworkflows/nf-core/fastq_align_hisat2/meta.yml b/subworkflows/nf-core/fastq_align_hisat2/meta.yml
@@ -10,11 +10,12 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - hisat2/align
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_sort_stats_samtools
 input:
   - meta:
       type: map

diff --git a/subworkflows/nf-core/fastq_align_star/meta.yml b/subworkflows/nf-core/fastq_align_star/meta.yml
@@ -6,13 +6,14 @@ keywords:
   - fasta
   - genome
   - reference
-modules:
+components:
   - star/align
   - samtools/sort
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_sort_stats_samtools
 input:
   - ch_reads:
       description: |

diff --git a/subworkflows/nf-core/fastq_contam_seqtk_kraken/meta.yml b/subworkflows/nf-core/fastq_contam_seqtk_kraken/meta.yml
@@ -5,8 +5,8 @@ keywords:
   - statistics
   - fastq
   - contamination
-modules:
-  - kraken/kraken2
+components:
+  - kraken2/kraken2
   - seqtk/sample
 input:
   - meta:

diff --git a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/meta.yml b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/meta.yml
@@ -1,5 +1,5 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: fgbio_create_umi_consensus
+name: fastq_create_umi_consensus_fgbio
 description: |
   This workflow uses the suite FGBIO to identify and remove UMI tags from FASTQ reads
   convert them to unmapped BAM file, map them to the reference genome,
@@ -10,14 +10,23 @@ keywords:
   - samblaster
   - samtools
   - bwa
-modules:
+components:
   - bwa/index
   - bwa/mem
+  - bwamem2/mem
+  - bwamem2/index
   - fgbio/fastqtobam
   - fgbio/groupreadsbyumi
   - fgbio/callmolecularconsensusreads
+  - fgbio/callduplexconsensusreads
+  - fgbio/filterconsensusreads
   - samblaster
   - samtools/bam2fq
+  - samtools/view
+  - samtools/sort
+  - samtools/index
+  - samtools/fastq
+  - fgbio/zipperbams
 input:
   - meta:
       type: map