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https://github.com/MillironX/nf-core_modules.git
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Module new version reporting fixes (#753)
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Fix IQ tree * Fix picard markdup and merge sam * Fix plink/vcf version * Fix plink version output * Fix prokka version command * Fix pydamage * Try fixing markduplicates * Fix snpEff * Fix vcftools version * Fix pydamage and filtersamreads test run * Fix MarkDuplicates tests * Add missing unsorted checks * Remove MD5 sym due to stochasicity in BAM file
This commit is contained in:
James A. Fellows Yates
GitHub
parent
3c5492b4a3
commit
e971f538a9
16 changed files with 23 additions and 19 deletions
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@ -41,7 +41,7 @@ process IQTREE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(iqtree -version 2>&1 | sed 's/^IQ-TREE multicore version \\([0-9\\.]*\\) .*\$/\\1/')
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${getSoftwareName(task.process)}: \$(echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version //;s/ .*//')
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END_VERSIONS
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"""
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}
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@ -47,7 +47,7 @@ process PICARD_MARKDUPLICATES {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(picard MarkDuplicates --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
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${getSoftwareName(task.process)}: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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}
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@ -45,7 +45,7 @@ process PICARD_MERGESAMFILES {
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OUTPUT=${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(picard MergeSamFiles --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
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${getSoftwareName(task.process)}: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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} else {
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@ -53,7 +53,7 @@ process PICARD_MERGESAMFILES {
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ln -s ${bam_files[0]} ${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(picard MergeSamFiles --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
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${getSoftwareName(task.process)}: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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}
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@ -41,7 +41,7 @@ process PLINK_VCF {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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plink: \$( plink --version 2>&1 | sed 's/^PLINK //' | sed 's/..-bit.*//' )
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plink: \$(echo \$(plink --version 2>&1) | sed 's/^PLINK v//' | sed 's/..-bit.*//' )
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END_VERSIONS
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"""
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}
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@ -53,7 +53,7 @@ process PROKKA {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(prokka --version 2>&1 | sed 's/^.*prokka //')
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${getSoftwareName(task.process)}: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
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END_VERSIONS
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"""
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}
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@ -37,7 +37,7 @@ process PYDAMAGE_ANALYZE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(pydamage --version 2>&1 | sed -e 's/pydamage, version //g')
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${getSoftwareName(task.process)}: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g')
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END_VERSIONS
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"""
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}
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@ -37,7 +37,7 @@ process PYDAMAGE_FILTER {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(pydamage --version 2>&1 | sed -e 's/pydamage, version //g')
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${getSoftwareName(task.process)}: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g')
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END_VERSIONS
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"""
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}
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@ -54,7 +54,7 @@ process SNPEFF {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(snpEff -version 2>&1)
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${getSoftwareName(task.process)}: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
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END_VERSIONS
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"""
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}
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@ -126,7 +126,7 @@ process VCFTOOLS {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(vcftools --version 2>&1 | sed 's/^.*vcftools //; s/Using.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
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END_VERSIONS
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"""
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}
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@ -1,4 +1,4 @@
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- name: iqtree
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- name: iqtree test workflow
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command: nextflow run ./tests/modules/iqtree -entry test_iqtree -c tests/config/nextflow.config
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tags:
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- iqtree
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@ -8,7 +8,7 @@
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md5sum: b44a6ca04811a9470c7813c3c9465fd5
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- name: picard filtersamreads_readlist
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- name: picard filtersamreads readlist
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command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c tests/config/nextflow.config
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tags:
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- picard
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@ -3,6 +3,7 @@
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nextflow.enable.dsl = 2
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include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [:] )
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include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [args : '--ASSUME_SORT_ORDER queryname' ] )
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workflow test_picard_markduplicates_sorted_bam {
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input = [ [ id:'test', single_end:false ], // meta map
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@ -17,5 +18,5 @@ workflow test_picard_markduplicates_unsorted_bam {
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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PICARD_MARKDUPLICATES ( input )
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PICARD_MARKDUPLICATES_UNSORTED ( input )
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}
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@ -1,4 +1,4 @@
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- name: picard markduplicates on sorted bam
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- name: picard markduplicates sorted bam
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command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
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tags:
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- picard
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@ -7,9 +7,13 @@
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- path: ./output/picard/test.MarkDuplicates.metrics.txt
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- path: ./output/picard/test.bam
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md5sum: b520ccdc3a9edf3c6a314983752881f2
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- name: picard markduplicates on unsorted bam
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- name: picard markduplicates unsorted bam
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command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
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tags:
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- picard
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- picard/markduplicates
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exit_code: 1
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files:
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- path: ./output/picard/test.MarkDuplicates.metrics.txt
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- path: ./output/picard/test.bam
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md5sum: 46a6fc76048ba801d328f869ac9db020
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@ -5,4 +5,3 @@
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- picard/mergesamfiles
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files:
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- path: ./output/picard/test.bam
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md5sum: 82bb91735aff82eae4f0b631114e9e15
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@ -1,4 +1,4 @@
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- name: test_pydamage_analyze
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- name: pydamage analyze test workflow
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command: nextflow run tests/modules/pydamage/analyze -entry test_pydamage -c tests/config/nextflow.config
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tags:
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- pydamage
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@ -1,4 +1,4 @@
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- name: test_pydamage_filter
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- name: pydamage filter test workflow
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command: nextflow run tests/modules/pydamage/filter -entry test_pydamage -c tests/config/nextflow.config
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tags:
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- pydamage
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