From 179b8ff84f318e9111febfce8c405a7d383380fd Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 19 Dec 2022 12:08:37 +0000 Subject: [PATCH 01/14] Template update for nf-core/tools version 2.7.2 --- .github/workflows/fix-linting.yml | 4 +- .github/workflows/linting_comment.yml | 2 +- lib/WorkflowMain.groovy | 2 +- modules.json | 6 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 2 +- .../templates/dumpsoftwareversions.py | 99 ++++++++++--------- modules/nf-core/fastqc/main.nf | 40 +++----- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 3 - nextflow_schema.json | 6 -- workflows/sarek.nf | 2 +- 12 files changed, 82 insertions(+), 88 deletions(-) mode change 100644 => 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 6e76e699a3..0529d32d0b 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -34,9 +34,9 @@ jobs: id: prettier_status run: | if prettier --check ${GITHUB_WORKSPACE}; then - echo "name=result::pass" >> $GITHUB_OUTPUT + echo "result=pass" >> $GITHUB_OUTPUT else - echo "name=result::fail" >> $GITHUB_OUTPUT + echo "result=fail" >> $GITHUB_OUTPUT fi - name: Run 'prettier --write' diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 3963518629..0bbcd30f23 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -18,7 +18,7 @@ jobs: - name: Get PR number id: pr_number - run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT + run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment uses: marocchino/sticky-pull-request-comment@v2 diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 78f4e2f6ed..cec16506b6 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -72,7 +72,7 @@ class WorkflowMain { NfcoreTemplate.checkConfigProvided(workflow, log) // Check that conda channels are set-up correctly - if (params.enable_conda) { + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { Utils.checkCondaChannels(log) } diff --git a/modules.json b/modules.json index e9df5add7a..0cb2b6d3d9 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 82c77605c2..2b909e77cd 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK { tag "$samplesheet" label 'process_single' - conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : 'quay.io/biocontainers/python:3.8.3' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index cebb6e0589..3df21765b9 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py old mode 100644 new mode 100755 index 787bdb7b1b..e55b8d43a9 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -1,5 +1,9 @@ #!/usr/bin/env python + +"""Provide functions to merge multiple versions.yml files.""" + + import platform from textwrap import dedent @@ -7,6 +11,7 @@ def _make_versions_html(versions): + """Generate a tabular HTML output of all versions for MultiQC.""" html = [ dedent( """\\ @@ -45,47 +50,53 @@ def _make_versions_html(versions): return "\\n".join(html) -versions_this_module = {} -versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, -} - -with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - -# aggregate versions by the module name (derived from fully-qualified process name) -versions_by_module = {} -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. " - ) - except KeyError: - versions_by_module[module] = process_versions - -versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", -} - -versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), -} - -with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) -with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - -with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) +def main(): + """Load all version files and generate merged output.""" + versions_this_module = {} + versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, + } + + with open("$versions") as f: + versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module + + # aggregate versions by the module name (derived from fully-qualified process name) + versions_by_module = {} + for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + + versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + } + + versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://github.com/${workflow.manifest.name}", + "plot_type": "html", + "description": "are collected at run time from the software output.", + "data": _make_versions_html(versions_by_module), + } + + with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) + with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + + with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False) + + +if __name__ == "__main__": + main() diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 05730368b2..9ae5838158 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : 'quay.io/biocontainers/fastqc:0.11.9--0' }" @@ -20,30 +20,22 @@ process FASTQC { script: def args = task.ext.args ?: '' - // Add soft-links to original FastQs for consistent naming in pipeline def prefix = task.ext.prefix ?: "${meta.id}" - if (meta.single_end) { - """ - [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz - fastqc $args --threads $task.cpus ${prefix}.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } else { - """ - [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz - [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz - fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } + // Make list of old name and new name pairs to use for renaming in the bash while loop + def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } + def rename_to = old_new_pairs*.join(' ').join(' ') + def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + """ + printf "%s %s\\n" $rename_to | while read old_name new_name; do + [ -f "\${new_name}" ] || ln -s \$old_name \$new_name + done + fastqc $args --threads $task.cpus $renamed_files + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ stub: def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index a8159a57bf..68f66bea74 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,7 +1,7 @@ process MULTIQC { label 'process_single' - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/nextflow.config b/nextflow.config index 76f546abe5..361675a92b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -39,7 +39,6 @@ params { validate_params = true show_hidden_params = false schema_ignore_params = 'genomes' - enable_conda = false // Config options @@ -81,7 +80,6 @@ try { profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { - params.enable_conda = true conda.enabled = true docker.enabled = false singularity.enabled = false @@ -90,7 +88,6 @@ profiles { charliecloud.enabled = false } mamba { - params.enable_conda = true conda.enabled = true conda.useMamba = true docker.enabled = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 5b8f7ddd14..7f7e4c1341 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -263,12 +263,6 @@ "description": "Show all params when using `--help`", "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "enable_conda": { - "type": "boolean", - "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.", - "hidden": true, - "fa_icon": "fas fa-bacon" } } } diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 27a86ee3e1..7ccddd6fb3 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -82,7 +82,7 @@ workflow SAREK { ch_versions = ch_versions.mix(FASTQC.out.versions.first()) CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml') + ch_versions.unique().collectFile(name: 'collated_versions.yml') ) // From c0da7014ce8581931c469d180cd48072a374423b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Dec 2022 16:28:13 +0100 Subject: [PATCH 02/14] update modules [] --- CHANGELOG.md | 2 + modules.json | 164 +++++++++--------- modules/nf-core/bcftools/concat/main.nf | 19 +- modules/nf-core/bcftools/concat/meta.yml | 1 + modules/nf-core/bcftools/mpileup/main.nf | 2 +- modules/nf-core/bcftools/sort/main.nf | 14 +- modules/nf-core/bcftools/stats/main.nf | 14 +- modules/nf-core/bwa/index/main.nf | 2 +- modules/nf-core/bwa/mem/main.nf | 2 +- modules/nf-core/bwamem2/index/main.nf | 2 +- modules/nf-core/bwamem2/index/meta.yml | 2 +- modules/nf-core/bwamem2/mem/main.nf | 2 +- modules/nf-core/cat/cat/main.nf | 2 +- modules/nf-core/cat/fastq/main.nf | 2 +- modules/nf-core/cnvkit/antitarget/main.nf | 2 +- modules/nf-core/cnvkit/batch/main.nf | 161 ++++------------- modules/nf-core/cnvkit/reference/main.nf | 2 +- .../controlfreec/assesssignificance/main.nf | 2 +- modules/nf-core/controlfreec/freec/main.nf | 2 +- .../nf-core/controlfreec/freec2bed/main.nf | 2 +- .../nf-core/controlfreec/freec2circos/main.nf | 2 +- .../nf-core/controlfreec/makegraph/main.nf | 2 +- .../templates/dumpsoftwareversions.py | 3 +- modules/nf-core/deepvariant/main.nf | 8 +- .../nf-core/dragmap/align/dragmap-align.diff | 19 -- modules/nf-core/dragmap/align/main.nf | 6 +- .../dragmap/hashtable/dragmap-hashtable.diff | 14 -- modules/nf-core/dragmap/hashtable/main.nf | 2 +- modules/nf-core/ensemblvep/main.nf | 2 +- modules/nf-core/fastp/main.nf | 2 +- .../fgbio/callmolecularconsensusreads/main.nf | 2 +- modules/nf-core/fgbio/fastqtobam/main.nf | 2 +- modules/nf-core/fgbio/groupreadsbyumi/main.nf | 2 +- modules/nf-core/freebayes/main.nf | 2 +- modules/nf-core/gatk4/applybqsr/main.nf | 2 +- modules/nf-core/gatk4/applybqsrspark/main.nf | 2 +- modules/nf-core/gatk4/applyvqsr/main.nf | 2 +- .../nf-core/gatk4/baserecalibrator/main.nf | 2 +- .../gatk4/baserecalibratorspark/main.nf | 2 +- .../gatk4/calculatecontamination/main.nf | 2 +- .../nf-core/gatk4/cnnscorevariants/main.nf | 8 +- .../gatk4/createsequencedictionary/main.nf | 4 +- .../gatk4/estimatelibrarycomplexity/main.nf | 2 +- .../nf-core/gatk4/filtermutectcalls/main.nf | 2 +- .../gatk4/filtervarianttranches/main.nf | 2 +- .../nf-core/gatk4/gatherbqsrreports/main.nf | 2 +- .../gatk4/gatherpileupsummaries/main.nf | 2 +- .../nf-core/gatk4/genomicsdbimport/main.nf | 38 +++- modules/nf-core/gatk4/genotypegvcfs/main.nf | 15 +- .../nf-core/gatk4/getpileupsummaries/main.nf | 2 +- modules/nf-core/gatk4/haplotypecaller/main.nf | 19 +- .../nf-core/gatk4/intervallisttobed/main.nf | 2 +- .../gatk4/learnreadorientationmodel/main.nf | 2 +- .../markduplicates/gatk4-markduplicates.diff | 45 ----- modules/nf-core/gatk4/markduplicates/main.nf | 4 +- .../nf-core/gatk4/markduplicatesspark/main.nf | 2 +- .../nf-core/gatk4/mergemutectstats/main.nf | 2 +- modules/nf-core/gatk4/mergevcfs/main.nf | 2 +- modules/nf-core/gatk4/mutect2/main.nf | 2 +- .../nf-core/gatk4/variantrecalibrator/main.nf | 2 +- modules/nf-core/manta/germline/main.nf | 2 +- modules/nf-core/manta/somatic/main.nf | 2 +- modules/nf-core/manta/tumoronly/main.nf | 2 +- modules/nf-core/mosdepth/main.nf | 2 +- .../nf-core/msisensorpro/msi_somatic/main.nf | 2 +- modules/nf-core/msisensorpro/scan/main.nf | 2 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/multiqc.diff | 42 ----- modules/nf-core/samblaster/main.nf | 2 +- modules/nf-core/samtools/bam2fq/main.nf | 2 +- modules/nf-core/samtools/collatefastq/main.nf | 2 +- modules/nf-core/samtools/convert/main.nf | 2 +- modules/nf-core/samtools/faidx/main.nf | 2 +- modules/nf-core/samtools/index/main.nf | 2 +- modules/nf-core/samtools/merge/main.nf | 2 +- modules/nf-core/samtools/mpileup/main.nf | 2 +- modules/nf-core/samtools/stats/main.nf | 2 +- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/snpeff/main.nf | 2 +- modules/nf-core/strelka/germline/main.nf | 2 +- modules/nf-core/strelka/somatic/main.nf | 2 +- modules/nf-core/svdb/merge/main.nf | 2 +- modules/nf-core/tabix/bgziptabix/main.nf | 2 +- modules/nf-core/tabix/tabix/main.nf | 2 +- modules/nf-core/tiddit/sv/main.nf | 2 +- modules/nf-core/untar/main.nf | 2 +- modules/nf-core/unzip/main.nf | 2 +- modules/nf-core/vcftools/main.nf | 2 +- 88 files changed, 314 insertions(+), 424 deletions(-) delete mode 100644 modules/nf-core/dragmap/align/dragmap-align.diff delete mode 100644 modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff delete mode 100644 modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff delete mode 100644 modules/nf-core/multiqc/multiqc.diff diff --git a/CHANGELOG.md b/CHANGELOG.md index 013e5109f1..822fd30d95 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#860](https://github.com/nf-core/sarek/pull/860) - Replace local subworkflow with nf-core version - vcf_annotate_snpeff - [#865](https://github.com/nf-core/sarek/pull/865) - Replace local subworkflow with nf-core version - vcf_annotate_ensemblvep - [#874](https://github.com/nf-core/sarek/pull/874) - Update all modules +- [#890](https://github.com/nf-core/sarek/pull/890) - Sync `TEMPLATE` with `tools` `2.7.1` +- [#898](https://github.com/nf-core/sarek/pull/898) - Sync `TEMPLATE` with `tools` `2.7.2` ### Fixed diff --git a/modules.json b/modules.json index 770c334625..3182966d99 100644 --- a/modules.json +++ b/modules.json @@ -12,411 +12,411 @@ }, "bcftools/concat": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bcftools/mpileup": { "branch": "master", - "git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", - "git_sha": "78cf39939fbe160a1410c44a6c5946f9a4c56e7e", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bcftools/stats": { "branch": "master", - "git_sha": "78cf39939fbe160a1410c44a6c5946f9a4c56e7e", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bwa/index": { "branch": "master", - "git_sha": "9518fa4f65f3fb8cde24fde7d40333b39ec8fd65", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", - "git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bwamem2/index": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bwamem2/mem": { "branch": "master", - "git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "cat/cat": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "cnvkit/antitarget": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "cnvkit/batch": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "8f2dbc4736bb43346642ab42b2264bad35d924fc", "installed_by": ["modules"] }, "cnvkit/reference": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "controlfreec/assesssignificance": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "controlfreec/freec": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", 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"7578005a576f3ac1b0d4f10c037dde34cdedfb67", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "gatk4/mergemutectstats": { "branch": "master", - "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "c25943553f62be5f907e3c12c42eaf0a1b40746d", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "gatk4/mutect2": { "branch": "master", - "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "gatk4/variantrecalibrator": { "branch": "master", - "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "manta/germline": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "manta/somatic": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "manta/tumoronly": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "mosdepth": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "msisensorpro/msi_somatic": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "msisensorpro/scan": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": 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"samtools/faidx": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "samtools/mpileup": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "samtools/view": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "snpeff": { "branch": "master", - "git_sha": "262f7951d491a7f60ac1ae4a558fc2d725be9fc9", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules", "vcf_annotate_snpeff"] }, "strelka/germline": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "strelka/somatic": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", - "git_sha": "4a8a2caf44b87734b41ea4c67f508c14f0745ee7", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, "tiddit/sv": { "branch": "master", - "git_sha": "89f98091ac9e1653657b9e324e394b158d723a4f", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "unzip": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "vcftools": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index d2a58a557a..7d02cec5d2 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -2,13 +2,13 @@ process BCFTOOLS_CONCAT { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) + conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': + 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" input: - tuple val(meta), path(vcfs), path(tbi) + tuple val(meta), path(vcfs, stageAs: "?/*"), path(tbi, stageAs: "?/*") output: tuple val(meta), path("*.gz"), emit: vcf @@ -32,4 +32,15 @@ process BCFTOOLS_CONCAT { bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index 167dbe5a05..e8c83cd685 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -46,3 +46,4 @@ output: pattern: "versions.yml" authors: - "@abhi18av" + - "@nvnieuwk" diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index ffb6aa4a52..c9e42c4dd5 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -2,7 +2,7 @@ process BCFTOOLS_MPILEUP { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::bcftools=1.16" : null) + conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 6441def7cb..13d75b271a 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -2,7 +2,7 @@ process BCFTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::bcftools=1.16" : null) + conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" @@ -32,4 +32,16 @@ process BCFTOOLS_SORT { bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index 9db624ebf2..51e9c91c70 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -2,7 +2,7 @@ process BCFTOOLS_STATS { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::bcftools=1.16" : null) + conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" @@ -39,4 +39,16 @@ process BCFTOOLS_STATS { bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.bcftools_stats.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 6d70fc1598..7ccf3110f1 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -2,7 +2,7 @@ process BWA_INDEX { tag "$fasta" label 'process_single' - conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) + conda "bioconda::bwa=0.7.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' }" diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 363d1f2e0e..cbf34c2579 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -2,7 +2,7 @@ process BWA_MEM { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.16.1" : null) + conda "bioconda::bwa=0.7.17 bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' : 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' }" diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 0b7ad1991e..a236121b2a 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -2,7 +2,7 @@ process BWAMEM2_INDEX { tag "$fasta" label 'process_single' - conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) + conda "bioconda::bwa-mem2=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : 'quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0' }" diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml index a6b11ae5fd..40c26c3873 100644 --- a/modules/nf-core/bwamem2/index/meta.yml +++ b/modules/nf-core/bwamem2/index/meta.yml @@ -6,7 +6,7 @@ keywords: - genome - reference tools: - - bwa: + - bwamem2: description: | BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome. diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 84b99dfa02..489b17043a 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -2,7 +2,7 @@ process BWAMEM2_MEM { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.16.1" : null) + conda "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' : 'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' }" diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 40e53f3eda..840af4b9c6 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -2,7 +2,7 @@ process CAT_CAT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null) + conda "conda-forge::pigz=2.3.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : 'quay.io/biocontainers/pigz:2.3.4' }" diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 4fa365d33e..8a0b5600c2 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -2,7 +2,7 @@ process CAT_FASTQ { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "conda-forge::sed=4.7" : null) + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index bf6461bdb0..f5cd1186ee 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -2,7 +2,7 @@ process CNVKIT_ANTITARGET { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) + conda "bioconda::cnvkit=0.9.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': 'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index ac3ace4f69..e0c2557574 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -2,7 +2,7 @@ process CNVKIT_BATCH { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1' : null) + conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' : 'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' }" @@ -13,6 +13,7 @@ process CNVKIT_BATCH { path fasta_fai path targets path reference + val panel_of_normals output: tuple val(meta), path("*.bed"), emit: bed @@ -63,133 +64,39 @@ process CNVKIT_BATCH { } } - def target_args = targets ? "--targets $targets" : "" - def reference_args = reference ? "--reference $reference" : "" + // generation of panel of normals + def generate_pon = panel_of_normals ? true : false - // somatic_mode cram_input - if (tumor_cram && normal_cram){ - """ - samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out - samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out - - cnvkit.py \\ - batch \\ - $tumor_out \\ - $normal_args \\ - $fasta_args \\ - $reference_args \\ - $target_args \\ - --processes $task.cpus \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") - END_VERSIONS - """ - } - // somatic_mode bam_input - else if (tumor_bam && normal_bam){ - """ - cnvkit.py \\ - batch \\ - $tumor_out \\ - $normal_args \\ - $fasta_args \\ - $reference_args \\ - $target_args \\ - --processes $task.cpus \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") - END_VERSIONS - """ - } - // tumor_only_mode cram_input - else if(tumor_cram && !normal_exists){ - """ - samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out - - cnvkit.py \\ - batch \\ - $tumor_out \\ - $normal_args \\ - $fasta_args \\ - $reference_args \\ - $target_args \\ - --processes $task.cpus \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") - END_VERSIONS - """ - } - // tumor_only bam_input - else if(tumor_bam && !normal_exists){ - """ - cnvkit.py \\ - batch \\ - $tumor_out \\ - $normal_args \\ - $fasta_args \\ - $reference_args \\ - $target_args \\ - --processes $task.cpus \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") - END_VERSIONS - """ - } - // germline mode cram_input - // normal_args must be --normal [] - else if (normal_cram && !tumor_exists){ - """ - samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out - - cnvkit.py \\ - batch \\ - $tumor_out \\ - $normal_args \\ - $fasta_args \\ - $reference_args \\ - $target_args \\ - --processes $task.cpus \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") - END_VERSIONS - """ - } - // germline mode bam_input - else if (normal_bam && !tumor_exists){ - """ - cnvkit.py \\ - batch \\ - $tumor_out \\ - $normal_args \\ - $fasta_args \\ - $reference_args \\ - $target_args \\ - --processes $task.cpus \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") - END_VERSIONS - """ + if (generate_pon && !tumor_exists && normal_bam){ + def pon_input = normal.collect("$it").join(' ') + normal_args = "--normal $pon_input" } + def target_args = targets ? "--targets $targets" : "" + def reference_args = reference ? "--reference $reference" : "" + + def samtools_cram_convert = '' + samtools_cram_convert += normal_cram ? " samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out\n" : '' + samtools_cram_convert += tumor_cram ? " samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out\n" : '' + def versions = normal_cram || tumor_cram ? + "samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')\n cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g')" : + "cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g')" + """ + $samtools_cram_convert + + cnvkit.py \\ + batch \\ + $tumor_out \\ + $normal_args \\ + $fasta_args \\ + $reference_args \\ + $target_args \\ + --processes $task.cpus \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ${versions} + END_VERSIONS + """ } diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index 10458f2786..f04bdb2126 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -2,7 +2,7 @@ process CNVKIT_REFERENCE { tag "$fasta" label 'process_low' - conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) + conda "bioconda::cnvkit=0.9.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': 'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index 4bdb00b386..fadbe73f9a 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) + conda "bioconda::control-freec=11.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 857ffdee17..78c8b58bce 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_FREEC { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) + conda "bioconda::control-freec=11.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index aefc200e81..9a70da674a 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_FREEC2BED { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) + conda "bioconda::control-freec=11.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index 8f9be30097..42e4d8fcaa 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_FREEC2CIRCOS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) + conda "bioconda::control-freec=11.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index a8954d726a..3c9afe5b3e 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -2,7 +2,7 @@ process CONTROLFREEC_MAKEGRAPH { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) + conda "bioconda::control-freec=11.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index e55b8d43a9..da03340857 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -4,11 +4,10 @@ """Provide functions to merge multiple versions.yml files.""" +import yaml import platform from textwrap import dedent -import yaml - def _make_versions_html(versions): """Generate a tabular HTML output of all versions for MultiQC.""" diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf index de48d9c1e4..7e11b766d9 100644 --- a/modules/nf-core/deepvariant/main.nf +++ b/modules/nf-core/deepvariant/main.nf @@ -2,13 +2,13 @@ process DEEPVARIANT { tag "$meta.id" label 'process_medium' + container "google/deepvariant:1.4.0" - if (params.enable_conda) { - exit 1, "Conda environments cannot be used with DeepVariant at the moment. Please use Docker or Singularity containers." + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + exit 1, "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "google/deepvariant:1.4.0" - input: tuple val(meta), path(input), path(index), path(intervals) path(fasta) diff --git a/modules/nf-core/dragmap/align/dragmap-align.diff b/modules/nf-core/dragmap/align/dragmap-align.diff deleted file mode 100644 index 90f2a15e43..0000000000 --- a/modules/nf-core/dragmap/align/dragmap-align.diff +++ /dev/null @@ -1,19 +0,0 @@ -Changes in module 'nf-core/dragmap/align' ---- modules/nf-core/dragmap/align/main.nf -+++ modules/nf-core/dragmap/align/main.nf -@@ -2,10 +2,10 @@ - tag "$meta.id" - label 'process_high' - -- conda (params.enable_conda ? "bioconda::dragmap=1.3.0 bioconda::samtools=1.16.1 conda-forge::pigz=2.3.4" : null) -+ conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0': -- 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0' }" -+ 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': -+ 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }" - - input: - tuple val(meta) , path(reads) - -************************************************************ diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index 082b189183..22e4b7c145 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -2,10 +2,10 @@ process DRAGMAP_ALIGN { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) + conda "bioconda::dragmap=1.3.0 bioconda::samtools=1.16.1 conda-forge::pigz=2.3.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': - 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0': + 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0' }" input: tuple val(meta) , path(reads) diff --git a/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff b/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff deleted file mode 100644 index 9f948b4852..0000000000 --- a/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff +++ /dev/null @@ -1,14 +0,0 @@ -Changes in module 'nf-core/dragmap/hashtable' ---- modules/nf-core/dragmap/hashtable/main.nf -+++ modules/nf-core/dragmap/hashtable/main.nf -@@ -2,7 +2,7 @@ - tag "$fasta" - label 'process_high' - -- conda (params.enable_conda ? "bioconda::dragmap=1.3.0" : null) -+ conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/dragmap:1.3.0--h72d16da_1': - 'quay.io/biocontainers/dragmap:1.3.0--h72d16da_1' }" - -************************************************************ diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index a0fb1d7731..e64ea487f1 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -2,7 +2,7 @@ process DRAGMAP_HASHTABLE { tag "$fasta" label 'process_high' - conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) + conda "bioconda::dragmap=1.3.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dragmap:1.3.0--h72d16da_1': 'quay.io/biocontainers/dragmap:1.3.0--h72d16da_1' }" diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index a6049034e6..02132ababf 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -2,7 +2,7 @@ process ENSEMBLVEP { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::ensembl-vep=108.2" : null) + conda "bioconda::ensembl-vep=108.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ensembl-vep:108.2--pl5321h4a94de4_0' : 'quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0' }" diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 207258ad75..e1ed9288de 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -2,7 +2,7 @@ process FASTP { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) + conda "bioconda::fastp=0.23.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : 'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }" diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 88c5ab4c1a..edbbfab294 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -2,7 +2,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) + conda "bioconda::fgbio=2.0.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index a3279491cf..ea55c07e23 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -2,7 +2,7 @@ process FGBIO_FASTQTOBAM { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) + conda "bioconda::fgbio=2.0.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 3014355c4f..b05c4cd82a 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -2,7 +2,7 @@ process FGBIO_GROUPREADSBYUMI { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) + conda "bioconda::fgbio=2.0.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index dfc65a3bc3..35ced9f1ad 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -2,7 +2,7 @@ process FREEBAYES { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::freebayes=1.3.6" : null) + conda "bioconda::freebayes=1.3.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hbfe0e7f_2' : 'quay.io/biocontainers/freebayes:1.3.6--hbfe0e7f_2' }" diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index d3e251a282..9dc6ac68ad 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -2,7 +2,7 @@ process GATK4_APPLYBQSR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/applybqsrspark/main.nf b/modules/nf-core/gatk4/applybqsrspark/main.nf index 9b47dc916f..0790d2abb4 100644 --- a/modules/nf-core/gatk4/applybqsrspark/main.nf +++ b/modules/nf-core/gatk4/applybqsrspark/main.nf @@ -2,7 +2,7 @@ process GATK4_APPLYBQSR_SPARK { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" : null) + conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" container 'broadinstitute/gatk:4.3.0.0' input: diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 6d18463d8d..f9bb2bf720 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -2,7 +2,7 @@ process GATK4_APPLYVQSR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 222dfae9da..b668a1fc90 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -2,7 +2,7 @@ process GATK4_BASERECALIBRATOR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/baserecalibratorspark/main.nf b/modules/nf-core/gatk4/baserecalibratorspark/main.nf index d923721515..4fdf1b27f3 100644 --- a/modules/nf-core/gatk4/baserecalibratorspark/main.nf +++ b/modules/nf-core/gatk4/baserecalibratorspark/main.nf @@ -2,7 +2,7 @@ process GATK4_BASERECALIBRATOR_SPARK { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" : null) + conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" container 'broadinstitute/gatk:4.3.0.0' input: diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index a270c03773..c2a6a3d171 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -2,7 +2,7 @@ process GATK4_CALCULATECONTAMINATION { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf index 319ab43887..0aaead007f 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -3,11 +3,13 @@ process GATK4_CNNSCOREVARIANTS { label 'process_low' //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - if (params.enable_conda) { - exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers." - } container "broadinstitute/gatk:4.3.0.0" //Biocontainers is missing a package + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + exit 1, "GATK4_CNNSCOREVARIANTS module does not support Conda. Please use Docker / Singularity / Podman instead." + } + input: tuple val(meta), path(vcf), path(tbi), path(aligned_input), path(intervals) path fasta diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index fb78cdf5dc..bc324adaca 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -2,7 +2,7 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" @@ -41,7 +41,7 @@ process GATK4_CREATESEQUENCEDICTIONARY { stub: """ - touch test.dict + touch ${fasta.baseName}.dict cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 9d56bb3e57..123313835a 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -2,7 +2,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 130c83b654..f3585bb306 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -2,7 +2,7 @@ process GATK4_FILTERMUTECTCALLS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 5a2117e980..ed6af4e664 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -2,7 +2,7 @@ process GATK4_FILTERVARIANTTRANCHES { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index f560d47670..1de9754eb0 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -2,7 +2,7 @@ process GATK4_GATHERBQSRREPORTS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index 05e7f13d53..ff669de9df 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -2,7 +2,7 @@ process GATK4_GATHERPILEUPSUMMARIES { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 45f2e75878..f11a8e56b4 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -2,7 +2,7 @@ process GATK4_GENOMICSDBIMPORT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" @@ -31,6 +31,7 @@ process GATK4_GENOMICSDBIMPORT { genomicsdb_command = "--genomicsdb-workspace-path ${prefix}" interval_command = interval_file ? "--intervals ${interval_file}" : "--intervals ${interval_value}" + updated_db = "" // settings changed for running get intervals list mode if run_intlist is true if (run_intlist) { @@ -64,4 +65,39 @@ process GATK4_GENOMICSDBIMPORT { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + + genomicsdb_command = "--genomicsdb-workspace-path ${prefix}" + interval_command = interval_file ? "--intervals ${interval_file}" : "--intervals ${interval_value}" + updated_db = "" + + // settings changed for running get intervals list mode if run_intlist is true + if (run_intlist) { + genomicsdb_command = "--genomicsdb-update-workspace-path ${wspace}" + interval_command = "--output-interval-list-to-file ${prefix}.interval_list" + } + + // settings changed for running update gendb mode. input_command same as default, update_db forces module to emit the updated gendb + if (run_updatewspace) { + genomicsdb_command = "--genomicsdb-update-workspace-path ${wspace}" + interval_command = '' + updated_db = "${wspace}" + } + + def stub_genomicsdb = genomicsdb_command == "--genomicsdb-workspace-path ${prefix}" ? "touch ${prefix}" : "" + def stub_interval = interval_command == "--output-interval-list-to-file ${prefix}.interval_list" ? "touch ${prefix}.interval_list" : "" + def stub_update = updated_db != "" ? "touch ${wspace}" : "" + + """ + ${stub_genomicsdb} + ${stub_interval} + ${stub_update} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 043e006f70..74fe434cf3 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -2,7 +2,7 @@ process GATK4_GENOTYPEGVCFS { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" @@ -51,4 +51,17 @@ process GATK4_GENOTYPEGVCFS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 99b2595ca9..a9130f17aa 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -2,7 +2,7 @@ process GATK4_GETPILEUPSUMMARIES { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 51572176df..c011376a3e 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -2,7 +2,7 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" @@ -55,4 +55,21 @@ process GATK4_HAPLOTYPECALLER { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def bamout_command = args.contains("--bam-writer-type") ? "--bam-output ${prefix.replaceAll('.g\\s*$', '')}.realigned.bam" : "" + + def stub_realigned_bam = bamout_command ? "touch ${prefix.replaceAll('.g\\s*$', '')}.realigned.bam" : "" + """ + touch ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + ${stub_realigned_bam} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 901b9301c1..3a2d596ac9 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -2,7 +2,7 @@ process GATK4_INTERVALLISTTOBED { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index 3f206296f5..f93753b91e 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -2,7 +2,7 @@ process GATK4_LEARNREADORIENTATIONMODEL { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff deleted file mode 100644 index 8ba713052b..0000000000 --- a/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff +++ /dev/null @@ -1,45 +0,0 @@ -Changes in module 'nf-core/gatk4/markduplicates' ---- modules/nf-core/gatk4/markduplicates/main.nf -+++ modules/nf-core/gatk4/markduplicates/main.nf -@@ -2,10 +2,10 @@ - tag "$meta.id" - label 'process_medium' - -- conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) -+ conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0 bioconda::samtools=1.16.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': -- 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" -+ 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0': -+ 'quay.io/biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0' }" - - input: - tuple val(meta), path(bam) -@@ -38,20 +38,20 @@ - """ - 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 -+ samtools view -Ch -T ${fasta} -o ${prefix} ${prefix}.bam -+ rm ${prefix}.bam -+ samtools index ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') -+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS - """ --} -+} -************************************************************ diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 10ca04f100..4b52e5e613 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -2,7 +2,7 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0 bioconda::samtools=1.16.1" : null) + conda "bioconda::gatk4=4.3.0.0 bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0': 'quay.io/biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0' }" @@ -54,4 +54,4 @@ process GATK4_MARKDUPLICATES { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/nf-core/gatk4/markduplicatesspark/main.nf b/modules/nf-core/gatk4/markduplicatesspark/main.nf index a632c65f78..bb30057c76 100644 --- a/modules/nf-core/gatk4/markduplicatesspark/main.nf +++ b/modules/nf-core/gatk4/markduplicatesspark/main.nf @@ -2,7 +2,7 @@ process GATK4_MARKDUPLICATES_SPARK { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" : null) + conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" container 'broadinstitute/gatk:4.3.0.0' input: diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index c666d3c60e..28bb61332e 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -2,7 +2,7 @@ process GATK4_MERGEMUTECTSTATS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 08fb3969e3..d418468ffe 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -2,7 +2,7 @@ process GATK4_MERGEVCFS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 693340d9eb..c2085266ca 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -2,7 +2,7 @@ process GATK4_MUTECT2 { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index dd317a9bbd..d0d92fc270 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -2,7 +2,7 @@ process GATK4_VARIANTRECALIBRATOR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda "bioconda::gatk4=4.3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index 5f2964fbd0..2feb6ed29b 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -2,7 +2,7 @@ process MANTA_GERMLINE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) + conda "bioconda::manta=1.6.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }" diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index 0b40965b7c..c559c8851b 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -2,7 +2,7 @@ process MANTA_SOMATIC { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) + conda "bioconda::manta=1.6.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }" diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index 759f9cb9ec..3fea008fc4 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -2,7 +2,7 @@ process MANTA_TUMORONLY { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) + conda "bioconda::manta=1.6.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }" diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index d7e3c92904..511d29ba47 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -2,7 +2,7 @@ process MOSDEPTH { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) + conda "bioconda::mosdepth=0.3.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : 'quay.io/biocontainers/mosdepth:0.3.3--hdfd78af_1'}" diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index e2da70de7c..0713aa4b27 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -2,7 +2,7 @@ process MSISENSORPRO_MSI_SOMATIC { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) + conda "bioconda::msisensor-pro=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : 'quay.io/biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index 752606d620..efeda36e4e 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -2,7 +2,7 @@ process MSISENSORPRO_SCAN { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) + conda "bioconda::msisensor-pro=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : 'quay.io/biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 68f66bea74..7d43cd35bf 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -8,9 +8,7 @@ process MULTIQC { input: path multiqc_files, stageAs: "?/*" - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) + tuple path(multiqc_config), path(multiqc_logo) output: path "*multiqc_report.html", emit: report diff --git a/modules/nf-core/multiqc/multiqc.diff b/modules/nf-core/multiqc/multiqc.diff deleted file mode 100644 index f6c829984a..0000000000 --- a/modules/nf-core/multiqc/multiqc.diff +++ /dev/null @@ -1,42 +0,0 @@ -Changes in module 'nf-core/multiqc' ---- modules/nf-core/multiqc/main.nf -+++ modules/nf-core/multiqc/main.nf -@@ -1,16 +1,14 @@ - process MULTIQC { -- label 'process_single' -+ label 'process_medium' - -- conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) -+ conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : -- 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" -+ 'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1' : -+ 'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }" - - input: - path multiqc_files, stageAs: "?/*" -- path(multiqc_config) -- path(extra_multiqc_config) -- path(multiqc_logo) -+ tuple path(multiqc_config), path(multiqc_logo) - - output: - path "*multiqc_report.html", emit: report -@@ -24,13 +22,11 @@ - script: - def args = task.ext.args ?: '' - def config = multiqc_config ? "--config $multiqc_config" : '' -- def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - """ - multiqc \\ - --force \\ -+ $config \\ - $args \\ -- $config \\ -- $extra_config \\ - . - - cat <<-END_VERSIONS > versions.yml - -************************************************************ diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index 64e498431e..2177d81fd3 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -2,7 +2,7 @@ process SAMBLASTER { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.16.1" : null) + conda "bioconda::samblaster=0.1.26 bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:cee56b506ceb753d4bbef7e05b81e1bfc25d937f-0' : 'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:cee56b506ceb753d4bbef7e05b81e1bfc25d937f-0' }" diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index a6bd59d93f..0b06352533 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_BAM2FQ { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 8d6b1fb730..e464aee0b1 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_COLLATEFASTQ { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index ab4833a45e..7efebb8e51 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_CONVERT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 2830963e88..ce6580d25d 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_FAIDX { tag "$fasta" label 'process_single' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 8577dc9df2..8b95687a96 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 89dd072a9f..a80ff3a227 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_MERGE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index 6c6b1bf61d..28092683ac 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_MPILEUP { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 5d2fd68a04..0a2a364015 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_STATS { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 314c8b729d..729c85e54e 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_VIEW { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index ac615bf73e..bab7050cf7 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -2,7 +2,7 @@ process SNPEFF { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::snpeff=5.1" : null) + conda "bioconda::snpeff=5.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' : 'quay.io/biocontainers/snpeff:5.1--hdfd78af_2' }" diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 1f59bee157..5b837f6393 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -2,7 +2,7 @@ process STRELKA_GERMLINE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) + conda "bioconda::strelka=2.9.10" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : 'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }" diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index 08b298a463..74c9c443b6 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -2,7 +2,7 @@ process STRELKA_SOMATIC { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) + conda "bioconda::strelka=2.9.10" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : 'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }" diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 7dd926537f..8544daff99 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -1,7 +1,7 @@ process SVDB_MERGE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::svdb=2.8.1 bioconda::samtools=1.16.1" : null) + conda "bioconda::svdb=2.8.1 bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:af6f8534cd538a85ff43a2eae1b52b143e7abd05-0': 'quay.io/biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:af6f8534cd538a85ff43a2eae1b52b143e7abd05-0' }" diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 0d05984add..d3a3bbffce 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -2,7 +2,7 @@ process TABIX_BGZIPTABIX { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) + conda "bioconda::tabix=1.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 21b2e79f48..9a404db931 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -2,7 +2,7 @@ process TABIX_TABIX { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) + conda "bioconda::tabix=1.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 7faefa99c7..45f9588a9e 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -2,7 +2,7 @@ process TIDDIT_SV { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::tiddit=3.3.2" : null) + conda "bioconda::tiddit=3.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tiddit:3.3.2--py310hc2b7f4b_0' : 'quay.io/biocontainers/tiddit:3.3.2--py310hc2b7f4b_0' }" diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 71eea7b2c6..16bccc9059 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ process UNTAR { tag "$archive" label 'process_single' - conda (params.enable_conda ? "conda-forge::sed=4.7" : null) + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index bb645ca63f..18c1f08c86 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -2,7 +2,7 @@ process UNZIP { tag "$archive" label 'process_single' - conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) + conda "bioconda::p7zip=15.09" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4' : 'quay.io/biocontainers/p7zip:15.09--h2d50403_4' }" diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index feefb0e3f8..637543c0db 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -2,7 +2,7 @@ process VCFTOOLS { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) + conda "bioconda::vcftools=0.1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4' : 'quay.io/biocontainers/vcftools:0.1.16--he513fc3_4' }" From 35125c5ec97a8fdf111b04bc899552a25ff64013 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Dec 2022 16:39:24 +0100 Subject: [PATCH 03/14] patch modules --- .../nf-core/dragmap/align/dragmap-align.diff | 19 ++++++++ modules/nf-core/dragmap/align/main.nf | 6 +-- .../markduplicates/gatk4-markduplicates.diff | 45 +++++++++++++++++++ 3 files changed, 67 insertions(+), 3 deletions(-) create mode 100644 modules/nf-core/dragmap/align/dragmap-align.diff create mode 100644 modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff diff --git a/modules/nf-core/dragmap/align/dragmap-align.diff b/modules/nf-core/dragmap/align/dragmap-align.diff new file mode 100644 index 0000000000..7c472c71a0 --- /dev/null +++ b/modules/nf-core/dragmap/align/dragmap-align.diff @@ -0,0 +1,19 @@ +Changes in module 'nf-core/dragmap/align' +--- modules/nf-core/dragmap/align/main.nf ++++ modules/nf-core/dragmap/align/main.nf +@@ -2,10 +2,10 @@ + tag "$meta.id" + label 'process_high' + +- conda "bioconda::dragmap=1.3.0 bioconda::samtools=1.16.1 conda-forge::pigz=2.3.4" ++ conda "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0': +- 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0' }" ++ 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': ++ 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }" + + input: + tuple val(meta) , path(reads) + +************************************************************ diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index 22e4b7c145..6138f58392 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -2,10 +2,10 @@ process DRAGMAP_ALIGN { tag "$meta.id" label 'process_high' - conda "bioconda::dragmap=1.3.0 bioconda::samtools=1.16.1 conda-forge::pigz=2.3.4" + conda "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0': - 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': + 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }" input: tuple val(meta) , path(reads) diff --git a/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff new file mode 100644 index 0000000000..5f511493ac --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff @@ -0,0 +1,45 @@ +Changes in module 'nf-core/gatk4/markduplicates' +--- modules/nf-core/gatk4/markduplicates/main.nf ++++ modules/nf-core/gatk4/markduplicates/main.nf +@@ -2,10 +2,10 @@ + tag "$meta.id" + label 'process_medium' + +- conda "bioconda::gatk4=4.3.0.0" ++ conda "bioconda::gatk4=4.3.0.0 bioconda::samtools=1.16.1" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': +- 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" ++ 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0': ++ 'quay.io/biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0' }" + + input: + tuple val(meta), path(bam) +@@ -38,20 +38,20 @@ + """ + gatk --java-options "-Xmx${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 ++ samtools view -Ch -T ${fasta} -o ${prefix} ${prefix}.bam ++ rm ${prefix}.bam ++ samtools index ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') ++ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + } + +************************************************************ From 44fee16bf33ef4dd33d2d09ab1d0e0c35aa7886a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Dec 2022 16:48:35 +0100 Subject: [PATCH 04/14] better patch --- .../nf-core/gatk4/markduplicates/gatk4-markduplicates.diff | 4 ++-- modules/nf-core/gatk4/markduplicates/main.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff index 5f511493ac..5856135cf6 100644 --- a/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff +++ b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff @@ -40,6 +40,6 @@ Changes in module 'nf-core/gatk4/markduplicates' + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ - } - +-} ++} ************************************************************ diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 4b52e5e613..19757d84b8 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -54,4 +54,4 @@ process GATK4_MARKDUPLICATES { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ -} +} \ No newline at end of file From dd681c4f628562f3f412a40e2ebb154119840d23 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Dec 2022 17:12:46 +0100 Subject: [PATCH 05/14] no pon generation in sarek --- subworkflows/local/bam_variant_calling_cnvkit/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/bam_variant_calling_cnvkit/main.nf b/subworkflows/local/bam_variant_calling_cnvkit/main.nf index 14892898ed..4f7781013d 100644 --- a/subworkflows/local/bam_variant_calling_cnvkit/main.nf +++ b/subworkflows/local/bam_variant_calling_cnvkit/main.nf @@ -17,7 +17,8 @@ workflow BAM_VARIANT_CALLING_CNVKIT { main: ch_versions = Channel.empty() - CNVKIT_BATCH(cram_recalibrated, fasta, fasta_fai, targets, reference) + generate_pon = false + CNVKIT_BATCH(cram_recalibrated, fasta, fasta_fai, targets, reference, generate_pon) ch_versions = ch_versions.mix(CNVKIT_BATCH.out.versions) From e8da460a5cf479c19737d03606b15643a6a0d3fe Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Dec 2022 17:19:31 +0100 Subject: [PATCH 06/14] fix last modules --- modules.json | 3 +-- modules/nf-core/ascat/main.nf | 2 +- modules/nf-core/multiqc/main.nf | 4 +++- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/modules.json b/modules.json index 3182966d99..e250fd69e7 100644 --- a/modules.json +++ b/modules.json @@ -316,8 +316,7 @@ "multiqc": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"], - "patch": "modules/nf-core/multiqc/multiqc.diff" + "installed_by": ["modules"] }, "samblaster": { "branch": "master", diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index df6141d010..88ee819d14 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -2,7 +2,7 @@ process ASCAT { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null) + conda "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0': 'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0' }" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 7d43cd35bf..68f66bea74 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -8,7 +8,9 @@ process MULTIQC { input: path multiqc_files, stageAs: "?/*" - tuple path(multiqc_config), path(multiqc_logo) + path(multiqc_config) + path(extra_multiqc_config) + path(multiqc_logo) output: path "*multiqc_report.html", emit: report From 4804afca30ed5d7ed31864fb68a0e417e554b4d2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Dec 2022 17:39:08 +0100 Subject: [PATCH 07/14] nf-core bump-version --nextflow 22.10.1 --- .github/workflows/ci.yml | 2 +- .github/workflows/pytest-workflow.yml | 2 +- README.md | 4 ++-- nextflow.config | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 411ae0fcfc..2a95af93b3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false matrix: NXF_VER: - - "21.10.3" + - "22.10.1" - "latest-everything" test: - "default" diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 3ffff196ef..97800229c4 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -34,7 +34,7 @@ jobs: tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] profile: ["docker", "singularity", "conda"] NXF_VER: - - "21.10.3" + - "22.10.1" - "latest-everything" exclude: - profile: "conda" diff --git a/README.md b/README.md index 1ccfee3502..7b7e6dcfb6 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/sarek/results) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3476426-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3476425) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -49,7 +49,7 @@ By default, the pipeline currently performs the following: ## Quick Start -1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) +1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`) 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. diff --git a/nextflow.config b/nextflow.config index 1e53d3e098..23a655b0eb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -283,7 +283,7 @@ manifest { homePage = 'https://github.com/nf-core/sarek' description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' - nextflowVersion = '!>=21.10.3' + nextflowVersion = '!>=22.10.1' version = '3.2dev' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' } From 5564a293e6835ad7ef87e856d5719004a043bc7a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 19 Dec 2022 17:55:23 +0100 Subject: [PATCH 08/14] fix conda --- .github/workflows/ci.yml | 3 --- conf/test/test.config | 4 +++- modules/local/add_info_to_vcf/main.nf | 2 +- modules/local/build_intervals/main.nf | 2 +- modules/local/create_intervals_bed/main.nf | 2 +- 5 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2a95af93b3..19a00b7c74 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,9 +28,6 @@ jobs: test: - "default" profile: ["docker", "singularity", "conda"] - exclude: - - NXF_VER: "latest-everything" - profile: "conda" env: NXF_ANSI_LOG: false steps: diff --git a/conf/test/test.config b/conf/test/test.config index 18acff808e..26c5ee1822 100644 --- a/conf/test/test.config +++ b/conf/test/test.config @@ -93,13 +93,14 @@ process { if (System.getenv('PROFILE')) { if ("$PROFILE" == "conda") { conda.createTimeout = "120 min" - params.enable_conda = true + conda.enabled = true charliecloud.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false singularity.enabled = false } else if ("$PROFILE" == "docker") { + conda.enabled = false docker.enabled = true docker.userEmulation = { params.use_gatk_spark ? false : true }.call() charliecloud.enabled = false @@ -107,6 +108,7 @@ if (System.getenv('PROFILE')) { shifter.enabled = false singularity.enabled = false } else if ("$PROFILE" == "singularity") { + conda.enabled = false params.singularity_pull_docker_container = false singularity.autoMounts = true singularity.enabled = true diff --git a/modules/local/add_info_to_vcf/main.nf b/modules/local/add_info_to_vcf/main.nf index 91c4e6b3b4..c0ca9e918f 100644 --- a/modules/local/add_info_to_vcf/main.nf +++ b/modules/local/add_info_to_vcf/main.nf @@ -1,7 +1,7 @@ process ADD_INFO_TO_VCF { tag "$meta.id" - conda (params.enable_conda ? "anaconda::gawk=5.1.0" : null) + conda "anaconda::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : 'quay.io/biocontainers/gawk:5.1.0' }" diff --git a/modules/local/build_intervals/main.nf b/modules/local/build_intervals/main.nf index 9f14182ea1..9acb0cc7ea 100644 --- a/modules/local/build_intervals/main.nf +++ b/modules/local/build_intervals/main.nf @@ -1,7 +1,7 @@ process BUILD_INTERVALS { tag "$meta.id" - conda (params.enable_conda ? "anaconda::gawk=5.1.0" : null) + conda "anaconda::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : 'quay.io/biocontainers/gawk:5.1.0' }" diff --git a/modules/local/create_intervals_bed/main.nf b/modules/local/create_intervals_bed/main.nf index f46a0df091..f96a4c33fa 100644 --- a/modules/local/create_intervals_bed/main.nf +++ b/modules/local/create_intervals_bed/main.nf @@ -1,7 +1,7 @@ process CREATE_INTERVALS_BED { tag "$intervals" - conda (params.enable_conda ? "anaconda::gawk=5.1.0" : null) + conda "anaconda::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : 'quay.io/biocontainers/gawk:5.1.0' }" From c6fcf68dd496aef2f0ad9291c0aafbd1edb18d7a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 20 Dec 2022 09:12:46 +0100 Subject: [PATCH 09/14] fix vep test --- tests/test_annotation_vep.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_annotation_vep.yml b/tests/test_annotation_vep.yml index 3ed3df474f..fdfeda0f43 100644 --- a/tests/test_annotation_vep.yml +++ b/tests/test_annotation_vep.yml @@ -12,7 +12,7 @@ # test_VEP.ann.summary.html changes md5sums on reruns. contains: ["test.vcf.gzOutput filetest_VEP.ann.vcf.gz"] - name: Run VEP with fasta - command: nextflow run main.nf -profile test,annotation --tools vep --vep_include_fasta --skip_tools multiqc + command: nextflow run main.nf -profile test,annotation --tools vep --vep_include_fasta --skip_tools multiqc --outdir results tags: - annotation - vep From 30992001bb03b4f14d06cb5ab71a16248b75f45c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 20 Dec 2022 09:13:05 +0100 Subject: [PATCH 10/14] add conda back --- .github/workflows/pytest-workflow.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 97800229c4..36099a3f2c 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -37,8 +37,6 @@ jobs: - "22.10.1" - "latest-everything" exclude: - - profile: "conda" - NXF_VER: "latest-everything" - profile: "conda" tags: umi - profile: "conda" From f2932b70229cc7cdb885bef53b1283e1dc368fa9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 20 Dec 2022 14:38:53 +0100 Subject: [PATCH 11/14] update CHANGELOG + fix version of dragmap --- CHANGELOG.md | 3 +++ .../dragmap/hashtable/dragmap-hashtable.diff | 19 +++++++++++++++++++ modules/nf-core/dragmap/hashtable/main.nf | 6 +++--- 3 files changed, 25 insertions(+), 3 deletions(-) create mode 100644 modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff diff --git a/CHANGELOG.md b/CHANGELOG.md index 822fd30d95..b176647c59 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#874](https://github.com/nf-core/sarek/pull/874) - Update all modules - [#890](https://github.com/nf-core/sarek/pull/890) - Sync `TEMPLATE` with `tools` `2.7.1` - [#898](https://github.com/nf-core/sarek/pull/898) - Sync `TEMPLATE` with `tools` `2.7.2` +- [#898](https://github.com/nf-core/sarek/pull/898) - Nextflow minimal version is now `22.10.1` ### Fixed @@ -34,6 +35,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed +- [#898](https://github.com/nf-core/sarek/pull/898) - Params `enable_conda` was removed + ### Dependencies | Dependency | Old version | New version | diff --git a/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff b/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff new file mode 100644 index 0000000000..ffaf908cd9 --- /dev/null +++ b/modules/nf-core/dragmap/hashtable/dragmap-hashtable.diff @@ -0,0 +1,19 @@ +Changes in module 'nf-core/dragmap/hashtable' +--- modules/nf-core/dragmap/hashtable/main.nf ++++ modules/nf-core/dragmap/hashtable/main.nf +@@ -2,10 +2,10 @@ + tag "$fasta" + label 'process_high' + +- conda "bioconda::dragmap=1.3.0" ++ conda "bioconda::dragmap=1.2.1" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/dragmap:1.3.0--h72d16da_1': +- 'quay.io/biocontainers/dragmap:1.3.0--h72d16da_1' }" ++ 'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--h72d16da_1': ++ 'quay.io/biocontainers/dragmap:1.2.1--h72d16da_1' }" + + input: + tuple val(meta), path(fasta) + +************************************************************ diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index e64ea487f1..46d26c4d56 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -2,10 +2,10 @@ process DRAGMAP_HASHTABLE { tag "$fasta" label 'process_high' - conda "bioconda::dragmap=1.3.0" + conda "bioconda::dragmap=1.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/dragmap:1.3.0--h72d16da_1': - 'quay.io/biocontainers/dragmap:1.3.0--h72d16da_1' }" + 'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--h72d16da_1': + 'quay.io/biocontainers/dragmap:1.2.1--h72d16da_1' }" input: tuple val(meta), path(fasta) From 557e859b8172193b2b0864182faf4cd26d15d6ba Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 20 Dec 2022 16:56:44 +0100 Subject: [PATCH 12/14] bcftools/concat --- modules.json | 2 +- modules/nf-core/bcftools/concat/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index e250fd69e7..58b87f0404 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "bcftools/concat": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "582ff1755bdd205c65e2ba4c31e0a008dae299ec", "installed_by": ["modules"] }, "bcftools/mpileup": { diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 7d02cec5d2..c7c39d9fa0 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -8,7 +8,7 @@ process BCFTOOLS_CONCAT { 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" input: - tuple val(meta), path(vcfs, stageAs: "?/*"), path(tbi, stageAs: "?/*") + tuple val(meta), path(vcfs), path(tbi) output: tuple val(meta), path("*.gz"), emit: vcf From 71a03e627309fcec908258e4d5e6a339e9b41555 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 20 Dec 2022 17:07:25 +0100 Subject: [PATCH 13/14] update CHANGELOG [no ci] --- CHANGELOG.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b176647c59..7eeb06a07d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,9 +39,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Dependencies -| Dependency | Old version | New version | -| ---------- | ----------- | ----------- | -| `svdb` | 2.6.1 | 2.8.1 | +| Dependency | Old version | New version | +| ------------- | ----------- | ----------- | +| `bcftools` | 1.15.1 | 1.16 | +| `ensembl-vep` | 106.1 | 108.2 | +| `multiqc` | 1.13a | 1.13 | +| `svdb` | 2.6.1 | 2.8.1 | ## [3.1.1](https://github.com/nf-core/sarek/releases/tag/3.1.1) - Lilla Luleälven From a792145896865174f5a7e45ad76ee306aa0127b2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 3 Jan 2023 09:12:19 +0100 Subject: [PATCH 14/14] typos --- CHANGELOG.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7eeb06a07d..b3c999157f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,14 +10,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - [#864](https://github.com/nf-core/sarek/pull/864) - Added possibilities to export assembled haplotypes and locally realigned reads -- [#792](https://github.com/nf-core/sarek/pull/792) - Added the option `--concatenate_vcfs` for concatenating the germline vcf-files. Per default, the resulting vcf-files will be placed under `/variant_calling/concat`. +- [#792](https://github.com/nf-core/sarek/pull/792) - Added the option `--concatenate_vcfs` for concatenating the germline VCF files. Per default, the resulting vcf-files will be placed under `/variant_calling/concat` - [#889](https://github.com/nf-core/sarek/pull/889) - Added possibilities to skip variant filtering after Haplotypecaller ### Changed - [#859](https://github.com/nf-core/sarek/pull/859) - Back to dev -- [#860](https://github.com/nf-core/sarek/pull/860) - Replace local subworkflow with nf-core version - vcf_annotate_snpeff -- [#865](https://github.com/nf-core/sarek/pull/865) - Replace local subworkflow with nf-core version - vcf_annotate_ensemblvep +- [#860](https://github.com/nf-core/sarek/pull/860) - Replace local subworkflow with nf-core version - `vcf_annotate_snpeff` +- [#865](https://github.com/nf-core/sarek/pull/865) - Replace local subworkflow with nf-core version - `vcf_annotate_ensemblvep` - [#874](https://github.com/nf-core/sarek/pull/874) - Update all modules - [#890](https://github.com/nf-core/sarek/pull/890) - Sync `TEMPLATE` with `tools` `2.7.1` - [#898](https://github.com/nf-core/sarek/pull/898) - Sync `TEMPLATE` with `tools` `2.7.2` @@ -28,7 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#870](https://github.com/nf-core/sarek/pull/870) - Fix output for locally realigned reads from haplotypecaller - [#874](https://github.com/nf-core/sarek/pull/874) - Remove `CITATION.cff` - [#893](https://github.com/nf-core/sarek/pull/893) - Fix logic of when to execute tabix on dbsnp -- [#894](https://github.com/nf-core/sarek/pull/894) - Add description to --cnvkit_reference +- [#894](https://github.com/nf-core/sarek/pull/894) - Add description to `--cnvkit_reference` - [#894](https://github.com/nf-core/sarek/pull/894) - Remove methods description TODO prompt ### Deprecated