From 411df34906e633146e9ac663f00af1282927941b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 12:04:52 +0200 Subject: [PATCH 01/25] nf-core lint --- modules.json | 320 +++++++++++++++++++++++++-------------------------- 1 file changed, 160 insertions(+), 160 deletions(-) diff --git a/modules.json b/modules.json index 804374e532..1bc4a78c8b 100644 --- a/modules.json +++ b/modules.json @@ -6,324 +6,324 @@ "git_url": "https://github.com/nf-core/modules.git", "modules": { "ascat": { - "git_sha": "98ffb090029d17a9fb8de75dadcfe6bc8b6377ec", - "branch": "master" + "branch": "master", + "git_sha": "98ffb090029d17a9fb8de75dadcfe6bc8b6377ec" }, "bcftools/sort": { - "git_sha": "682f789f93070bd047868300dd018faf3d434e7c", - "branch": "master" + "branch": "master", + "git_sha": "682f789f93070bd047868300dd018faf3d434e7c" }, "bcftools/stats": { - "git_sha": "535975eb81c9e48eb0403c136b7f1dd7acb1afad", - "branch": "master" + "branch": "master", + "git_sha": "535975eb81c9e48eb0403c136b7f1dd7acb1afad" }, "bwa/index": { - 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"git_sha": "6b011dd14821385c282e030c6d993d2116aed23f", - "branch": "master" + "branch": "master", + "git_sha": "6b011dd14821385c282e030c6d993d2116aed23f" }, "tabix/bgziptabix": { - "git_sha": "9dbaffff88013bc21460a989cde7a5aa172c2e0b", - "branch": "master" + "branch": "master", + "git_sha": "9dbaffff88013bc21460a989cde7a5aa172c2e0b" }, "tabix/tabix": { - "git_sha": "b3e9b88e80880f450ad79a95b2b7aa05e1de5484", - "branch": "master" + "branch": "master", + "git_sha": "b3e9b88e80880f450ad79a95b2b7aa05e1de5484" }, "tiddit/sv": { - "git_sha": "b689b8ed88a9f89eb2f7c75d3eb0bace77ade109", - "branch": "master" + "branch": "master", + "git_sha": "b689b8ed88a9f89eb2f7c75d3eb0bace77ade109" }, "untar": { - "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5", - "branch": "master" + "branch": "master", + "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5" }, "unzip": { - "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918", - "branch": "master" + "branch": "master", + "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918" }, "vcftools": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" + "branch": "master", + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" } } } From 47ce0eecfbac431397b1bf673efa88d8a9655ea8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 12:05:50 +0200 Subject: [PATCH 02/25] nf-core modules update -a --- modules.json | 44 +++++++++---------- .../nf-core/modules/bcftools/stats/main.nf | 2 +- modules/nf-core/modules/bwamem2/index/main.nf | 6 +-- .../nf-core/modules/bwamem2/index/meta.yml | 12 ++++- modules/nf-core/modules/bwamem2/mem/main.nf | 2 +- modules/nf-core/modules/bwamem2/mem/meta.yml | 5 +++ modules/nf-core/modules/cat/fastq/main.nf | 29 ++++++++++++ .../custom/dumpsoftwareversions/main.nf | 2 +- .../templates/dumpsoftwareversions.py | 14 +++--- .../nf-core/modules/fgbio/fastqtobam/main.nf | 20 +++++---- .../nf-core/modules/fgbio/fastqtobam/meta.yml | 20 ++++----- .../modules/gatk4/markduplicates/main.nf | 21 ++++++--- .../modules/gatk4/markduplicates/meta.yml | 20 +++++++++ .../nf-core/modules/manta/germline/main.nf | 2 +- modules/nf-core/modules/manta/somatic/main.nf | 2 +- .../nf-core/modules/manta/tumoronly/main.nf | 2 +- .../nf-core/modules/samtools/convert/main.nf | 2 +- .../nf-core/modules/samtools/faidx/main.nf | 3 +- .../nf-core/modules/samtools/mpileup/main.nf | 2 +- .../nf-core/modules/samtools/stats/main.nf | 4 +- modules/nf-core/modules/samtools/view/main.nf | 2 +- .../nf-core/modules/strelka/germline/main.nf | 2 +- .../nf-core/modules/strelka/somatic/main.nf | 2 +- .../nf-core/modules/tabix/bgziptabix/main.nf | 2 +- modules/nf-core/modules/tabix/tabix/main.nf | 2 +- modules/nf-core/modules/untar/main.nf | 2 +- modules/nf-core/modules/unzip/main.nf | 2 +- modules/nf-core/modules/vcftools/main.nf | 2 +- 28 files changed, 151 insertions(+), 79 deletions(-) diff --git a/modules.json b/modules.json index 1bc4a78c8b..24231e3870 100644 --- a/modules.json +++ b/modules.json @@ -15,7 +15,7 @@ }, "bcftools/stats": { "branch": "master", - "git_sha": "535975eb81c9e48eb0403c136b7f1dd7acb1afad" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "bwa/index": { "branch": "master", @@ -27,11 +27,11 @@ }, "bwamem2/index": { "branch": "master", - "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe" + "git_sha": "d0ff29fca32ba795177584ebfd51dcd6b0d5f890" }, "bwamem2/mem": { "branch": "master", - "git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9" + "git_sha": "30b04859129f5f4235accdea9fdea8f1feb23809" }, "cat/cat": { "branch": "master", @@ -39,7 +39,7 @@ }, "cat/fastq": { "branch": "master", - "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9" + "git_sha": "b034029b59b1198075da8019074bc02051a6100e" }, "cnvkit/antitarget": { "branch": "master", @@ -75,7 +75,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "e5b44499efcf6f7fb24874886bac60591c5d94dd" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "deepvariant": { "branch": "master", @@ -107,7 +107,7 @@ }, "fgbio/fastqtobam": { "branch": "master", - "git_sha": "6720d88f4e46e67b9a225f06bfb10c8e8ae04a84" + "git_sha": "36049bf544c2f3fad7508778b76f56c5e0fe1ee7" }, "fgbio/groupreadsbyumi": { "branch": "master", @@ -195,7 +195,7 @@ }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "df2620cfc7e4c21b14ed03c1c928f09fbabf83c4" + "git_sha": "e726b1730dff525bde4a6839e544dabfea4cd7fd" }, "gatk4/markduplicatesspark": { "branch": "master", @@ -219,15 +219,15 @@ }, "manta/germline": { "branch": "master", - "git_sha": "ffedf09b6e84b479c9c901274f74bb33f3777243" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "manta/somatic": { "branch": "master", - "git_sha": "979e57b7ac6a405a395dd7a6dbe1a275c5bc226b" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "manta/tumoronly": { "branch": "master", - "git_sha": "979e57b7ac6a405a395dd7a6dbe1a275c5bc226b" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "mosdepth": { "branch": "master", @@ -259,11 +259,11 @@ }, "samtools/convert": { "branch": "master", - "git_sha": "da79396f066a96450d9cc9f115c17c9d738595fd" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "samtools/faidx": { "branch": "master", - "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "samtools/index": { "branch": "master", @@ -275,15 +275,15 @@ }, "samtools/mpileup": { "branch": "master", - "git_sha": "454e0acc09de7cdcc90007420bfe8afa251286fb" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "samtools/stats": { "branch": "master", - "git_sha": "f48a24770e24358e58de66e9b805a70d77cd154b" + "git_sha": "f4eab7945952dc4934224309701a49913ea05ae6" }, "samtools/view": { "branch": "master", - "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "snpeff": { "branch": "master", @@ -291,11 +291,11 @@ }, "strelka/germline": { "branch": "master", - "git_sha": "e5b44499efcf6f7fb24874886bac60591c5d94dd" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "strelka/somatic": { "branch": "master", - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "svdb/merge": { "branch": "master", @@ -303,11 +303,11 @@ }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "9dbaffff88013bc21460a989cde7a5aa172c2e0b" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "tabix/tabix": { "branch": "master", - "git_sha": "b3e9b88e80880f450ad79a95b2b7aa05e1de5484" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "tiddit/sv": { "branch": "master", @@ -315,15 +315,15 @@ }, "untar": { "branch": "master", - "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "unzip": { "branch": "master", - "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" }, "vcftools": { "branch": "master", - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" + "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247" } } } diff --git a/modules/nf-core/modules/bcftools/stats/main.nf b/modules/nf-core/modules/bcftools/stats/main.nf index c42ed29a8e..95251d13a9 100644 --- a/modules/nf-core/modules/bcftools/stats/main.nf +++ b/modules/nf-core/modules/bcftools/stats/main.nf @@ -1,6 +1,6 @@ process BCFTOOLS_STATS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/bwamem2/index/main.nf b/modules/nf-core/modules/bwamem2/index/main.nf index 900f27d472..6b63ea59a8 100644 --- a/modules/nf-core/modules/bwamem2/index/main.nf +++ b/modules/nf-core/modules/bwamem2/index/main.nf @@ -8,11 +8,11 @@ process BWAMEM2_INDEX { 'quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0' }" input: - path fasta + tuple val(meta), path(fasta) output: - path "bwamem2" , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("bwamem2"), emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/modules/bwamem2/index/meta.yml b/modules/nf-core/modules/bwamem2/index/meta.yml index 1b52448d0e..a6b11ae5fd 100644 --- a/modules/nf-core/modules/bwamem2/index/meta.yml +++ b/modules/nf-core/modules/bwamem2/index/meta.yml @@ -14,14 +14,24 @@ tools: documentation: https://github.com/bwa-mem2/bwa-mem2#usage licence: ["MIT"] input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Input genome fasta file output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - index: type: file description: BWA genome index files - pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}" + pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/modules/bwamem2/mem/main.nf b/modules/nf-core/modules/bwamem2/mem/main.nf index 978c4019b6..08dc5dfb8c 100644 --- a/modules/nf-core/modules/bwamem2/mem/main.nf +++ b/modules/nf-core/modules/bwamem2/mem/main.nf @@ -9,7 +9,7 @@ process BWAMEM2_MEM { input: tuple val(meta), path(reads) - path index + tuple val(meta2), path(index) val sort_bam output: diff --git a/modules/nf-core/modules/bwamem2/mem/meta.yml b/modules/nf-core/modules/bwamem2/mem/meta.yml index 25c97f91fe..a465551048 100644 --- a/modules/nf-core/modules/bwamem2/mem/meta.yml +++ b/modules/nf-core/modules/bwamem2/mem/meta.yml @@ -37,6 +37,11 @@ input: description: use samtools sort (true) or samtools view (false) pattern: "true or false" output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - bam: type: file description: Output BAM file containing read alignments diff --git a/modules/nf-core/modules/cat/fastq/main.nf b/modules/nf-core/modules/cat/fastq/main.nf index b685489596..d275f19c1e 100644 --- a/modules/nf-core/modules/cat/fastq/main.nf +++ b/modules/nf-core/modules/cat/fastq/main.nf @@ -48,4 +48,33 @@ process CAT_FASTQ { """ } } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def readList = reads.collect{ it.toString() } + if (meta.single_end) { + if (readList.size > 1) { + """ + touch ${prefix}.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } else { + if (readList.size > 2) { + """ + touch ${prefix}_1.merged.fastq.gz + touch ${prefix}_2.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } + } diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf index 203e485aec..34b50b9f84 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf @@ -1,5 +1,5 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_low' + label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null) diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index 787bdb7b1b..d139039254 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -1,10 +1,9 @@ #!/usr/bin/env python +import yaml import platform from textwrap import dedent -import yaml - def _make_versions_html(versions): html = [ @@ -59,12 +58,11 @@ def _make_versions_html(versions): for process, process_versions in versions_by_process.items(): module = process.split(":")[-1] try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) + assert versions_by_module[module] == process_versions, ( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) except KeyError: versions_by_module[module] = process_versions diff --git a/modules/nf-core/modules/fgbio/fastqtobam/main.nf b/modules/nf-core/modules/fgbio/fastqtobam/main.nf index 76cfc0752d..a3279491cf 100644 --- a/modules/nf-core/modules/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/modules/fgbio/fastqtobam/main.nf @@ -9,11 +9,11 @@ process FGBIO_FASTQTOBAM { input: tuple val(meta), path(reads) - val read_structure output: - tuple val(meta), path("*_umi_converted.bam"), emit: umibam - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam") , emit: bam , optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -21,17 +21,19 @@ process FGBIO_FASTQTOBAM { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def sample_name = args.contains("--sample") ? "" : "--sample ${prefix}" + def library_name = args.contains("--library") ? "" : "--library ${prefix}" + def output = prefix =~ /\.(bam|cram)$/ ? prefix : "${prefix}.bam" """ fgbio \\ --tmp-dir=. \\ FastqToBam \\ - -i $reads \\ - -o "${prefix}_umi_converted.bam" \\ - --read-structures $read_structure \\ - --sample $meta.id \\ - --library $meta.id \\ - $args + ${args} \\ + --input ${reads} \\ + --output ${output} \\ + ${sample_name} \\ + ${library_name} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/modules/fgbio/fastqtobam/meta.yml b/modules/nf-core/modules/fgbio/fastqtobam/meta.yml index 3081cafc83..6769fc1521 100644 --- a/modules/nf-core/modules/fgbio/fastqtobam/meta.yml +++ b/modules/nf-core/modules/fgbio/fastqtobam/meta.yml @@ -1,6 +1,6 @@ name: fgbio_fastqtobam description: | - Using the FGBIO tools, converts FASTQ files sequenced with UMIs into BAM files, moving the UMI barcode into the RX field of the BAM file + Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads keywords: - fastqtobam - fgbio @@ -19,15 +19,6 @@ input: description: pair of reads to be converted into BAM file pattern: "*.{fastq.gz}" - - read_structure: - type: string - description: | - A read structure should always be provided for each of the fastq files. - If single end, the string will contain only one structure (i.e. "2M11S+T"), if paired-end the string - will contain two structures separated by a blank space (i.e. "2M11S+T 2M11S+T"). - If the read does not contain any UMI, the structure will be +T (i.e. only template of any length). - https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures - output: - meta: type: map @@ -38,10 +29,15 @@ output: type: file description: File containing software version pattern: "*.{version.yml}" - - umibam: + - bam: type: file - description: Converted, unsorted BAM file with RX tag reporting UMI sequence (if any) + description: Unaligned, unsorted BAM file pattern: "*.{bam}" + - cram: + type: file + description: Unaligned, unsorted CRAM file + pattern: "*.{cram}" authors: - "@lescai" + - "@matthdsm" diff --git a/modules/nf-core/modules/gatk4/markduplicates/main.nf b/modules/nf-core/modules/gatk4/markduplicates/main.nf index 68e4a21ae3..63805c929d 100644 --- a/modules/nf-core/modules/gatk4/markduplicates/main.nf +++ b/modules/nf-core/modules/gatk4/markduplicates/main.nf @@ -9,20 +9,25 @@ process GATK4_MARKDUPLICATES { input: tuple val(meta), path(bam) + path fasta + path fasta_fai output: - tuple val(meta), path("*.bam") , emit: bam - tuple val(meta), path("*.bai") , optional:true, emit: bai + tuple val(meta), path("*cram"), emit: cram, optional: true + tuple val(meta), path("*bam"), emit: bam, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.bai"), emit: bai, optional: true tuple val(meta), path("*.metrics"), emit: metrics - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def input_list = bam.collect{"--INPUT $it"}.join(' ') + def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3 if (!task.memory) { @@ -33,11 +38,17 @@ process GATK4_MARKDUPLICATES { """ gatk --java-options "-Xmx${avail_mem}g" MarkDuplicates \\ $input_list \\ - --OUTPUT ${prefix}.bam \\ + --OUTPUT ${prefix} \\ --METRICS_FILE ${prefix}.metrics \\ --TMP_DIR . \\ + ${reference} \\ $args + + if [[ ${prefix} == *.cram ]]; then + mv ${prefix}.bai ${prefix}.crai + fi + cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') diff --git a/modules/nf-core/modules/gatk4/markduplicates/meta.yml b/modules/nf-core/modules/gatk4/markduplicates/meta.yml index 93877f479b..ddf98d2f5a 100644 --- a/modules/nf-core/modules/gatk4/markduplicates/meta.yml +++ b/modules/nf-core/modules/gatk4/markduplicates/meta.yml @@ -26,6 +26,14 @@ input: type: file description: Sorted BAM file pattern: "*.{bam}" + - fasta: + type: file + description: Fasta file + pattern: "*.{fasta}" + - fasta_fai: + type: file + description: Fasta index file + pattern: "*.{fai}" output: - meta: @@ -41,6 +49,18 @@ output: type: file description: Marked duplicates BAM file pattern: "*.{bam}" + - cram: + type: file + description: Marked duplicates CRAM file + pattern: "*.{cram}" + - bai: + type: file + description: BAM index file + pattern: "*.{bam.bai}" + - crai: + type: file + description: CRAM index file + pattern: "*.{cram.crai}" - metrics: type: file description: Duplicate metrics file generated by GATK diff --git a/modules/nf-core/modules/manta/germline/main.nf b/modules/nf-core/modules/manta/germline/main.nf index c680dc9d3d..5f2964fbd0 100644 --- a/modules/nf-core/modules/manta/germline/main.nf +++ b/modules/nf-core/modules/manta/germline/main.nf @@ -1,6 +1,6 @@ process MANTA_GERMLINE { tag "$meta.id" - label 'process_high' + label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/manta/somatic/main.nf b/modules/nf-core/modules/manta/somatic/main.nf index 6313c38bdd..0b40965b7c 100644 --- a/modules/nf-core/modules/manta/somatic/main.nf +++ b/modules/nf-core/modules/manta/somatic/main.nf @@ -1,6 +1,6 @@ process MANTA_SOMATIC { tag "$meta.id" - label 'process_high' + label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/manta/tumoronly/main.nf b/modules/nf-core/modules/manta/tumoronly/main.nf index 3361cf82be..759f9cb9ec 100644 --- a/modules/nf-core/modules/manta/tumoronly/main.nf +++ b/modules/nf-core/modules/manta/tumoronly/main.nf @@ -1,6 +1,6 @@ process MANTA_TUMORONLY { tag "$meta.id" - label 'process_high' + label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/samtools/convert/main.nf b/modules/nf-core/modules/samtools/convert/main.nf index e0e7d725d7..eea00179c6 100644 --- a/modules/nf-core/modules/samtools/convert/main.nf +++ b/modules/nf-core/modules/samtools/convert/main.nf @@ -1,6 +1,6 @@ process SAMTOOLS_CONVERT { tag "$meta.id" - label 'process_medium' + label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/samtools/faidx/main.nf b/modules/nf-core/modules/samtools/faidx/main.nf index fdce7d9b8b..36b3538e55 100644 --- a/modules/nf-core/modules/samtools/faidx/main.nf +++ b/modules/nf-core/modules/samtools/faidx/main.nf @@ -1,6 +1,6 @@ process SAMTOOLS_FAIDX { tag "$fasta" - label 'process_low' + label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -22,6 +22,7 @@ process SAMTOOLS_FAIDX { """ samtools \\ faidx \\ + $args \\ $fasta cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/modules/samtools/mpileup/main.nf b/modules/nf-core/modules/samtools/mpileup/main.nf index 34a1b508e3..fe8e32b4ce 100644 --- a/modules/nf-core/modules/samtools/mpileup/main.nf +++ b/modules/nf-core/modules/samtools/mpileup/main.nf @@ -1,6 +1,6 @@ process SAMTOOLS_MPILEUP { tag "$meta.id" - label 'process_medium' + label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/samtools/stats/main.nf b/modules/nf-core/modules/samtools/stats/main.nf index 89b92d79eb..9b0c386789 100644 --- a/modules/nf-core/modules/samtools/stats/main.nf +++ b/modules/nf-core/modules/samtools/stats/main.nf @@ -1,6 +1,6 @@ process SAMTOOLS_STATS { tag "$meta.id" - label 'process_low' + label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -25,7 +25,7 @@ process SAMTOOLS_STATS { """ samtools \\ stats \\ - --threads ${task.cpus-1} \\ + --threads ${task.cpus} \\ ${reference} \\ ${input} \\ > ${prefix}.stats diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/modules/samtools/view/main.nf index 55194e887f..59ded5c3b8 100644 --- a/modules/nf-core/modules/samtools/view/main.nf +++ b/modules/nf-core/modules/samtools/view/main.nf @@ -1,6 +1,6 @@ process SAMTOOLS_VIEW { tag "$meta.id" - label 'process_medium' + label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/strelka/germline/main.nf b/modules/nf-core/modules/strelka/germline/main.nf index 02364273d6..1f59bee157 100644 --- a/modules/nf-core/modules/strelka/germline/main.nf +++ b/modules/nf-core/modules/strelka/germline/main.nf @@ -1,6 +1,6 @@ process STRELKA_GERMLINE { tag "$meta.id" - label 'process_high' + label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/strelka/somatic/main.nf b/modules/nf-core/modules/strelka/somatic/main.nf index b61c09bd8c..08b298a463 100644 --- a/modules/nf-core/modules/strelka/somatic/main.nf +++ b/modules/nf-core/modules/strelka/somatic/main.nf @@ -1,6 +1,6 @@ process STRELKA_SOMATIC { tag "$meta.id" - label 'process_high' + label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/tabix/bgziptabix/main.nf b/modules/nf-core/modules/tabix/bgziptabix/main.nf index 03e3b0c320..0d05984add 100644 --- a/modules/nf-core/modules/tabix/bgziptabix/main.nf +++ b/modules/nf-core/modules/tabix/bgziptabix/main.nf @@ -1,6 +1,6 @@ process TABIX_BGZIPTABIX { tag "$meta.id" - label 'process_medium' + label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/tabix/tabix/main.nf b/modules/nf-core/modules/tabix/tabix/main.nf index e155e4685a..21b2e79f48 100644 --- a/modules/nf-core/modules/tabix/tabix/main.nf +++ b/modules/nf-core/modules/tabix/tabix/main.nf @@ -1,6 +1,6 @@ process TABIX_TABIX { tag "$meta.id" - label 'process_medium' + label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/untar/main.nf b/modules/nf-core/modules/untar/main.nf index 29ab10a505..4128652008 100644 --- a/modules/nf-core/modules/untar/main.nf +++ b/modules/nf-core/modules/untar/main.nf @@ -1,6 +1,6 @@ process UNTAR { tag "$archive" - label 'process_low' + label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/unzip/main.nf b/modules/nf-core/modules/unzip/main.nf index 8476a2eba4..bb645ca63f 100644 --- a/modules/nf-core/modules/unzip/main.nf +++ b/modules/nf-core/modules/unzip/main.nf @@ -1,6 +1,6 @@ process UNZIP { tag "$archive" - label 'process_low' + label 'process_single' conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/modules/vcftools/main.nf b/modules/nf-core/modules/vcftools/main.nf index 78b95fae3f..feefb0e3f8 100644 --- a/modules/nf-core/modules/vcftools/main.nf +++ b/modules/nf-core/modules/vcftools/main.nf @@ -1,6 +1,6 @@ process VCFTOOLS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? From bad181a5710185e16f7f46f7b89b7dd4b7f6d34b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 12:07:14 +0200 Subject: [PATCH 03/25] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6c53610ca6..f9f36cf723 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#723](https://github.com/nf-core/sarek/pull/723) - Sync `TEMPLATE` with `tools` `2.5.1` - [#730](https://github.com/nf-core/sarek/pull/730) - Reduce number of tests - [#731](https://github.com/nf-core/sarek/pull/731) - Run the somatic test as default on `-profile test_full`, the germline can be tested with `-profile test_full_somatic` +- [#734](https://github.com/nf-core/sarek/pull/734) - nf-core modules update -a ### Fixed From 342494dcd35645b0ee1f17cac2bc7d84995b2359 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 13:15:15 +0200 Subject: [PATCH 04/25] un-update markduplicates --- modules.json | 2 +- .../modules/gatk4/markduplicates/main.nf | 21 +++++-------------- .../modules/gatk4/markduplicates/meta.yml | 20 ------------------ 3 files changed, 6 insertions(+), 37 deletions(-) diff --git a/modules.json b/modules.json index 24231e3870..c2064ca0b7 100644 --- a/modules.json +++ b/modules.json @@ -195,7 +195,7 @@ }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "e726b1730dff525bde4a6839e544dabfea4cd7fd" + "git_sha": "df2620cfc7e4c21b14ed03c1c928f09fbabf83c4" }, "gatk4/markduplicatesspark": { "branch": "master", diff --git a/modules/nf-core/modules/gatk4/markduplicates/main.nf b/modules/nf-core/modules/gatk4/markduplicates/main.nf index 63805c929d..68e4a21ae3 100644 --- a/modules/nf-core/modules/gatk4/markduplicates/main.nf +++ b/modules/nf-core/modules/gatk4/markduplicates/main.nf @@ -9,25 +9,20 @@ process GATK4_MARKDUPLICATES { input: tuple val(meta), path(bam) - path fasta - path fasta_fai output: - tuple val(meta), path("*cram"), emit: cram, optional: true - tuple val(meta), path("*bam"), emit: bam, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.bai"), emit: bai, optional: true + tuple val(meta), path("*.bam") , emit: bam + tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.metrics"), emit: metrics - path "versions.yml", emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def input_list = bam.collect{"--INPUT $it"}.join(' ') - def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3 if (!task.memory) { @@ -38,17 +33,11 @@ process GATK4_MARKDUPLICATES { """ gatk --java-options "-Xmx${avail_mem}g" MarkDuplicates \\ $input_list \\ - --OUTPUT ${prefix} \\ + --OUTPUT ${prefix}.bam \\ --METRICS_FILE ${prefix}.metrics \\ --TMP_DIR . \\ - ${reference} \\ $args - - if [[ ${prefix} == *.cram ]]; then - mv ${prefix}.bai ${prefix}.crai - fi - cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') diff --git a/modules/nf-core/modules/gatk4/markduplicates/meta.yml b/modules/nf-core/modules/gatk4/markduplicates/meta.yml index ddf98d2f5a..93877f479b 100644 --- a/modules/nf-core/modules/gatk4/markduplicates/meta.yml +++ b/modules/nf-core/modules/gatk4/markduplicates/meta.yml @@ -26,14 +26,6 @@ input: type: file description: Sorted BAM file pattern: "*.{bam}" - - fasta: - type: file - description: Fasta file - pattern: "*.{fasta}" - - fasta_fai: - type: file - description: Fasta index file - pattern: "*.{fai}" output: - meta: @@ -49,18 +41,6 @@ output: type: file description: Marked duplicates BAM file pattern: "*.{bam}" - - cram: - type: file - description: Marked duplicates CRAM file - pattern: "*.{cram}" - - bai: - type: file - description: BAM index file - pattern: "*.{bam.bai}" - - crai: - type: file - description: CRAM index file - pattern: "*.{cram.crai}" - metrics: type: file description: Duplicate metrics file generated by GATK From 6db3cb016818362335df24d47edf3a394f7718cc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 13:29:33 +0200 Subject: [PATCH 05/25] fix bwamem2_index input and output --- subworkflows/local/prepare_genome.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 58d140aff1..8f922693e9 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -45,9 +45,9 @@ workflow PREPARE_GENOME { ch_versions = Channel.empty() - BWAMEM1_INDEX(fasta) // If aligner is bwa-mem - BWAMEM2_INDEX(fasta) // If aligner is bwa-mem2 - DRAGMAP_HASHTABLE(fasta) // If aligner is dragmap + BWAMEM1_INDEX(fasta) // If aligner is bwa-mem + BWAMEM2_INDEX(fasta.map{ it -> [[id:it[0].baseName], it] }) // If aligner is bwa-mem2 + DRAGMAP_HASHTABLE(fasta) // If aligner is dragmap GATK4_CREATESEQUENCEDICTIONARY(fasta) MSISENSORPRO_SCAN(fasta.map{ it -> [[id:it[0].baseName], it] }) @@ -112,13 +112,13 @@ workflow PREPARE_GENOME { emit: bwa = BWAMEM1_INDEX.out.index // path: bwa/* - bwamem2 = BWAMEM2_INDEX.out.index // path: bwamem2/* + bwamem2 = BWAMEM2_INDEX.out.index.map{ meta, index -> [index] }.collect() // path: bwamem2/* hashtable = DRAGMAP_HASHTABLE.out.hashmap // path: dragmap/* dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai germline_resource_tbi = TABIX_GERMLINE_RESOURCE.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: germline_resource.vcf.gz.tbi - known_snps_tbi = TABIX_KNOWN_SNPS.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi + known_snps_tbi = TABIX_KNOWN_SNPS.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi msisensorpro_scan = MSISENSORPRO_SCAN.out.list.map{ meta, list -> [list] } // path: genome_msi.list pon_tbi = TABIX_PON.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: pon.vcf.gz.tbi From a3080286fbcca499bcc3b6cd02f5fca3138d5ec9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 13:36:30 +0200 Subject: [PATCH 06/25] fix input for bwamem2_mem module --- subworkflows/nf-core/gatk4/mapping/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/nf-core/gatk4/mapping/main.nf b/subworkflows/nf-core/gatk4/mapping/main.nf index 8c820677ff..bc89fdb394 100644 --- a/subworkflows/nf-core/gatk4/mapping/main.nf +++ b/subworkflows/nf-core/gatk4/mapping/main.nf @@ -20,9 +20,9 @@ workflow GATK4_MAPPING { ch_reports = Channel.empty() // Only one of the following should be run - BWAMEM1_MEM(ch_reads, ch_map_index, sort) // If aligner is bwa-mem - BWAMEM2_MEM(ch_reads, ch_map_index, sort) // If aligner is bwa-mem2 - DRAGMAP_ALIGN(ch_reads, ch_map_index, sort) // If aligner is dragmap + BWAMEM1_MEM(ch_reads, ch_map_index, sort) // If aligner is bwa-mem + BWAMEM2_MEM(ch_reads, ch_map_index.map{ it -> [[id:it[0].baseName], it] }, sort) // If aligner is bwa-mem2 + DRAGMAP_ALIGN(ch_reads, ch_map_index, sort) // If aligner is dragmap // Get the bam files from the aligner // Only one aligner is run From 81cf09c63a33db2c5562d14f97ed52643429ed3a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 13:52:29 +0200 Subject: [PATCH 07/25] code polish --- subworkflows/local/prepare_genome.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 8f922693e9..f2652b6f5c 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -51,11 +51,11 @@ workflow PREPARE_GENOME { GATK4_CREATESEQUENCEDICTIONARY(fasta) MSISENSORPRO_SCAN(fasta.map{ it -> [[id:it[0].baseName], it] }) - SAMTOOLS_FAIDX(fasta.map{ it -> [[id:it[0].getName()], it] }) + SAMTOOLS_FAIDX(fasta.map{ it -> [[id:it[0].baseName], it] }) // the following are flattened and mapped in case the user supplies more than one value for the param // written for KNOWN_INDELS, but preemptively applied to the rest - // [file1,file2] becomes [[meta1,file1],[meta2,file2]] + // [file1, file2] becomes [[meta1, file1],[meta2, file2]] // outputs are collected to maintain a single channel for relevant TBI files TABIX_DBSNP(dbsnp.flatten().map{ it -> [[id:it.baseName], it] }) TABIX_GERMLINE_RESOURCE(germline_resource.flatten().map{ it -> [[id:it.baseName], it] }) From 0473fc3516046ba70fb9bebc87d9ebc3a828daa0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 15:21:50 +0200 Subject: [PATCH 08/25] fix md5sum in default --- tests/test_default.yml | 8 ++++---- tests/test_targeted.yml | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/test_default.yml b/tests/test_default.yml index e2cef4b222..80794a291b 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -49,9 +49,9 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b1c2a861f64e20a94108a6de3b76c582 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5528d952f5dc74a39f28e27165bf96be + md5sum: 811d834ff8849e69e7c5925dc2a34257 - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary md5sum: dd87f507da7de20d5318841af312493b - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count @@ -121,6 +121,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b1c2a861f64e20a94108a6de3b76c582 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: f7005dd4646700e107bfc00e36c432fe + md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38 diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml index e4aba5ab9e..fe019605a9 100644 --- a/tests/test_targeted.yml +++ b/tests/test_targeted.yml @@ -53,7 +53,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats md5sum: ecad3c41de5b82f6bc0c429e7b24958e @@ -100,6 +100,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz md5sum: 38fe39894abe62e38f8ac214cba64f2b - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5528d952f5dc74a39f28e27165bf96be + md5sum: 811d834ff8849e69e7c5925dc2a34257 From ec3f8807856be15f4346ce68c9b0b2b2d67148ec Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 15:23:32 +0200 Subject: [PATCH 09/25] fix md5sum in aligner --- tests/test_aligner.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_aligner.yml b/tests/test_aligner.yml index 4d913cbb4f..ff73b59197 100644 --- a/tests/test_aligner.yml +++ b/tests/test_aligner.yml @@ -70,9 +70,9 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b1c2a861f64e20a94108a6de3b76c582 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5528d952f5dc74a39f28e27165bf96be + md5sum: 811d834ff8849e69e7c5925dc2a34257 - name: Run dragmap command: nextflow run main.nf -profile test,docker --aligner dragmap --save_reference tags: @@ -160,6 +160,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: d5f1c9389ecf52ba839e834780a94549 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: f2ae8b531aa1fb2fbffe9a92e4c81493 + md5sum: 9f64e86202f2291b33c0e8c3e7981193 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: f7bab59db4fb8ab49eea71b668d351d5 + md5sum: a63f247fb403d8679c8f96f3a128aba0 From 9adb528960eb063944275db5407f97d80437a75b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 15:25:06 +0200 Subject: [PATCH 10/25] fix md5sum in alignment_to_fastq --- tests/test_bam_remap.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_bam_remap.yml b/tests/test_bam_remap.yml index c30613f946..630c6cefad 100644 --- a/tests/test_bam_remap.yml +++ b/tests/test_bam_remap.yml @@ -44,6 +44,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 5201890d36c1dd127b930373b6e823e5 + md5sum: d6634d51a009e3da43b2349e424b2d9f - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: bb2fc6118a1404c45f9e828600df8fb1 + md5sum: 91915547ff9e654c106a42e5edfd9405 From 1bb4245ad9e970ee87dfaeb6410a4971f7f33888 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 15:55:39 +0200 Subject: [PATCH 11/25] fix md5sum for gatk_spark --- tests/test_gatk_spark.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_gatk_spark.yml b/tests/test_gatk_spark.yml index cd35041ddc..f54aaa3aea 100644 --- a/tests/test_gatk_spark.yml +++ b/tests/test_gatk_spark.yml @@ -45,6 +45,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz md5sum: c259a9fd73f576626c3a29841c2dc019 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 2e4edbad7d0fb88d7834114a2d5ab534 + md5sum: b573b2e930c5f68e7e4910faf9e51e44 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 996b6f18a9ad4aa4ebc8a38f559471a0 + md5sum: a75731dca9b42d87d9997ea44aaf82fc From a1a16a84b2c127c5bb423f27cf5a3fb229f52f33 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 15:56:44 +0200 Subject: [PATCH 12/25] fix md5sum for markduplicates --- tests/test_markduplicates.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_markduplicates.yml b/tests/test_markduplicates.yml index 7c8fef9ffb..563a3b35bf 100644 --- a/tests/test_markduplicates.yml +++ b/tests/test_markduplicates.yml @@ -45,9 +45,9 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi # binary changes md5sums on reruns. - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 06fdce012030eeb6d1c1c529b382c564 + md5sum: a0ecedb6be28639e276d38e4ac18935b - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: c37a9db008f05a0aaf591f0bb41ef387 + md5sum: 69d2bab6fdbe21ec5c598dc404a3df00 - name: Run markduplicates starting from CRAM command: nextflow run main.nf -profile test,markduplicates_cram tags: @@ -95,9 +95,9 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi # binary changes md5sums on reruns. - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 06fdce012030eeb6d1c1c529b382c564 + md5sum: a0ecedb6be28639e276d38e4ac18935b - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: c37a9db008f05a0aaf591f0bb41ef387 + md5sum: 69d2bab6fdbe21ec5c598dc404a3df00 - path: results/samtools/test.bam # binary changes md5sums on reruns. - path: results/samtools/test.bam.bai From 7bbd6e1ae3f586841659e84c06fd1a0bc712fde8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 15:57:47 +0200 Subject: [PATCH 13/25] fix md5sum for save_bam_mapped --- tests/test_save_bam_mapped.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_save_bam_mapped.yml b/tests/test_save_bam_mapped.yml index abf388b8ee..71629918cc 100644 --- a/tests/test_save_bam_mapped.yml +++ b/tests/test_save_bam_mapped.yml @@ -51,6 +51,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b1c2a861f64e20a94108a6de3b76c582 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5528d952f5dc74a39f28e27165bf96be + md5sum: 811d834ff8849e69e7c5925dc2a34257 From 2958fd550a9deff434e8807053b6a728bb62060c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 15:59:08 +0200 Subject: [PATCH 14/25] fix md5sum for recalibrate --- tests/test_recalibrate.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_recalibrate.yml b/tests/test_recalibrate.yml index 2a7d47a4c6..91341c9119 100644 --- a/tests/test_recalibrate.yml +++ b/tests/test_recalibrate.yml @@ -27,7 +27,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 1787b3a12b134fe35ab166431f107fc4 + md5sum: a0841c41460d0d4bdc2a1a777ee7e7c2 - name: Run Recalibration starting from cram command: nextflow run main.nf -profile test,recalibrate_cram tags: @@ -53,7 +53,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 1787b3a12b134fe35ab166431f107fc4 + md5sum: a0841c41460d0d4bdc2a1a777ee7e7c2 - name: Run Recalibration starting from bam and skip baserecalibration command: nextflow run main.nf -profile test,recalibrate_bam,skip_bqsr --tools strelka tags: From 046c272479d741dd84a15e17b22da577909b8e99 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 16:00:20 +0200 Subject: [PATCH 15/25] fix md5sum for prepare_recalibration --- tests/test_prepare_recalibration.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_prepare_recalibration.yml b/tests/test_prepare_recalibration.yml index 283ccdb350..0becfe55cb 100644 --- a/tests/test_prepare_recalibration.yml +++ b/tests/test_prepare_recalibration.yml @@ -31,7 +31,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 61fd75f684ee1b98fd29d7005199762e + md5sum: 71af990f7acad8bf24d37e88c4adcded - name: Run prepare_recalibration starting from cram command: nextflow run main.nf -profile test,prepare_recalibration_cram tags: @@ -59,7 +59,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 61fd75f684ee1b98fd29d7005199762e + md5sum: 71af990f7acad8bf24d37e88c4adcded - name: Run prepare_recalibration starting from bam and skip baserecalibration command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr --tools strelka tags: From e0cbd9c0fdcbb8f3356a4798888bd893f4f05a95 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 16:07:32 +0200 Subject: [PATCH 16/25] fix md5sum for skip_markduplicates --- tests/test_skip_markduplicates.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml index dd9bdceaa2..2974bebd09 100644 --- a/tests/test_skip_markduplicates.yml +++ b/tests/test_skip_markduplicates.yml @@ -47,9 +47,9 @@ - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi md5sum: e3235323f455414ee3acc7144e659caf - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 58deb5e1d74a991f863136a218c8f56c + md5sum: 55ddd2d98552a1483bf2a965f19d8da4 - path: results/reports/samtools/test/test.sorted.cram.stats - md5sum: 494976d0d5b3ca029c986cf9e79bb7b3 + md5sum: 59d921ed3970e19145fbae75966de3e3 - path: results/csv/markduplicates.csv should_exist: false - path: results/csv/markduplicates_no_table.csv @@ -97,9 +97,9 @@ - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 61fd75f684ee1b98fd29d7005199762e + md5sum: 71af990f7acad8bf24d37e88c4adcded - path: results/reports/samtools/test/test.sorted.cram.stats - md5sum: 9fc99b31174fc1ea50cd7644c50f42aa + md5sum: ac78da9dde7bae6849c0e2488bf7506a - path: results/csv/markduplicates.csv should_exist: false - path: results/csv/markduplicates_no_table.csv @@ -141,9 +141,9 @@ - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 61fd75f684ee1b98fd29d7005199762e + md5sum: 71af990f7acad8bf24d37e88c4adcded - path: results/reports/samtools/test/test.sorted.cram.stats - md5sum: a0105eedd6ff6c840f0853434addb0c1 + md5sum: 42b536ada66f772bb4dfd741098b2783 - path: results/csv/markduplicates.csv should_exist: false - path: results/csv/markduplicates_no_table.csv From bb568f4f61748b8cfd71cc24425b4ba960ad8969 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 16:08:21 +0200 Subject: [PATCH 17/25] fix md5sum for split_fastq --- tests/test_split_fastq.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_split_fastq.yml b/tests/test_split_fastq.yml index 72c76a743c..d067e67166 100644 --- a/tests/test_split_fastq.yml +++ b/tests/test_split_fastq.yml @@ -52,6 +52,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: 1b65ac38cd96783394e0cf9b7bdd5bc2 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 013094be804395f1168077076accd078 + md5sum: 44c873922c844b85c0920d22c98b08cf - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: c0bf46dc246b21320f77ef4f395eca0c + md5sum: 5ad46c4c701943dfc67604ed34c1c69e From a0323d31c4e9bb4524f148be16c9789fd1bad54a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 16:09:12 +0200 Subject: [PATCH 18/25] fix md5sum for targeted --- tests/test_targeted.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml index fe019605a9..ce1e3b36eb 100644 --- a/tests/test_targeted.yml +++ b/tests/test_targeted.yml @@ -55,7 +55,7 @@ - path: results/reports/samtools/test/test.md.cram.stats md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: ecad3c41de5b82f6bc0c429e7b24958e + md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98 - name: Run intervals false pipeline command: nextflow run main.nf -profile test --intervals false From fc0c11c317b1a1777525777a295f970f120d7255 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 16:09:54 +0200 Subject: [PATCH 19/25] fix md5sum for trimming --- tests/test_trimming.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_trimming.yml b/tests/test_trimming.yml index 8111c398c0..ccbdb831f6 100644 --- a/tests/test_trimming.yml +++ b/tests/test_trimming.yml @@ -50,6 +50,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: a5ad8f917979f62eacfff1461529dbaa - path: results/reports/samtools/test/test.md.cram.stats - md5sum: bba23d14aa20be36bf87bedf91c8832c + md5sum: 7382e028335a2b057cb54ea160c4be7b - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: deb6f58a0d339e821e98c25b456f7eb7 + md5sum: 5adeae7e9ce068009e88bacba549096e From c51fc8ec34129c74d4aa7ef06664fb428fd7d8ce Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 16:11:13 +0200 Subject: [PATCH 20/25] fix md5sum for tumor_normal_pair --- tests/test_pair.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_pair.yml b/tests/test_pair.yml index ce3063881f..409f585baf 100644 --- a/tests/test_pair.yml +++ b/tests/test_pair.yml @@ -78,10 +78,10 @@ - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi md5sum: d5f1c9389ecf52ba839e834780a94549 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5528d952f5dc74a39f28e27165bf96be + md5sum: 811d834ff8849e69e7c5925dc2a34257 - path: results/reports/samtools/test2/test2.md.cram.stats - md5sum: ad42bfa581dddc911ebd36d386a330a3 + md5sum: 60152dbf1e109d4c407c151204388109 - path: results/reports/samtools/test2/test2.recal.cram.stats - md5sum: 9cc426e4cf249288b61816f806f74bfd + md5sum: 2907543ab51cabd97318b15cf035c867 From 54537b3e032b161c5983d7a9b62bb62a1b11cf5b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 16:32:14 +0200 Subject: [PATCH 21/25] fix umi tests --- conf/modules.config | 1 + .../nf-core/fgbio_create_umi_consensus/main.nf | 11 +++++------ workflows/sarek.nf | 4 ---- 3 files changed, 6 insertions(+), 10 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index e21a7b1845..5bb85de2b3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -301,6 +301,7 @@ process { // UMI Subworkflow withName: 'FASTQTOBAM'{ + ext.args = { "--read-structures '$params.umi_read_structure'" } publishDir = [ //specify to avoid publishing, overwritten otherwise enabled: false diff --git a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf index 030397a966..df5302619e 100644 --- a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf +++ b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf @@ -18,22 +18,21 @@ workflow CREATE_UMI_CONSENSUS { reads // channel: [mandatory] [ val(meta), [ reads ] ] fasta // channel: [mandatory] /path/to/reference/fasta map_index // channel: [mandatory] Pre-computed mapping index - read_structure // string: [mandatory] "read_structure" groupreadsbyumi_strategy // string: [mandatory] grouping strategy - default: "Adjacency" main: ch_versions = Channel.empty() - // using information in val(read_structure) FASTQ reads are converted into - // a tagged unmapped BAM file (uBAM) - FASTQTOBAM(reads, read_structure) + // params.umi_read_structure is passed out as ext.args + // FASTQ reads are converted into a tagged unmapped BAM file (uBAM) + FASTQTOBAM(reads) // in order to map uBAM using BWA MEM, we need to convert uBAM to FASTQ // TODO check if DRAGMAP works well with BAM inputs // but keep the appropriate UMI tags in the FASTQ comment field and produce // an interleaved FASQT file (hence, split = false) split = false - BAM2FASTQ(FASTQTOBAM.out.umibam, split) + BAM2FASTQ(FASTQTOBAM.out.bam, split) // appropriately tagged interleaved FASTQ reads are mapped to the reference // bams will not be sorted (hence, sort = false) @@ -60,7 +59,7 @@ workflow CREATE_UMI_CONSENSUS { ch_versions = ch_versions.mix(SAMBLASTER.out.versions) emit: - umibam = FASTQTOBAM.out.umibam // channel: [ val(meta), [ bam ] ] + umibam = FASTQTOBAM.out.bam // channel: [ val(meta), [ bam ] ] groupbam = GROUPREADSBYUMI.out.bam // channel: [ val(meta), [ bam ] ] consensusbam = CALLUMICONSENSUS.out.bam // channel: [ val(meta), [ bam ] ] versions = ch_versions // channel: [ versions.yml ] diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 057fee0a1a..19dd7165db 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -189,9 +189,6 @@ if (params.spliceai_snv && params.spliceai_snv_tbi && params.spliceai_indel && p vep_extra_files.add(file(params.spliceai_snv_tbi, checkIfExists: true)) } -// Initialize value channels based on params, not defined within the params.genomes[params.genome] scope -umi_read_structure = params.umi_read_structure ? "${params.umi_read_structure}" : Channel.empty() - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT LOCAL/NF-CORE MODULES/SUBWORKFLOWS @@ -414,7 +411,6 @@ workflow SAREK { ch_input_fastq, fasta, ch_map_index, - umi_read_structure, params.group_by_umi_strategy ) From e0ace928133e764c239966321dac25e8da847963 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 16:43:35 +0200 Subject: [PATCH 22/25] fix params --- conf/modules.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 5bb85de2b3..24e9e7e618 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -301,7 +301,8 @@ process { // UMI Subworkflow withName: 'FASTQTOBAM'{ - ext.args = { "--read-structures '$params.umi_read_structure'" } + ext.prefix = {"${meta.id}"} + ext.args = { "--read-structures $params.umi_read_structure" } publishDir = [ //specify to avoid publishing, overwritten otherwise enabled: false From 48f2f61c6c9a6f389be9fc94e7b6a7555319b8e3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 17:09:39 +0200 Subject: [PATCH 23/25] fix md5sum for umi --- tests/test_umi.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 4446586014..673d6cdd54 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -46,9 +46,9 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 072daded4cd3bd08f2c94ef1f1478052 + md5sum: 9c424aaae1d200f67a1ecc3e55ad5a6a - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 1537c827260f24e3fa0f0dc257580b41 + md5sum: e64175125c512651b2819ced400bc846 # - name: Run UMI TSO test # command: nextflow run main.nf -profile test,umi_tso # tags: From 0c734fc392511af821291af280b182f3040a5423 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 17:32:42 +0200 Subject: [PATCH 24/25] fix md5sum for save_output_as_bam --- tests/test_save_output_bam.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_save_output_bam.yml b/tests/test_save_output_bam.yml index 5051d723b3..2f29413999 100644 --- a/tests/test_save_output_bam.yml +++ b/tests/test_save_output_bam.yml @@ -45,9 +45,9 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b1c2a861f64e20a94108a6de3b76c582 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5528d952f5dc74a39f28e27165bf96be + md5sum: 811d834ff8849e69e7c5925dc2a34257 - name: Run save_output_as_bam with gatk4 spark command: nextflow run main.nf -profile test,use_gatk_spark --save_output_as_bam tags: @@ -96,6 +96,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: cf85ba4692f016af70db2a594d9effdf - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 2e4edbad7d0fb88d7834114a2d5ab534 + md5sum: b573b2e930c5f68e7e4910faf9e51e44 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 996b6f18a9ad4aa4ebc8a38f559471a0 + md5sum: a75731dca9b42d87d9997ea44aaf82fc From 805cc1df0d34f7ef9ac0fe726f41e5654b5ea927 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 7 Sep 2022 18:20:01 +0200 Subject: [PATCH 25/25] fix md5sum for freebayes --- tests/test_tools.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/tests/test_tools.yml b/tests/test_tools.yml index a3f54dc1e5..9d3c289be1 100644 --- a/tests/test_tools.yml +++ b/tests/test_tools.yml @@ -406,9 +406,9 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: ecad3c41de5b82f6bc0c429e7b24958e + md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98 - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary md5sum: 43d53e36cbb1091f915b2499e545b41e - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count @@ -480,9 +480,9 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b1c2a861f64e20a94108a6de3b76c582 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: f7005dd4646700e107bfc00e36c432fe + md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38 - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary md5sum: 76c5919541536c12b5c8a6094d6d78d5 - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count @@ -597,13 +597,13 @@ - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: ecad3c41de5b82f6bc0c429e7b24958e + md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98 - path: results/reports/samtools/test2/test2.md.cram.stats - md5sum: ad42bfa581dddc911ebd36d386a330a3 + md5sum: 60152dbf1e109d4c407c151204388109 - path: results/reports/samtools/test2/test2.recal.cram.stats - md5sum: d5ecf9b3e13d5de98fcbc2e8f2cb02be + md5sum: 53a0b34b67fdf90ea68fac8ea744b576 - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary md5sum: 43d53e36cbb1091f915b2499e545b41e - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count @@ -712,13 +712,13 @@ - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi md5sum: 4205a09ede17cdbdaad45e3553f73105 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: dcf70bbcfb92e01027978f28d2035d78 + md5sum: 52411f93d9b5382342b40a351c2e313c - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: f7005dd4646700e107bfc00e36c432fe + md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38 - path: results/reports/samtools/test2/test2.md.cram.stats - md5sum: ad42bfa581dddc911ebd36d386a330a3 + md5sum: 60152dbf1e109d4c407c151204388109 - path: results/reports/samtools/test2/test2.recal.cram.stats - md5sum: 5dd3570db59cce7f7addd0257e858289 + md5sum: 029b903797dc228e56d6ab74e677fa21 - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary md5sum: 76c5919541536c12b5c8a6094d6d78d5 - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count