From f883a060a93fdcf9a02e53c7736101a19a56e52f Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:08:19 +0200 Subject: [PATCH 01/25] Update ataqv version --- modules/nf-core/ataqv/ataqv/main.nf | 2 +- modules/nf-core/ataqv/ataqv/meta.yml | 49 +++++++++++++++------------- modules/nf-core/ataqv/mkarv/main.nf | 2 +- modules/nf-core/ataqv/mkarv/meta.yml | 16 +++++---- 4 files changed, 37 insertions(+), 32 deletions(-) diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index 2dbb95ea1687..aadd44eef110 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -18,7 +18,7 @@ process ATAQV_ATAQV { output: tuple val(meta), path("*.ataqv.json"), emit: json tuple val(meta), path("*.problems") , emit: problems, optional: true - tuple val("${task.process}"), val('ataqv'), eval("echo \$(ataqv --version)"), emit: versions_ataqv, topic: versions + tuple val("${task.process}"), val('ataqv'), eval("ataqv --version"), emit: versions_ataqv, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ataqv/ataqv/meta.yml b/modules/nf-core/ataqv/ataqv/meta.yml index 71ca36dc5d57..dbcf210e21fc 100644 --- a/modules/nf-core/ataqv/ataqv/meta.yml +++ b/modules/nf-core/ataqv/ataqv/meta.yml @@ -6,10 +6,10 @@ keywords: - ataqv tools: - ataqv: - description: ataqv is a toolkit for measuring and comparing ATAC-seq results. - It was written to help understand how well ATAC-seq assays have worked, and - to make it easier to spot differences that might be caused by library prep or - sequencing. + description: ataqv is a toolkit for measuring and comparing ATAC-seq + results. It was written to help understand how well ATAC-seq assays have + worked, and to make it easier to spot differences that might be caused by + library prep or sequencing. homepage: https://github.com/ParkerLab/ataqv/blob/master/README.rst documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst tool_dev_url: https://github.com/ParkerLab/ataqv @@ -30,8 +30,8 @@ input: ontologies: [] - bai: type: file - description: BAM index file with the same prefix as bam file. Required if tss_file - input is provided. + description: BAM index file with the same prefix as bam file. Required if + tss_file input is provided. pattern: "*.bam.bai" ontologies: [] - peak_file: @@ -41,30 +41,31 @@ input: ontologies: [] - organism: type: string - description: The subject of the experiment, which determines the list of autosomes - (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv). + description: The subject of the experiment, which determines the list of + autosomes (see "Reference Genome Configuration" section at + https://github.com/ParkerLab/ataqv). - mito_name: type: string description: Name of the mitochondrial sequence. - tss_file: type: file - description: A BED file of transcription start sites for the experiment organism. - If supplied, a TSS enrichment score will be calculated according to the ENCODE - data standards. This calculation requires that the BAM file of alignments be - indexed. + description: A BED file of transcription start sites for the experiment + organism. If supplied, a TSS enrichment score will be calculated according + to the ENCODE data standards. This calculation requires that the BAM file + of alignments be indexed. pattern: "*.bed" ontologies: [] - excl_regs_file: type: file - description: A BED file containing excluded regions. Peaks or TSS overlapping - these will be ignored. + description: A BED file containing excluded regions. Peaks or TSS + overlapping these will be ignored. pattern: "*.bed" ontologies: [] - autosom_ref_file: type: file - description: A file containing autosomal reference names, one per line. The names - must match the reference names in the alignment file exactly, or the metrics - based on counts of autosomal alignments will be wrong. + description: A file containing autosomal reference names, one per line. The + names must match the reference names in the alignment file exactly, or the + metrics based on counts of autosomal alignments will be wrong. ontologies: [] output: json: @@ -85,10 +86,10 @@ output: e.g. [ id:'test', single_end:false ] - "*.problems": type: file - description: If given, problematic reads will be logged to a file per read - group, with names derived from the read group IDs, with ".problems" appended. - If no read groups are found, the reads will be written to one file named - after the BAM file. + description: If given, problematic reads will be logged to a file per + read group, with names derived from the read group IDs, with + ".problems" appended. If no read groups are found, the reads will be + written to one file named after the BAM file. pattern: "*.problems" ontologies: [] versions_ataqv: @@ -98,9 +99,10 @@ output: - ataqv: type: string description: The name of the tool - - echo \$(ataqv --version): + - ataqv --version: type: eval description: The expression to obtain the version of the tool + topics: versions: - - ${task.process}: @@ -109,9 +111,10 @@ topics: - ataqv: type: string description: The name of the tool - - echo \$(ataqv --version): + - ataqv --version: type: eval description: The expression to obtain the version of the tool + authors: - "@i-pletenev" maintainers: diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index a26c111e7b82..cf812d6138ac 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -11,7 +11,7 @@ process ATAQV_MKARV { output: path "html" , emit: html - tuple val("${task.process}"), val('ataqv'), eval('echo \$(ataqv --version)'), emit: versions_ataqv, topic: versions + tuple val("${task.process}"), val('ataqv'), eval("ataqv --version"), emit: versions_ataqv, topic: versions // tuple val("${task.process}"), val('mkarv'), eval('mkarv --version'), emit: versions_mkarv, topic: versions //Use this when version string has been fixed when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ataqv/mkarv/meta.yml b/modules/nf-core/ataqv/mkarv/meta.yml index 8027f1a686dd..11bec4337606 100644 --- a/modules/nf-core/ataqv/mkarv/meta.yml +++ b/modules/nf-core/ataqv/mkarv/meta.yml @@ -7,10 +7,10 @@ keywords: - mkarv tools: - "ataqv": - description: "ataqv is a toolkit for measuring and comparing ATAC-seq results.\ - \ It was written to help understand how well ATAC-seq assays have worked, and\ - \ to make it easier to spot differences that might be caused by library prep\ - \ or sequencing." + description: "ataqv is a toolkit for measuring and comparing ATAC-seq results. + It was written to help understand how well ATAC-seq assays have worked, and + to make it easier to spot differences that might be caused by library prep or + sequencing." homepage: "https://github.com/ParkerLab/ataqv/blob/master/README.rst" documentation: "https://github.com/ParkerLab/ataqv/blob/master/README.rst" tool_dev_url: "https://github.com/ParkerLab/ataqv" @@ -23,7 +23,7 @@ input: description: JSON files pattern: "*.json" ontologies: - - edam: http://edamontology.org/format_3464 + - edam: http://edamontology.org/format_3464 # JSON output: html: - html: @@ -37,9 +37,10 @@ output: - ataqv: type: string description: The name of the tool - - echo \$(ataqv --version): + - ataqv --version: type: eval description: The expression to obtain the version of the tool + versions_mkarv: - - ${task.process}: type: string @@ -58,9 +59,10 @@ topics: - ataqv: type: string description: The name of the tool - - echo \$(ataqv --version): + - ataqv --version: type: eval description: The expression to obtain the version of the tool + - - ${task.process}: type: string description: The name of the process From 615a026a69eb396b4f03d602a055c00bdb3f86b2 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:09:09 +0200 Subject: [PATCH 02/25] Update leafcutter version --- modules/nf-core/leafcutter/clusterregtools/main.nf | 3 ++- .../nf-core/leafcutter/clusterregtools/meta.yml | 14 ++++++++------ .../clusterregtools/tests/main.nf.test.snap | 6 +++--- 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/modules/nf-core/leafcutter/clusterregtools/main.nf b/modules/nf-core/leafcutter/clusterregtools/main.nf index f9a38f2e2a03..64f5e30ef2ed 100644 --- a/modules/nf-core/leafcutter/clusterregtools/main.nf +++ b/modules/nf-core/leafcutter/clusterregtools/main.nf @@ -16,7 +16,8 @@ process LEAFCUTTER_CLUSTERREGTOOLS { tuple val(meta), path("*_sortedlibs") , emit: sortedlibs tuple val(meta), path("*_perind*.counts.gz") , emit: counts tuple val(meta), path("*_perind_numers*.counts.gz") , emit: numers - tuple val("${task.process}"), val('leafcutter'), eval("echo 'leafcutter 2.0.3'"), topic: versions, emit: versions_leafcutter + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('leafcutter'), val("2.0.3"), topic: versions, emit: versions_leafcutter when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/leafcutter/clusterregtools/meta.yml b/modules/nf-core/leafcutter/clusterregtools/meta.yml index 54b22a6e595a..b28ec5cb64b7 100644 --- a/modules/nf-core/leafcutter/clusterregtools/meta.yml +++ b/modules/nf-core/leafcutter/clusterregtools/meta.yml @@ -96,9 +96,10 @@ output: - leafcutter: type: string description: The name of the tool - - echo 'leafcutter 2.0.3': - type: eval - description: The expression to obtain the version of the tool + - 2.0.3: + type: string + description: The version of the tool + topics: versions: - - ${task.process}: @@ -107,9 +108,10 @@ topics: - leafcutter: type: string description: The name of the tool - - echo 'leafcutter 2.0.3': - type: eval - description: The expression to obtain the version of the tool + - 2.0.3: + type: string + description: The version of the tool + authors: - "@JTL-lab" maintainers: diff --git a/modules/nf-core/leafcutter/clusterregtools/tests/main.nf.test.snap b/modules/nf-core/leafcutter/clusterregtools/tests/main.nf.test.snap index 66b52fc52bc7..4c0aa1e2ece9 100644 --- a/modules/nf-core/leafcutter/clusterregtools/tests/main.nf.test.snap +++ b/modules/nf-core/leafcutter/clusterregtools/tests/main.nf.test.snap @@ -49,7 +49,7 @@ [ "LEAFCUTTER_CLUSTERREGTOOLS", "leafcutter", - "leafcutter 2.0.3" + "2.0.3" ] ], "counts": [ @@ -99,7 +99,7 @@ [ "LEAFCUTTER_CLUSTERREGTOOLS", "leafcutter", - "leafcutter 2.0.3" + "2.0.3" ] ] } @@ -160,7 +160,7 @@ [ "LEAFCUTTER_CLUSTERREGTOOLS", "leafcutter", - "leafcutter 2.0.3" + "2.0.3" ] ] } From 7a9796b537877db27e090a7322a86cad31d7c95d Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:09:52 +0200 Subject: [PATCH 03/25] Update authentict version --- modules/nf-core/authentict/deam2cont/main.nf | 2 +- modules/nf-core/authentict/deam2cont/meta.yml | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/authentict/deam2cont/main.nf b/modules/nf-core/authentict/deam2cont/main.nf index 7f2be9a2ccc9..5047cf8d1886 100644 --- a/modules/nf-core/authentict/deam2cont/main.nf +++ b/modules/nf-core/authentict/deam2cont/main.nf @@ -14,7 +14,7 @@ process AUTHENTICT_DEAM2CONT { output: tuple val(meta), path("*.txt"), emit: txt - tuple val("${task.process}"), val('authentict'), eval("echo \$(AuthentiCT --version 2>&1)"), emit: versions_authentict, topic: versions + tuple val("${task.process}"), val('authentict'), eval("AuthentiCT --version"), emit: versions_authentict, topic: versions tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //'"), emit: versions_samtools, topic: versions when: diff --git a/modules/nf-core/authentict/deam2cont/meta.yml b/modules/nf-core/authentict/deam2cont/meta.yml index d693149c4bc1..4d57c7d8a054 100644 --- a/modules/nf-core/authentict/deam2cont/meta.yml +++ b/modules/nf-core/authentict/deam2cont/meta.yml @@ -71,9 +71,10 @@ output: - authentict: type: string description: The name of the tool - - echo \$(AuthentiCT --version 2>&1): + - AuthentiCT --version: type: eval description: The expression to obtain the version of the tool + versions_samtools: - - ${task.process}: type: string @@ -92,9 +93,10 @@ topics: - authentict: type: string description: The name of the tool - - echo \$(AuthentiCT --version 2>&1): + - AuthentiCT --version: type: eval description: The expression to obtain the version of the tool + - - ${task.process}: type: string description: The name of the process From c94e2c775d3d4fa81172b75b181512b79975cbf0 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:11:00 +0200 Subject: [PATCH 04/25] Update links version --- modules/nf-core/links/main.nf | 16 +++------------- modules/nf-core/links/meta.yml | 16 +++++++++------- 2 files changed, 12 insertions(+), 20 deletions(-) diff --git a/modules/nf-core/links/main.nf b/modules/nf-core/links/main.nf index 089d6682a00d..3936b81d1560 100644 --- a/modules/nf-core/links/main.nf +++ b/modules/nf-core/links/main.nf @@ -22,7 +22,7 @@ process LINKS { tuple val(meta), path("*.assembly_correspondence.tsv"), emit: assembly_correspondence tuple val(meta), path("*.simplepair_checkpoint.tsv"), emit: simplepair_checkpoint, optional: true tuple val(meta), path("*.tigpair_checkpoint.tsv"), emit: tigpair_checkpoint - tuple val("${task.process}"), val('liftoff'), eval("echo \$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//')"), emit: versions_links, topic: versions + tuple val("${task.process}"), val('liftoff'), eval("LINKS | sed -n 's/LINKS v//p'"), emit: versions_links, topic: versions when: task.ext.when == null || task.ext.when @@ -53,14 +53,9 @@ process LINKS { LINKS -f assembly.fa \\ -s readfile.fof \\ - -j $nthreads \\ + -j ${nthreads} \\ -b ${prefix} \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - LINKS: \$(echo \$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//')) - END_VERSIONS + ${args} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" @@ -76,10 +71,5 @@ process LINKS { touch ${prefix}.assembly_correspondence.tsv touch ${prefix}.simplepair_checkpoint.tsv touch ${prefix}.tigpair_checkpoint.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - LINKS: \$(echo \$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//')) - END_VERSIONS """ } diff --git a/modules/nf-core/links/meta.yml b/modules/nf-core/links/meta.yml index 9cdcde4f8c52..021d3cfb84ff 100644 --- a/modules/nf-core/links/meta.yml +++ b/modules/nf-core/links/meta.yml @@ -42,7 +42,7 @@ input: scaffolding pattern: "*.{fq,fastq,fq.gz,fastq.gz}" ontologies: - - edam: http://edamontology.org/format_1930 + - edam: http://edamontology.org/format_1930 # FASTQ output: log: - - meta: @@ -70,7 +70,7 @@ output: that distance. pattern: "*.pairing_distribution.csv" ontologies: - - edam: http://edamontology.org/format_3752 + - edam: http://edamontology.org/format_3752 # CSV pairing_issues: - - meta: type: map @@ -146,7 +146,7 @@ output: links ratio, gap or overlap pattern: "*.assembly_correspondence.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV simplepair_checkpoint: - - meta: type: map @@ -159,7 +159,7 @@ output: .gv graph pattern: "*.simplepair_checkpoint.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV tigpair_checkpoint: - - meta: type: map @@ -179,7 +179,7 @@ output: 4) scaffold with output of ARCS pattern: "*.tigpair_checkpoint.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV versions_links: - - ${task.process}: type: string @@ -187,9 +187,10 @@ output: - liftoff: type: string description: The name of the tool - - echo \$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//'): + - LINKS | sed -n 's/LINKS v//p': type: eval description: The expression to obtain the version of the tool + topics: versions: - - ${task.process}: @@ -198,9 +199,10 @@ topics: - liftoff: type: string description: The name of the tool - - echo \$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//'): + - LINKS | sed -n 's/LINKS v//p': type: eval description: The expression to obtain the version of the tool + authors: - "@nschan" maintainers: From 029eb0bfab63928b7be52058477c246d1d7e8713 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:15:33 +0200 Subject: [PATCH 05/25] Update arcashla --- modules/nf-core/arcashla/extract/main.nf | 3 ++- modules/nf-core/arcashla/extract/meta.yml | 32 +++++++++++++---------- 2 files changed, 20 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/arcashla/extract/main.nf b/modules/nf-core/arcashla/extract/main.nf index 51589d14f4dd..afda527ee08e 100644 --- a/modules/nf-core/arcashla/extract/main.nf +++ b/modules/nf-core/arcashla/extract/main.nf @@ -16,7 +16,8 @@ process ARCASHLA_EXTRACT { tuple val(meta), path("temp_files/**.sam") , emit: intermediate_sam , optional: true tuple val(meta), path("temp_files/**.bam") , emit: intermediate_bam , optional: true tuple val(meta), path("temp_files/**.sorted.bam"), emit: intermediate_sorted_bam, optional: true - tuple val("${task.process}"), val('arcashla'), eval('echo 0.5.0'), emit: versions_arcashla, topic: versions + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('arcashla'), val('0.5.0'), emit: versions_arcashla, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/arcashla/extract/meta.yml b/modules/nf-core/arcashla/extract/meta.yml index 7a4ec9bec972..619d42f482a1 100644 --- a/modules/nf-core/arcashla/extract/meta.yml +++ b/modules/nf-core/arcashla/extract/meta.yml @@ -1,6 +1,6 @@ name: "arcashla_extract" -description: Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome - 6 alternates. +description: Extracts reads mapped to chromosome 6 and any HLA decoys or + chromosome 6 alternates. keywords: - HLA - genotype @@ -13,7 +13,8 @@ tools: documentation: "https://github.com/RabadanLab/arcasHLA" tool_dev_url: "https://github.com/RabadanLab/arcasHLA" doi: "10.1093/bioinformatics/btz474" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" input: - - meta: @@ -23,8 +24,8 @@ input: e.g. [ id:'test', single_end:false ] - bam: type: file - description: BAM file. If the BAM file is not indexed, this tool will run samtools - index before extracting reads. + description: BAM file. If the BAM file is not indexed, this tool will run + samtools index before extracting reads. pattern: "*.bam" ontologies: - edam: "http://edamontology.org/format_2572" # BAM @@ -37,7 +38,8 @@ output: e.g. [ id:'test', single_end:false ] - "*.fq.gz": type: file - description: FASTQ file(s) containing chromosome 6 reads and related HLA sequences + description: FASTQ file(s) containing chromosome 6 reads and related HLA + sequences pattern: "*.fq.gz" ontologies: - edam: "http://edamontology.org/format_1930" # FASTQ @@ -85,26 +87,28 @@ output: ontologies: - edam: "http://edamontology.org/format_2572" # BAM versions_arcashla: - - - "${task.process}": + - - ${task.process}: type: string description: The name of the process - - "arcashla": + - arcashla: type: string description: The name of the tool - - "echo 0.5.0": - type: eval + - 0.5.0: + type: string description: The expression to obtain the version of the tool + topics: versions: - - - "${task.process}": + - - ${task.process}: type: string description: The name of the process - - "arcashla": + - arcashla: type: string description: The name of the tool - - "echo 0.5.0": - type: eval + - 0.5.0: + type: string description: The expression to obtain the version of the tool + authors: - "@christopher-mohr" maintainers: From d5a7daafb595fad38cebfa39669bbd562b022f21 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:17:00 +0200 Subject: [PATCH 06/25] Update bamcmp --- modules/nf-core/bamcmp/main.nf | 4 +-- modules/nf-core/bamcmp/meta.yml | 53 +++++++++++++++++---------------- 2 files changed, 30 insertions(+), 27 deletions(-) diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index 2cb0048374d8..9815312d9950 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -1,7 +1,6 @@ process BAMCMP { label 'process_low' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e5ee3676abe7e65f65eca55e8dbc76f4dd195a44679cd1a785943d7a0d598f1/data' : @@ -13,7 +12,8 @@ process BAMCMP { output: tuple val(meta), path("${prefix}.bam") , emit: primary_filtered_bam tuple val(meta), path("${prefix2}.bam"), emit: contamination_bam - tuple val("${task.process}"), val('bamcmp'), eval('echo 2.2'), topic: versions, emit: versions_bamcmp + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('bamcmp'), val('2.2'), topic: versions, emit: versions_bamcmp tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: diff --git a/modules/nf-core/bamcmp/meta.yml b/modules/nf-core/bamcmp/meta.yml index 0533577d233d..0f901800df13 100644 --- a/modules/nf-core/bamcmp/meta.yml +++ b/modules/nf-core/bamcmp/meta.yml @@ -1,7 +1,7 @@ name: bamcmp -description: Bamcmp (Bam Compare) is a tool for assigning reads between a primary - genome and a contamination genome. For instance, filtering out mouse reads from - patient derived xenograft mouse models (PDX). +description: Bamcmp (Bam Compare) is a tool for assigning reads between a + primary genome and a contamination genome. For instance, filtering out mouse + reads from patient derived xenograft mouse models (PDX). keywords: - filter - xenograft @@ -11,16 +11,17 @@ keywords: - mouse tools: - bamcmp: - description: Bamcmp is a tool for deconvolving host and graft reads, using two - bam files. Reads should be mapped to two genomes, and the mapped, sorted bam - files supplied to the tool. It is highly recommended to use the "-s as" option - not the "-s mapq" option, else reads which multimap to the contamination genome - will be spuriously kept. + description: Bamcmp is a tool for deconvolving host and graft reads, using + two bam files. Reads should be mapped to two genomes, and the mapped, + sorted bam files supplied to the tool. It is highly recommended to use the + "-s as" option not the "-s mapq" option, else reads which multimap to the + contamination genome will be spuriously kept. homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp doi: "10.1158/1541-7786.MCR-16-0431" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" input: - - meta: @@ -30,14 +31,14 @@ input: e.g. [ id:'test'] - primary_aligned_bam: type: file - description: BAM/CRAM/SAM file with the reads aligned to the primary genome - (the one you want to keep) + description: BAM/CRAM/SAM file with the reads aligned to the primary + genome (the one you want to keep) pattern: "*.{bam,cram,sam}" ontologies: [] - contaminant_aligned_bam: type: file - description: BAM/CRAM/SAM file with the reads aligned to the contaminant genome - (the one you want to filter out) + description: BAM/CRAM/SAM file with the reads aligned to the contaminant + genome (the one you want to filter out) pattern: "*.{bam,cram,sam}" ontologies: [] output: @@ -47,8 +48,8 @@ output: description: Groovy Map containing sample information - ${prefix}.bam: type: file - description: Bam file containing the reads which align better to the primary - genome. + description: Bam file containing the reads which align better to the + primary genome. pattern: "*.{bam,cram,sam}" ontologies: [] contamination_bam: @@ -57,8 +58,8 @@ output: description: Groovy Map containing sample information - ${prefix2}.bam: type: file - description: Bam file containing the reads which align better to the contaminant - genome. + description: Bam file containing the reads which align better to the + contaminant genome. pattern: "*.{bam,cram,sam}" ontologies: [] versions_bamcmp: @@ -68,9 +69,10 @@ output: - bamcmp: type: string description: The tool name - - echo 2.2: + - "2.2": type: string - description: The version used (constant) + description: The version of the tool + versions_samtools: - - ${task.process}: type: string @@ -78,8 +80,8 @@ output: - samtools: type: string description: The tool name - - "samtools version | sed '1!d;s/.* //'": - type: string + - samtools version | sed '1!d;s/.* //': + type: eval description: The command used to generate the version of the tool topics: versions: @@ -89,17 +91,18 @@ topics: - bamcmp: type: string description: The tool name - - echo 2.2: + - "2.2": type: string - description: The version used (constant) + description: The version of the tool + - - ${task.process}: type: string description: The process the versions were collected from - samtools: type: string description: The tool name - - "samtools version | sed '1!d;s/.* //'": - type: string + - samtools version | sed '1!d;s/.* //': + type: eval description: The command used to generate the version of the tool authors: - "@kmurat1" From 263e27bbe458aab41dcabf9a754fc04fd6bff583 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:18:40 +0200 Subject: [PATCH 07/25] Update busco/phylogenomics --- modules/nf-core/busco/phylogenomics/main.nf | 2 +- modules/nf-core/busco/phylogenomics/meta.yml | 14 ++++++++------ 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/busco/phylogenomics/main.nf b/modules/nf-core/busco/phylogenomics/main.nf index ff790ba2e863..9bba33abeace 100644 --- a/modules/nf-core/busco/phylogenomics/main.nf +++ b/modules/nf-core/busco/phylogenomics/main.nf @@ -14,7 +14,7 @@ process BUSCO_PHYLOGENOMICS { tuple val(meta), path("${prefix}/gene_trees_single_copy/"), emit: gene_trees tuple val(meta), path("${prefix}/supermatrix/") , emit: supermatrix // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - tuple val("${task.process}"), val('busco_phylogenomics'), eval('echo 20240919'), emit: versions_buscophylogenomics, topic: versions + tuple val("${task.process}"), val('busco_phylogenomics'), val('20240919'), emit: versions_buscophylogenomics, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/busco/phylogenomics/meta.yml b/modules/nf-core/busco/phylogenomics/meta.yml index fb8845bb5011..3b144df36dfe 100644 --- a/modules/nf-core/busco/phylogenomics/meta.yml +++ b/modules/nf-core/busco/phylogenomics/meta.yml @@ -52,9 +52,10 @@ output: - busco_phylogenomics: type: string description: The name of the tool - - echo 20240919: - type: eval - description: The expression to obtain the version of the tool + - "20240919": + type: string + description: The version of the tool + topics: versions: - - ${task.process}: @@ -63,9 +64,10 @@ topics: - busco_phylogenomics: type: string description: The name of the tool - - echo 20240919: - type: eval - description: The expression to obtain the version of the tool + - "20240919": + type: string + description: The version of the tool + authors: - "@vagkaratzas" maintainers: From 88a727fb816e044f30c0c5fc3f673bf51f7e9254 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:20:09 +0200 Subject: [PATCH 08/25] Update vafe --- modules/nf-core/cafe/main.nf | 5 +++-- modules/nf-core/cafe/meta.yml | 14 ++++++++------ 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/cafe/main.nf b/modules/nf-core/cafe/main.nf index 62cd26495f9a..fe4cddf98531 100644 --- a/modules/nf-core/cafe/main.nf +++ b/modules/nf-core/cafe/main.nf @@ -1,6 +1,6 @@ process CAFE { label 'process_high' - // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cafe:5.1.0--h43eeafb_0': @@ -16,7 +16,8 @@ process CAFE { path("$prefix/*.tre") , emit: cafe_significant_trees path("$prefix/*_report.cafe") , emit: cafe_report path("$prefix/*results.txt") , emit: cafe_results - tuple val("${task.process}"), val('cafe'), eval('echo 5.1.0'), emit: versions_cafe, topic: versions + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('cafe'), val('5.1.0'), emit: versions_cafe, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/cafe/meta.yml b/modules/nf-core/cafe/meta.yml index e4d769a6952e..a27ba02bbd70 100644 --- a/modules/nf-core/cafe/meta.yml +++ b/modules/nf-core/cafe/meta.yml @@ -75,9 +75,10 @@ output: - cafe: type: string description: The name of the tool - - echo 5.1.0: - type: eval - description: The expression to obtain the version of the tool + - 5.1.0: + type: string + description: The version of the tool + topics: versions: - - ${task.process}: @@ -86,9 +87,10 @@ topics: - cafe: type: string description: The name of the tool - - echo 5.1.0: - type: eval - description: The expression to obtain the version of the tool + - 5.1.0: + type: string + description: The version of the tool + authors: - "@chriswyatt1" maintainers: From 33ff90891678c3477dbaa8f48811122dc6c17b0c Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:21:00 +0200 Subject: [PATCH 09/25] Update clusty --- modules/nf-core/clusty/main.nf | 2 +- modules/nf-core/clusty/meta.yml | 19 ++++++++++--------- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/modules/nf-core/clusty/main.nf b/modules/nf-core/clusty/main.nf index 9d448b99dd16..9ea0a9451c81 100644 --- a/modules/nf-core/clusty/main.nf +++ b/modules/nf-core/clusty/main.nf @@ -14,7 +14,7 @@ process CLUSTY { output: tuple val(meta), path("*.tsv"), emit: assignments - tuple val("${task.process}"), val('clusty'), eval('echo $(clusty --version 2>&1)'), topic: versions, emit: versions_clusty + tuple val("${task.process}"), val('clusty'), eval("clusty --version"), topic: versions, emit: versions_clusty when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/clusty/meta.yml b/modules/nf-core/clusty/meta.yml index dadd04d488ad..21d1a0a7581d 100644 --- a/modules/nf-core/clusty/meta.yml +++ b/modules/nf-core/clusty/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "clusty" description: Clusty is a tool for large-scale clustering using sparse distance matrices, suitable for datasets with millions of objects. @@ -16,7 +15,8 @@ tools: documentation: "https://github.com/refresh-bio/clusty" tool_dev_url: "https://github.com/refresh-bio/clusty" doi: "10.1038/s41592-025-02701-7" - licence: ["GPL v3-or-later"] + licence: + - "GPL v3-or-later" identifier: "" input: @@ -42,7 +42,6 @@ input: pattern: "*.tsv" ontologies: - edam: "http://edamontology.org/format_3475" # TSV - output: assignments: - - meta: @@ -63,9 +62,10 @@ output: - clusty: type: string description: The name of the tool - - "echo $(clusty --version 2>&1": - type: string - description: The version of the tool + - clusty --version: + type: eval + description: The expression to obtain the version of the tool + topics: versions: - - ${task.process}: @@ -74,9 +74,10 @@ topics: - clusty: type: string description: The name of the tool - - "echo $(clusty --version 2>&1": - type: string - description: The version of the tool + - clusty --version: + type: eval + description: The expression to obtain the version of the tool + authors: - "@Joon-Klaps" maintainers: From 02e3c78065e307d043776c11712e3e73d6e0966c Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:23:07 +0200 Subject: [PATCH 10/25] Update hlala --- modules/nf-core/hlala/preparegraph/main.nf | 5 +++-- modules/nf-core/hlala/preparegraph/meta.yml | 17 ++++++++++------- modules/nf-core/hlala/typing/main.nf | 3 ++- modules/nf-core/hlala/typing/meta.yml | 21 ++++++++++++--------- 4 files changed, 27 insertions(+), 19 deletions(-) diff --git a/modules/nf-core/hlala/preparegraph/main.nf b/modules/nf-core/hlala/preparegraph/main.nf index 68e70afceff2..2b5b8aea122f 100644 --- a/modules/nf-core/hlala/preparegraph/main.nf +++ b/modules/nf-core/hlala/preparegraph/main.nf @@ -12,8 +12,9 @@ process HLALA_PREPAREGRAPH { tuple val(meta), path(graph) output: - tuple val(meta), path("${graph}") , emit: graph - tuple val("${task.process}"), val('hla-la'), eval('echo 1.0.4'), emit: versions_hlala, topic: versions + tuple val(meta), path("${graph}"), emit: graph + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('hla-la'), val('1.0.4'), emit: versions_hlala, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/hlala/preparegraph/meta.yml b/modules/nf-core/hlala/preparegraph/meta.yml index fb3833424a3e..757823aa9d08 100644 --- a/modules/nf-core/hlala/preparegraph/meta.yml +++ b/modules/nf-core/hlala/preparegraph/meta.yml @@ -12,7 +12,8 @@ tools: documentation: "https://github.com/DiltheyLab/HLA-LA#running-hlala" tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" doi: "10.1093/bioinformatics/btz235" - licence: ["GPL"] + licence: + - "GPL" identifier: "" input: - - meta: @@ -40,9 +41,10 @@ output: - hla-la: type: string description: The name of the tool - - echo 1.0.4: - type: eval - description: The expression to obtain the version of the tool + - 1.0.4: + type: string + description: The version of the tool + topics: versions: - - ${task.process}: @@ -51,9 +53,10 @@ topics: - hla-la: type: string description: The name of the tool - - echo 1.0.4: - type: eval - description: The expression to obtain the version of the tool + - 1.0.4: + type: string + description: The version of the tool + authors: - "@mapo9" maintainers: diff --git a/modules/nf-core/hlala/typing/main.nf b/modules/nf-core/hlala/typing/main.nf index 82cb826ec4f7..f6649ebc73d9 100644 --- a/modules/nf-core/hlala/typing/main.nf +++ b/modules/nf-core/hlala/typing/main.nf @@ -21,7 +21,8 @@ process HLALA_TYPING { tuple val(meta), path("${prefix}/reads_per_level.txt") , emit: reads_per_level tuple val(meta), path("${prefix}/remapped_with_a.bam") , emit: remapped tuple val(meta), path("${prefix}/remapped_with_a.bam.bai") , emit: remapped_index - tuple val("${task.process}"), val('hla-la'), eval('echo 1.0.4'), emit: versions_hlala, topic: versions + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('hla-la'), val('1.0.4'), emit: versions_hlala, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/hlala/typing/meta.yml b/modules/nf-core/hlala/typing/meta.yml index 479f486d57a1..b271fcbfc602 100644 --- a/modules/nf-core/hlala/typing/meta.yml +++ b/modules/nf-core/hlala/typing/meta.yml @@ -1,6 +1,6 @@ name: "hlala_typing" -description: Performs HLA typing based on a population reference graph and employs - a new linear projection method to align reads to the graph. +description: Performs HLA typing based on a population reference graph and + employs a new linear projection method to align reads to the graph. keywords: - hla - hlala @@ -13,7 +13,8 @@ tools: documentation: "https://github.com/DiltheyLab/HLA-LA#running-hlala" tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" doi: "10.1093/bioinformatics/btz235" - licence: ["GPL"] + licence: + - "GPL" identifier: "" input: - - meta: @@ -150,9 +151,10 @@ output: - hla-la: type: string description: The name of the tool - - echo 1.0.4: - type: eval - description: The expression to obtain the version of the tool + - 1.0.4: + type: string + description: The version of the tool + topics: versions: - - ${task.process}: @@ -161,9 +163,10 @@ topics: - hla-la: type: string description: The name of the tool - - echo 1.0.4: - type: eval - description: The expression to obtain the version of the tool + - 1.0.4: + type: string + description: The version of the tool + authors: - "@mapo9" maintainers: From bf56d8dae3ef450ebee5a506e08b242fa9fbc368 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:25:58 +0200 Subject: [PATCH 11/25] Update merquryfk --- modules/nf-core/merquryfk/ploidyplot/main.nf | 4 +-- modules/nf-core/merquryfk/ploidyplot/meta.yml | 31 +++++++++++-------- 2 files changed, 20 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/merquryfk/ploidyplot/main.nf b/modules/nf-core/merquryfk/ploidyplot/main.nf index f9bee4df9dc4..23845938bed4 100644 --- a/modules/nf-core/merquryfk/ploidyplot/main.nf +++ b/modules/nf-core/merquryfk/ploidyplot/main.nf @@ -13,9 +13,9 @@ process MERQURYFK_PLOIDYPLOT { output: tuple val(meta), path("*.{png,pdf}"), emit: images // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - tuple val("${task.process}"), val('merquryfk'), eval('echo 1.1.1'), emit: versions_merquryfk, topic: versions + tuple val("${task.process}"), val('merquryfk'), val('1.1.1'), emit: versions_merquryfk, topic: versions // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - tuple val("${task.process}"), val('fastk'), eval('echo 1.1'), emit: versions_fastk, topic: versions + tuple val("${task.process}"), val('fastk'), val('1.1'), emit: versions_fastk, topic: versions tuple val("${task.process}"), val('R'), eval('R --version | sed "1!d; s/.*version //; s/ .*//"'), emit: versions_r, topic: versions when: diff --git a/modules/nf-core/merquryfk/ploidyplot/meta.yml b/modules/nf-core/merquryfk/ploidyplot/meta.yml index 28b373d9ad6b..ba42b00398e1 100644 --- a/modules/nf-core/merquryfk/ploidyplot/meta.yml +++ b/modules/nf-core/merquryfk/ploidyplot/meta.yml @@ -9,7 +9,8 @@ tools: description: "FastK based version of Merqury" homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" - licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + licence: + - "https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE" identifier: "" input: - - meta: @@ -46,9 +47,10 @@ output: - merquryfk: type: string description: The name of the tool - - echo 1.1.1: - type: eval - description: The expression to obtain the version of the tool + - 1.1.1: + type: string + description: The version of the tool + versions_fastk: - - ${task.process}: type: string @@ -56,9 +58,10 @@ output: - fastk: type: string description: The name of the tool - - echo 1.1: - type: eval - description: The expression to obtain the version of the tool + - "1.1": + type: string + description: The version of the tool + versions_r: - - ${task.process}: type: string @@ -77,18 +80,20 @@ topics: - merquryfk: type: string description: The name of the tool - - echo 1.1.1: - type: eval - description: The expression to obtain the version of the tool + - 1.1.1: + type: string + description: The version of the tool + - - ${task.process}: type: string description: The name of the process - fastk: type: string description: The name of the tool - - echo 1.1: - type: eval - description: The expression to obtain the version of the tool + - "1.1": + type: string + description: The version of the tool + - - ${task.process}: type: string description: The name of the process From 30a73b50691380fe101ae37e4e0026eca70e3d1f Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:26:13 +0200 Subject: [PATCH 12/25] Update arcashla --- modules/nf-core/arcashla/extract/meta.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/arcashla/extract/meta.yml b/modules/nf-core/arcashla/extract/meta.yml index 619d42f482a1..729afa41260b 100644 --- a/modules/nf-core/arcashla/extract/meta.yml +++ b/modules/nf-core/arcashla/extract/meta.yml @@ -95,7 +95,7 @@ output: description: The name of the tool - 0.5.0: type: string - description: The expression to obtain the version of the tool + description: The version of the tool topics: versions: @@ -107,7 +107,7 @@ topics: description: The name of the tool - 0.5.0: type: string - description: The expression to obtain the version of the tool + description: The version of the tool authors: - "@christopher-mohr" From d2918f0b6d4e62c261321e7736cc91ea424705c4 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:28:46 +0200 Subject: [PATCH 13/25] Update mitohifi --- .../mitohifi/findmitoreference/main.nf | 2 +- .../mitohifi/findmitoreference/meta.yml | 24 +++++++++------- modules/nf-core/mitohifi/mitohifi/main.nf | 2 +- modules/nf-core/mitohifi/mitohifi/meta.yml | 28 +++++++++++-------- 4 files changed, 33 insertions(+), 23 deletions(-) diff --git a/modules/nf-core/mitohifi/findmitoreference/main.nf b/modules/nf-core/mitohifi/findmitoreference/main.nf index 1e6e8d896921..ebdd46d530ba 100644 --- a/modules/nf-core/mitohifi/findmitoreference/main.nf +++ b/modules/nf-core/mitohifi/findmitoreference/main.nf @@ -19,7 +19,7 @@ process MITOHIFI_FINDMITOREFERENCE { tuple val(meta), path("*.fasta"), path("*.gb"), emit: reference // WARN: Incorrect version information is provided by tool on CLI. Please update this string when bumping container versions. // old version command: \$(mitohifi.py -v | sed 's/.* //') - tuple val("${task.process}"), val('mitohifi'), eval('echo 3.2.3'), emit: versions_mitohifi, topic: versions + tuple val("${task.process}"), val('mitohifi'), val('3.2.3'), emit: versions_mitohifi, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/mitohifi/findmitoreference/meta.yml b/modules/nf-core/mitohifi/findmitoreference/meta.yml index 657c03f0d3fb..039bf91b093b 100644 --- a/modules/nf-core/mitohifi/findmitoreference/meta.yml +++ b/modules/nf-core/mitohifi/findmitoreference/meta.yml @@ -14,12 +14,14 @@ keywords: - NCBI tools: - "findMitoReference.py": - description: Fetch mitochondrial genome in Fasta and Genbank format from NCBI + description: Fetch mitochondrial genome in Fasta and Genbank format from + NCBI homepage: https://github.com/marcelauliano/MitoHiFi documentation: https://github.com/marcelauliano/MitoHiFi tool_dev_url: https://github.com/marcelauliano/MitoHiFi doi: "10.1101/2022.12.23.521667" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:mitohifi input: - - meta: @@ -29,8 +31,8 @@ input: e.g. [ id:'test', single_end:false ] - species: type: string - description: Latin name of the species for which a mitochondrial genome should - be fetched + description: Latin name of the species for which a mitochondrial genome + should be fetched pattern: "[A-Z]?[a-z]* [a-z]*" output: reference: @@ -58,9 +60,10 @@ output: - mitohifi: type: string description: The name of the tool - - echo 3.2.3: - type: eval - description: The expression to obtain the version of the tool + - 3.2.3: + type: string + description: The version of the tool + topics: versions: - - ${task.process}: @@ -69,9 +72,10 @@ topics: - mitohifi: type: string description: The name of the tool - - echo 3.2.3: - type: eval - description: The expression to obtain the version of the tool + - 3.2.3: + type: string + description: The version of the tool + authors: - "@verku" maintainers: diff --git a/modules/nf-core/mitohifi/mitohifi/main.nf b/modules/nf-core/mitohifi/mitohifi/main.nf index 79a9713e9d06..d71a2700bbdf 100644 --- a/modules/nf-core/mitohifi/mitohifi/main.nf +++ b/modules/nf-core/mitohifi/mitohifi/main.nf @@ -32,7 +32,7 @@ process MITOHIFI_MITOHIFI { tuple val(meta), path("*") , emit: all_files // WARN: Incorrect version information is provided by tool on CLI. Please update this string when bumping container versions. // old version command: \$(mitohifi.py -v | sed 's/.* //') - tuple val("${task.process}"), val('mitohifi'), eval('echo 3.2.3'), emit: versions_mitohifi, topic: versions + tuple val("${task.process}"), val('mitohifi'), val('3.2.3'), emit: versions_mitohifi, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/mitohifi/mitohifi/meta.yml b/modules/nf-core/mitohifi/mitohifi/meta.yml index bdbad06a99a5..bb9a20b85b70 100644 --- a/modules/nf-core/mitohifi/mitohifi/meta.yml +++ b/modules/nf-core/mitohifi/mitohifi/meta.yml @@ -12,7 +12,8 @@ tools: documentation: https://github.com/marcelauliano/MitoHiFi tool_dev_url: https://github.com/marcelauliano/MitoHiFi doi: "10.1101/2022.12.23.521667" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:mitohifi input: - - meta: @@ -33,7 +34,8 @@ input: e.g. [ id:'test', single_end:false ] - ref_fa: type: file - description: Reference mitochondrial genome to align reads or contigs against + description: Reference mitochondrial genome to align reads or contigs + against pattern: "*.{fa,fasta}" ontologies: - edam: http://edamontology.org/format_1929 # FASTA @@ -113,7 +115,8 @@ output: e.g. [ id:'test', single_end:false ] - all_potential_contigs.fa: type: file - description: Fasta file containing sequences of all potential mitogenome contigs + description: Fasta file containing sequences of all potential mitogenome + contigs pattern: "all_potential_contigs.fa" ontologies: - edam: http://edamontology.org/format_1929 # FASTA @@ -145,7 +148,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "contigs_filtering/": + - contigs_filtering/: type: directory description: Contains files with initial blast matches pattern: "contigs_filtering/" @@ -155,7 +158,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "coverage_mapping/": + - coverage_mapping/: type: directory description: Contains statistics on coverage mapping pattern: "coverage_mapping/" @@ -215,9 +218,10 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "potential_contigs/": + - potential_contigs/: type: directory - description: Files with sequences and annotations of the potential contigs + description: Files with sequences and annotations of the potential + contigs pattern: "potential_contigs/" reads_mapping_and_assembly: - - meta: @@ -270,9 +274,10 @@ output: - mitohifi: type: string description: The name of the tool - - echo 3.2.3: - type: eval + - 3.2.3: + type: string description: The expression to obtain the version of the tool + topics: versions: - - ${task.process}: @@ -281,9 +286,10 @@ topics: - mitohifi: type: string description: The name of the tool - - echo 3.2.3: - type: eval + - 3.2.3: + type: string description: The expression to obtain the version of the tool + authors: - "@ksenia-krasheninnikova" - "@prototaxites" From a249a49e8281bfe810254c25d05a0c632f242b95 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:30:55 +0200 Subject: [PATCH 14/25] Update rapidnj --- modules/nf-core/rapidnj/main.nf | 3 +-- modules/nf-core/rapidnj/meta.yml | 14 ++++++++------ 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index 393b2cfe4bca..e78c1a91d99a 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -1,7 +1,6 @@ process RAPIDNJ { label 'process_medium' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' : @@ -14,7 +13,7 @@ process RAPIDNJ { path "*.sth" , emit: stockholm_alignment path "*.tre" , emit: phylogeny // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - tuple val("${task.process}"), val('rapidnj'), eval('echo 2.3.2'), emit: versions_rapidnj, topic: versions + tuple val("${task.process}"), val('rapidnj'), val('2.3.2'), emit: versions_rapidnj, topic: versions tuple val("${task.process}"), val('biopython'), eval('python -c "import Bio; print(Bio.__version__)"'), emit: versions_biopython, topic: versions when: diff --git a/modules/nf-core/rapidnj/meta.yml b/modules/nf-core/rapidnj/meta.yml index fae727a4d533..6fd0a067c353 100644 --- a/modules/nf-core/rapidnj/meta.yml +++ b/modules/nf-core/rapidnj/meta.yml @@ -46,9 +46,10 @@ output: - rapidnj: type: string description: The name of the tool - - echo 2.3.2: - type: eval - description: The expression to obtain the version of the tool + - 2.3.2: + type: string + description: The version of the tool + versions_biopython: - - ${task.process}: type: string @@ -67,9 +68,10 @@ topics: - rapidnj: type: string description: The name of the tool - - echo 2.3.2: - type: eval - description: The expression to obtain the version of the tool + - 2.3.2: + type: string + description: The version of the tool + - - ${task.process}: type: string description: The name of the process From 469d952117fecf058c0058128c508162e9eb1a64 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:32:02 +0200 Subject: [PATCH 15/25] Update slimfastq --- modules/nf-core/slimfastq/main.nf | 4 ++-- modules/nf-core/slimfastq/meta.yml | 14 ++++++++------ 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index 7a4f337e6f0a..5e321f977bc0 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -2,7 +2,6 @@ process SLIMFASTQ { tag "$meta.id" label 'process_low' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2': @@ -13,7 +12,8 @@ process SLIMFASTQ { output: tuple val(meta), path("*.sfq"), emit: sfq - tuple val("${task.process}"), val('slimfastq'), eval('echo 2.04'), emit: versions_slimfastq, topic: versions + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('slimfastq'), val('2.04'), emit: versions_slimfastq, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/slimfastq/meta.yml b/modules/nf-core/slimfastq/meta.yml index d48fae1511b5..e3c28db198b6 100644 --- a/modules/nf-core/slimfastq/meta.yml +++ b/modules/nf-core/slimfastq/meta.yml @@ -43,9 +43,10 @@ output: - slimfastq: type: string description: The name of the tool - - echo 2.04: - type: eval - description: The expression to obtain the version of the tool + - "2.04": + type: string + description: The version of the tool + topics: versions: - - ${task.process}: @@ -54,9 +55,10 @@ topics: - slimfastq: type: string description: The name of the tool - - echo 2.04: - type: eval - description: The expression to obtain the version of the tool + - "2.04": + type: string + description: The version of the tool + authors: - "@Midnighter" maintainers: From 9443e0010f8e725eb306a302ab7722864d3e3132 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 19 Jun 2026 15:32:59 +0200 Subject: [PATCH 16/25] Update telseq --- modules/nf-core/telseq/main.nf | 3 ++- modules/nf-core/telseq/meta.yml | 28 ++++++++++++++++------------ 2 files changed, 18 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/telseq/main.nf b/modules/nf-core/telseq/main.nf index 77c0b79aab91..b18a6bf2a9d9 100644 --- a/modules/nf-core/telseq/main.nf +++ b/modules/nf-core/telseq/main.nf @@ -13,7 +13,8 @@ process TELSEQ { output: tuple val(meta), path("*.telseq.tsv"), emit: output - tuple val("${task.process}"), val('telseq'), eval('echo 0.0.2'), emit: versions_telseq, topic: versions + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('telseq'), val('0.0.2'), emit: versions_telseq, topic: versions tuple val("${task.process}"), val('samtools'), eval("samtools --version | sed -n '1s/samtools //p'"), emit: versions_samtools, topic: versions when: diff --git a/modules/nf-core/telseq/meta.yml b/modules/nf-core/telseq/meta.yml index 4cedd96018a0..8f2af8894678 100644 --- a/modules/nf-core/telseq/meta.yml +++ b/modules/nf-core/telseq/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "telseq" description: "Telseq: a software for calculating telomere length" keywords: @@ -15,7 +14,8 @@ tools: documentation: "https://github.com/zd1/telseq" tool_dev_url: "https://github.com/zd1/telseq" doi: "10.1093/nar/gku181" - licence: ["GPL v3"] + licence: + - "GPL v3" args_id: "$args" identifier: "" - samtools: @@ -24,7 +24,8 @@ tools: documentation: http://www.htslib.org/doc/samtools.html tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 - licence: ["MIT"] + licence: + - "MIT" identifier: "biotools:samtools" input: - - meta: @@ -44,7 +45,8 @@ input: ontologies: [] - bed: type: file - description: Optional exome regions in BED format. These regions will be excluded + description: Optional exome regions in BED format. These regions will be + excluded pattern: "*.bed" ontologies: [] - - meta2: @@ -82,9 +84,10 @@ output: - telseq: type: string description: The name of the tool - - "echo 0.0.2": - type: eval - description: The expression to obtain the version of telseq + - 0.0.2: + type: string + description: The version of the tool + versions_samtools: - - ${task.process}: type: string @@ -92,7 +95,7 @@ output: - samtools: type: string description: The name of the tool - - "samtools --version | sed -n '1s/samtools //p'": + - samtools --version | sed -n '1s/samtools //p': type: eval description: The expression to obtain the version of samtools topics: @@ -103,16 +106,17 @@ topics: - telseq: type: string description: The name of the tool - - "echo 0.0.2": - type: eval - description: The expression to obtain the version of telseq + - 0.0.2: + type: string + description: The version of the tool + - - ${task.process}: type: string description: The name of the process - samtools: type: string description: The name of the tool - - "samtools --version | sed -n '1s/samtools //p'": + - samtools --version | sed -n '1s/samtools //p': type: eval description: The expression to obtain the version of samtools authors: From 23f0ef786fa4bcebafde831c4e1d9149070c898c Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Mon, 22 Jun 2026 19:05:24 +0200 Subject: [PATCH 17/25] Fix ataqv --- modules/nf-core/ataqv/ataqv/main.nf | 2 +- modules/nf-core/ataqv/ataqv/meta.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index aadd44eef110..62bb0f358554 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -18,7 +18,7 @@ process ATAQV_ATAQV { output: tuple val(meta), path("*.ataqv.json"), emit: json tuple val(meta), path("*.problems") , emit: problems, optional: true - tuple val("${task.process}"), val('ataqv'), eval("ataqv --version"), emit: versions_ataqv, topic: versions + tuple val("${task.process}"), val('ataqv'), eval("ataqv --version 2>&1 || true"), emit: versions_ataqv, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ataqv/ataqv/meta.yml b/modules/nf-core/ataqv/ataqv/meta.yml index dbcf210e21fc..001a8d992cf9 100644 --- a/modules/nf-core/ataqv/ataqv/meta.yml +++ b/modules/nf-core/ataqv/ataqv/meta.yml @@ -99,7 +99,7 @@ output: - ataqv: type: string description: The name of the tool - - ataqv --version: + - ataqv --version 2>&1 || true: type: eval description: The expression to obtain the version of the tool @@ -111,7 +111,7 @@ topics: - ataqv: type: string description: The name of the tool - - ataqv --version: + - ataqv --version 2>&1 || true: type: eval description: The expression to obtain the version of the tool From 310bd46c52bad63690693435964bfa67b32a094f Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Mon, 22 Jun 2026 19:23:22 +0200 Subject: [PATCH 18/25] Fix errors --- modules/nf-core/ataqv/mkarv/main.nf | 2 +- modules/nf-core/ataqv/mkarv/meta.yml | 4 ++-- modules/nf-core/clusty/main.nf | 2 +- modules/nf-core/clusty/meta.yml | 4 ++-- modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap | 6 ++---- modules/nf-core/links/main.nf | 2 +- modules/nf-core/links/meta.yml | 4 ++-- 7 files changed, 11 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index cf812d6138ac..2727062a462a 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -11,7 +11,7 @@ process ATAQV_MKARV { output: path "html" , emit: html - tuple val("${task.process}"), val('ataqv'), eval("ataqv --version"), emit: versions_ataqv, topic: versions + tuple val("${task.process}"), val('ataqv'), eval("ataqv --version 2>&1 || true"), emit: versions_ataqv, topic: versions // tuple val("${task.process}"), val('mkarv'), eval('mkarv --version'), emit: versions_mkarv, topic: versions //Use this when version string has been fixed when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ataqv/mkarv/meta.yml b/modules/nf-core/ataqv/mkarv/meta.yml index 11bec4337606..6ab6b3ce698c 100644 --- a/modules/nf-core/ataqv/mkarv/meta.yml +++ b/modules/nf-core/ataqv/mkarv/meta.yml @@ -37,7 +37,7 @@ output: - ataqv: type: string description: The name of the tool - - ataqv --version: + - ataqv --version 2>&1 || true: type: eval description: The expression to obtain the version of the tool @@ -59,7 +59,7 @@ topics: - ataqv: type: string description: The name of the tool - - ataqv --version: + - ataqv --version 2>&1 || true: type: eval description: The expression to obtain the version of the tool diff --git a/modules/nf-core/clusty/main.nf b/modules/nf-core/clusty/main.nf index 9ea0a9451c81..c0eeec3ebda9 100644 --- a/modules/nf-core/clusty/main.nf +++ b/modules/nf-core/clusty/main.nf @@ -14,7 +14,7 @@ process CLUSTY { output: tuple val(meta), path("*.tsv"), emit: assignments - tuple val("${task.process}"), val('clusty'), eval("clusty --version"), topic: versions, emit: versions_clusty + tuple val("${task.process}"), val('clusty'), eval("clusty --version 2>&1 || true"), topic: versions, emit: versions_clusty when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/clusty/meta.yml b/modules/nf-core/clusty/meta.yml index 21d1a0a7581d..4bbeee78e817 100644 --- a/modules/nf-core/clusty/meta.yml +++ b/modules/nf-core/clusty/meta.yml @@ -62,7 +62,7 @@ output: - clusty: type: string description: The name of the tool - - clusty --version: + - clusty --version 2>&1 || true: type: eval description: The expression to obtain the version of the tool @@ -74,7 +74,7 @@ topics: - clusty: type: string description: The name of the tool - - clusty --version: + - clusty --version 2>&1 || true: type: eval description: The expression to obtain the version of the tool diff --git a/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap b/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap index c649d88804e5..06025f53735e 100644 --- a/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap +++ b/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap @@ -219,8 +219,7 @@ "unzip/test/PRG_test/serializedGRAPH", "unzip/test/PRG_test/serializedGRAPH_preGapPathIndex", "unzip/test/PRG_test/translation", - "unzip/test/PRG_test/translation/100.txt", - "unzip/versions.yml" + "unzip/test/PRG_test/translation/100.txt" ], [ ".nextflow.log:md5,f22b6ca679424bea221fe100b4162b4a", @@ -262,8 +261,7 @@ "sequences.txt:md5,61a3df2ca23dbe8d35c65944784def76", "serializedGRAPH:md5,a88016a601377a967feb04c1bbeeba65", "serializedGRAPH_preGapPathIndex:md5,65ea9cd52a00ffd51a2460c6887b277e", - "100.txt:md5,8dd91725d9a2f1f71a82ae1d190aa840", - "versions.yml:md5,52c55ce814e8bc9edc5a6c625ed794b8" + "100.txt:md5,8dd91725d9a2f1f71a82ae1d190aa840" ] ], "meta": { diff --git a/modules/nf-core/links/main.nf b/modules/nf-core/links/main.nf index 3936b81d1560..7ba89f0888e1 100644 --- a/modules/nf-core/links/main.nf +++ b/modules/nf-core/links/main.nf @@ -22,7 +22,7 @@ process LINKS { tuple val(meta), path("*.assembly_correspondence.tsv"), emit: assembly_correspondence tuple val(meta), path("*.simplepair_checkpoint.tsv"), emit: simplepair_checkpoint, optional: true tuple val(meta), path("*.tigpair_checkpoint.tsv"), emit: tigpair_checkpoint - tuple val("${task.process}"), val('liftoff'), eval("LINKS | sed -n 's/LINKS v//p'"), emit: versions_links, topic: versions + tuple val("${task.process}"), val('liftoff'), eval("LINKS | sed -n 's/.*LINKS v//p'"), emit: versions_links, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/links/meta.yml b/modules/nf-core/links/meta.yml index 021d3cfb84ff..c9d57c1c3f96 100644 --- a/modules/nf-core/links/meta.yml +++ b/modules/nf-core/links/meta.yml @@ -187,7 +187,7 @@ output: - liftoff: type: string description: The name of the tool - - LINKS | sed -n 's/LINKS v//p': + - LINKS | sed -n 's/.*LINKS v//p': type: eval description: The expression to obtain the version of the tool @@ -199,7 +199,7 @@ topics: - liftoff: type: string description: The name of the tool - - LINKS | sed -n 's/LINKS v//p': + - LINKS | sed -n 's/.*LINKS v//p': type: eval description: The expression to obtain the version of the tool From 9359fd72087fb9b90d1984221c2741dea9dfd6d5 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Mon, 22 Jun 2026 20:07:44 +0200 Subject: [PATCH 19/25] Update links --- modules/nf-core/links/main.nf | 2 +- modules/nf-core/links/meta.yml | 4 ++-- modules/nf-core/links/tests/main.nf.test.snap | 18 +++++++++--------- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/links/main.nf b/modules/nf-core/links/main.nf index 7ba89f0888e1..607e6f77b406 100644 --- a/modules/nf-core/links/main.nf +++ b/modules/nf-core/links/main.nf @@ -22,7 +22,7 @@ process LINKS { tuple val(meta), path("*.assembly_correspondence.tsv"), emit: assembly_correspondence tuple val(meta), path("*.simplepair_checkpoint.tsv"), emit: simplepair_checkpoint, optional: true tuple val(meta), path("*.tigpair_checkpoint.tsv"), emit: tigpair_checkpoint - tuple val("${task.process}"), val('liftoff'), eval("LINKS | sed -n 's/.*LINKS v//p'"), emit: versions_links, topic: versions + tuple val("${task.process}"), val('liftoff'), eval("LINKS | sed '/LINKS/!d;s/.*LINKS v//;s/ .*//'"), emit: versions_links, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/links/meta.yml b/modules/nf-core/links/meta.yml index c9d57c1c3f96..10457ae635d2 100644 --- a/modules/nf-core/links/meta.yml +++ b/modules/nf-core/links/meta.yml @@ -187,7 +187,7 @@ output: - liftoff: type: string description: The name of the tool - - LINKS | sed -n 's/.*LINKS v//p': + - LINKS | sed '/LINKS/!d;s/.*LINKS v//;s/ .*//': type: eval description: The expression to obtain the version of the tool @@ -199,7 +199,7 @@ topics: - liftoff: type: string description: The name of the tool - - LINKS | sed -n 's/.*LINKS v//p': + - LINKS | sed '/LINKS/!d;s/.*LINKS v//;s/ .*//': type: eval description: The expression to obtain the version of the tool diff --git a/modules/nf-core/links/tests/main.nf.test.snap b/modules/nf-core/links/tests/main.nf.test.snap index a7870de45e2c..1a2216c7fa7e 100644 --- a/modules/nf-core/links/tests/main.nf.test.snap +++ b/modules/nf-core/links/tests/main.nf.test.snap @@ -47,10 +47,10 @@ ] } ], - "timestamp": "2026-02-17T16:35:15.663121765", + "timestamp": "2026-06-22T20:05:59.416630407", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.04.8" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "LINKS - stub": { @@ -232,10 +232,10 @@ ] } ], - "timestamp": "2026-02-16T11:20:02.239712752", + "timestamp": "2026-06-22T20:06:07.774638412", "meta": { - "nf-test": "0.9.4", - "nextflow": "26.01.1" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "LINKS - sarscov2 test data - contigs": { @@ -286,10 +286,10 @@ ] } ], - "timestamp": "2026-02-17T10:53:57.921992204", + "timestamp": "2026-06-22T20:05:49.786953783", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.04.8" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file From 0c9d80f4f9b63e842ee18472277e9130e4608bc2 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Mon, 22 Jun 2026 21:30:56 +0200 Subject: [PATCH 20/25] Update bamcmp --- modules/nf-core/bamcmp/environment.yml | 2 +- modules/nf-core/bamcmp/main.nf | 4 +- modules/nf-core/bamcmp/tests/main.nf.test | 2 +- .../nf-core/bamcmp/tests/main.nf.test.snap | 50 ++++--------------- 4 files changed, 14 insertions(+), 44 deletions(-) diff --git a/modules/nf-core/bamcmp/environment.yml b/modules/nf-core/bamcmp/environment.yml index 52e9a688d483..4b6cefa587dd 100644 --- a/modules/nf-core/bamcmp/environment.yml +++ b/modules/nf-core/bamcmp/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: - bioconda::bamcmp=2.2 - - bioconda::samtools=1.23 + - bioconda::samtools=1.23.1 diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index 9815312d9950..4a53cb6f1640 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -3,8 +3,8 @@ process BAMCMP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e5ee3676abe7e65f65eca55e8dbc76f4dd195a44679cd1a785943d7a0d598f1/data' : - 'community.wave.seqera.io/library/bamcmp_samtools:2f211ea999bb54f5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2bff3af963e5095327f326b428e917bd431b18ccaa4a977135f2bc4a0174a5aa/data' : + 'community.wave.seqera.io/library/bamcmp_samtools:c59f681ef07a5b74' }" input: tuple val(meta), path(primary_aligned_bam), path(contaminant_aligned_bam) diff --git a/modules/nf-core/bamcmp/tests/main.nf.test b/modules/nf-core/bamcmp/tests/main.nf.test index e1bf6cbfac6a..8aab8abe29ce 100644 --- a/modules/nf-core/bamcmp/tests/main.nf.test +++ b/modules/nf-core/bamcmp/tests/main.nf.test @@ -102,7 +102,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/bamcmp/tests/main.nf.test.snap b/modules/nf-core/bamcmp/tests/main.nf.test.snap index df943e2b2e9e..e2eef0218186 100644 --- a/modules/nf-core/bamcmp/tests/main.nf.test.snap +++ b/modules/nf-core/bamcmp/tests/main.nf.test.snap @@ -15,50 +15,20 @@ [ "BAMCMP", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-06-22T21:25:33.376806465", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-23T08:33:48.801733878" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "bamcmp - stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test_primary.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test_contaminant.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "BAMCMP", - "bamcmp", - "2.2" - ] - ], - "3": [ - [ - "BAMCMP", - "samtools", - "1.23" - ] - ], "contamination_bam": [ [ { @@ -86,15 +56,15 @@ [ "BAMCMP", "samtools", - "1.23" + "1.23.1" ] ] } ], + "timestamp": "2026-06-22T21:30:09.012984284", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-23T08:33:55.698960334" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file From 740e90e8e89cfb71d664fd75e7ea0c87bec62d4a Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Mon, 22 Jun 2026 22:40:34 +0200 Subject: [PATCH 21/25] Update hlala --- modules/nf-core/hlala/preparegraph/tests/main.nf.test | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/hlala/preparegraph/tests/main.nf.test b/modules/nf-core/hlala/preparegraph/tests/main.nf.test index 429e32a45cf5..d70f6511d368 100644 --- a/modules/nf-core/hlala/preparegraph/tests/main.nf.test +++ b/modules/nf-core/hlala/preparegraph/tests/main.nf.test @@ -42,7 +42,11 @@ nextflow_process { def stable_content = getAllFilesFromDir(outputDir, ignore: ['**/referenceGenome.fa.{bwt,pac,sa}','**/referenceGenome.fa_bowtie2idx*']) assertAll( { assert process.success }, - { assert snapshot(stable_name,stable_content).match() } + { assert snapshot( + stable_name, + stable_content, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } @@ -78,7 +82,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } From f11f21a896302d81a324a6cdd215e117c3bdd89f Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Tue, 23 Jun 2026 09:48:20 +0200 Subject: [PATCH 22/25] Update hlala --- .../preparegraph/tests/main.nf.test.snap | 89 ++++--------------- 1 file changed, 18 insertions(+), 71 deletions(-) diff --git a/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap b/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap index 06025f53735e..e101a0580370 100644 --- a/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap +++ b/modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap @@ -2,68 +2,6 @@ "homo_sapiens - prg - stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - [ - [ - "100_gene_HLA-A_9_exon_5.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "100_gene_HLA-A_9_exon_5.txt.graph:md5,d41d8cd98f00b204e9800998ecf8427e", - "graph.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "positions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "segments.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "extendedReferenceGenome.fa:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "1000G_B37_noChr.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "1000G_B38.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "B37_generic_noChr.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "PRG_MHC_GRCh38_withIMGT.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "100.fa:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "check_refSequence_length.pl:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa.amb:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa.ann:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa.pac:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa.sa:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa_bowtie2idx.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa_bowtie2idx.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa_bowtie2idx.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa_bowtie2idx.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa_bowtie2idx.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", - "referenceGenome.fa_bowtie2idx.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - - ], - [ - - ], - "sequences.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "serializedGRAPH:md5,d41d8cd98f00b204e9800998ecf8427e", - "serializedGRAPH_preGapPathIndex:md5,d41d8cd98f00b204e9800998ecf8427e", - [ - "100.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] - ], - "1": [ - [ - "HLALA_PREPAREGRAPH", - "hla-la", - "1.0.4" - ] - ], "graph": [ [ { @@ -128,11 +66,11 @@ ] } ], + "timestamp": "2026-06-22T23:06:07.873826521", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-04-23T20:25:20.521118567" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "homo_sapiens - prg": { "content": [ @@ -262,12 +200,21 @@ "serializedGRAPH:md5,a88016a601377a967feb04c1bbeeba65", "serializedGRAPH_preGapPathIndex:md5,65ea9cd52a00ffd51a2460c6887b277e", "100.txt:md5,8dd91725d9a2f1f71a82ae1d190aa840" - ] + ], + { + "versions_hlala": [ + [ + "HLALA_PREPAREGRAPH", + "hla-la", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-06-22T23:06:00.1838722", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-04-23T20:24:57.389656201" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file From 4a5464c1833a66a9d4c170476ebd863084cc8fef Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Tue, 23 Jun 2026 12:02:43 +0200 Subject: [PATCH 23/25] Add registry --- .nf-core.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.nf-core.yml b/.nf-core.yml index 0a298adfcb4b..b93759701b57 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,5 +1,7 @@ repository_type: modules org_path: nf-core +container-registry: + - ghcr.io/ bump-versions: rseqc/junctionannotation: False rseqc/bamstat: False From 19e696b4b0baeb3c7e84d02a7c91d591788bc60e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Louis=20Le=20N=C3=A9zet?= <58640615+LouisLeNezet@users.noreply.github.com> Date: Tue, 23 Jun 2026 12:08:09 +0200 Subject: [PATCH 24/25] Update .nf-core.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index b93759701b57..233ef5ed2fde 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,7 +1,7 @@ repository_type: modules org_path: nf-core container-registry: - - ghcr.io/ + - ghcr.io/marcelauliano/ bump-versions: rseqc/junctionannotation: False rseqc/bamstat: False From 158173e75557e0da11f83d5e8f117df5974c920d Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Tue, 23 Jun 2026 12:11:44 +0200 Subject: [PATCH 25/25] Add missing registry --- .nf-core.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.nf-core.yml b/.nf-core.yml index 233ef5ed2fde..dfecacdb4a69 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,6 +2,9 @@ repository_type: modules org_path: nf-core container-registry: - ghcr.io/marcelauliano/ + - ghcr.io/schapirolabor + - ghcr.io/nbisweden + - ghcr.io/scverse bump-versions: rseqc/junctionannotation: False rseqc/bamstat: False