mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
Fix more version commands (#750)
* Fix outstanding tests * Fix more version commands * Fix remaining modules
This commit is contained in:
Harshil Patel
GitHub
parent
43c2779258
commit
3c5492b4a3
39 changed files with 185 additions and 157 deletions
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@ -35,7 +35,7 @@ process BISMARK_SUMMARY {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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END_VERSIONS
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"""
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}
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@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = 0.1 // No version information printed
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def VERSION = '0.1' // No version information printed
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process CHROMAP_CHROMAP {
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tag "$meta.id"
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@ -43,7 +43,7 @@ process GRAPHMAP2_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(graphmap2 align 2>&1 | sed 's/^.*Version: v//; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -36,7 +36,7 @@ process GRAPHMAP2_INDEX {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(graphmap2 align 2>&1 | sed 's/^.*Version: v//; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -29,10 +29,14 @@ process GUNZIP {
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def software = getSoftwareName(task.process)
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gunzip = archive.toString() - '.gz'
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"""
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gunzip -f $options.args $archive
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gunzip \\
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-f \\
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$options.args \\
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$archive
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(gunzip --version 2>&1 | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
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END_VERSIONS
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"""
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}
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@ -44,7 +44,7 @@ process IVAR_CONSENSUS {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -40,7 +40,7 @@ process IVAR_TRIM {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar 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 IVAR_VARIANTS {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -50,7 +50,7 @@ process KRAKEN2_KRAKEN2 {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(kraken2 --version 2>&1 | sed 's/^.*Kraken version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -39,7 +39,7 @@ process LOFREQ_CALL {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
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END_VERSIONS
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"""
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}
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@ -41,7 +41,7 @@ process LOFREQ_CALLPARALLEL {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
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END_VERSIONS
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"""
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}
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@ -37,7 +37,7 @@ process LOFREQ_FILTER {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
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END_VERSIONS
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"""
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}
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@ -37,7 +37,7 @@ process LOFREQ_INDELQUAL {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^.*lofreq //; s/Using.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
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END_VERSIONS
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"""
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}
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@ -40,7 +40,7 @@ process MINIA {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(minia --version 2>&1 | sed 's/^.*Minia version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(minia --version 2>&1) | sed 's/^.*Minia version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -42,7 +42,7 @@ process PRESEQ_LCEXTRAP {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(preseq 2>&1 | sed 's/^.*Version: //; s/Usage:.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
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END_VERSIONS
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"""
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}
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@ -58,7 +58,7 @@ process QUALIMAP_BAMQC {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(qualimap 2>&1 | sed 's/^.*QualiMap v.//; s/Built.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
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END_VERSIONS
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"""
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}
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@ -33,7 +33,7 @@ process TABIX_BGZIP {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -34,7 +34,7 @@ process TABIX_BGZIPTABIX {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -32,7 +32,7 @@ process TABIX_TABIX {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = '377' // No version information printed
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process UCSC_WIGTOBIGWIG {
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tag '$wig'
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label 'process_medium'
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@ -38,7 +40,7 @@ process UCSC_WIGTOBIGWIG {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(wigToBigWig 2>&1 | sed 's/wigToBigWig v //; s/ - Convert.*\$//')
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${getSoftwareName(task.process)}: \$(echo "$VERSION")
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END_VERSIONS
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"""
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}
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@ -22,17 +22,21 @@ process UNTAR {
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path archive
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output:
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path "$untar" , emit: untar
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path "versions.yml" , emit: version
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path "$untar" , emit: untar
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path "versions.yml", emit: version
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script:
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def software = getSoftwareName(task.process)
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untar = archive.toString() - '.tar.gz'
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"""
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tar -xzvf $options.args $archive
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tar \\
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-xzvf \\
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$options.args \\
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$archive
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(tar --version 2>&1 | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
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END_VERSIONS
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"""
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}
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@ -40,7 +40,7 @@ process UNZIP {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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7za: \$( 7za --help) grep Version | sed 's/.*p7zip Version//; s/(.*//' )
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7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
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END_VERSIONS
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"""
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}
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@ -3,18 +3,23 @@
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
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include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
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include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
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include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf' addParams( options: [:] )
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workflow test_bwa_sampe {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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Channel
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.fromList(
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[
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[ id:'test', single_end:false ],
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[ [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
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]
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).collect()
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.set { input }
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BWA_INDEX ( fasta )
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BWA_ALN ( input, BWA_INDEX.out.index )
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BWA_SAMPE ( BWA_ALN.out.sai, BWA_INDEX.out.index )
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BWA_SAMPE ( input.join(BWA_ALN.out.sai), BWA_INDEX.out.index )
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}
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@ -3,17 +3,20 @@
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
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include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
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include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
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include { BWA_SAMSE } from '../../../../modules/bwa/samse/main.nf' addParams( options: [:] )
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workflow test_bwa_samse {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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Channel
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.fromList(
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[ [ id:'test', single_end:true ],
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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).collect()
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.set { input }
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BWA_INDEX ( fasta )
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BWA_ALN ( input, BWA_INDEX.out.index )
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BWA_SAMSE ( BWA_ALN.out.sai, BWA_INDEX.out.index )
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BWA_SAMSE ( input.join(BWA_ALN.out.sai, by:[0]), BWA_INDEX.out.index )
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}
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@ -2,9 +2,8 @@
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nextflow.enable.dsl = 2
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include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:] )
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include { BWAMETH_ALIGN as BWAMETH_ALIGN_SE } from '../../../../modules/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../modules/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:] )
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include { BWAMETH_ALIGN } from '../../../../modules/bwameth/align/main.nf' addParams( options: [:] )
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//
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// Test with single-end data
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@ -16,7 +15,7 @@ workflow test_bwameth_align_single_end {
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BWAMETH_INDEX ( fasta )
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BWAMETH_ALIGN_SE ( input, BWAMETH_INDEX.out.index )
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BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
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}
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//
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@ -30,5 +29,5 @@ workflow test_bwameth_align_paired_end {
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BWAMETH_INDEX ( fasta )
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BWAMETH_ALIGN_PE ( input, BWAMETH_INDEX.out.index )
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BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
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}
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@ -4,7 +4,7 @@
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- bwameth
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- bwameth/align
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files:
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- path: output/test_single_end/test.bam
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- path: output/bwameth/test.bam
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- name: bwameth align paired-end test workflow
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command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config
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@ -12,5 +12,5 @@
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- bwameth
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- bwameth/align
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files:
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- path: output/test_paired_end/test.bam
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- path: output/bwameth/test.bam
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' addParams( options: [:] )
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include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' addParams( options: [publish_dir:'genmap'] )
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workflow test_genmap_index {
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@ -4,45 +4,45 @@
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- genmap
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- genmap/index
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files:
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- path: output/index/genmap/index.ids.concat
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- path: output/genmap/genmap/index.ids.concat
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md5sum: da6caa25f62c5407ccdfbcce1fa92408
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- path: output/index/genmap/index.ids.limits
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- path: output/genmap/genmap/index.ids.limits
|
||||
md5sum: f82636c5da188aec131d3a809473eff1
|
||||
- path: output/index/genmap/index.info.concat
|
||||
- path: output/genmap/genmap/index.info.concat
|
||||
md5sum: 8ba5273aa9e58722bf45b9cc39fc6bfe
|
||||
- path: output/index/genmap/index.info.limits
|
||||
- path: output/genmap/genmap/index.info.limits
|
||||
md5sum: 3522f2811f4ddf04598809fc84a1459e
|
||||
- path: output/index/genmap/index.lf.drp
|
||||
- path: output/genmap/genmap/index.lf.drp
|
||||
md5sum: dd85d6a23af2c7adf2695658e3056c08
|
||||
- path: output/index/genmap/index.lf.drp.sbl
|
||||
- path: output/genmap/genmap/index.lf.drp.sbl
|
||||
md5sum: f1d3ff8443297732862df21dc4e57262
|
||||
- path: output/index/genmap/index.lf.drs
|
||||
- path: output/genmap/genmap/index.lf.drs
|
||||
md5sum: 93b885adfe0da089cdf634904fd59f71
|
||||
- path: output/index/genmap/index.lf.drv
|
||||
- path: output/genmap/genmap/index.lf.drv
|
||||
md5sum: e06b605496bd91b32afa3c4f56d934ac
|
||||
- path: output/index/genmap/index.lf.drv.sbl
|
||||
- path: output/genmap/genmap/index.lf.drv.sbl
|
||||
md5sum: 8dd6bb7329a71449b0a1b292b5999164
|
||||
- path: output/index/genmap/index.lf.pst
|
||||
- path: output/genmap/genmap/index.lf.pst
|
||||
md5sum: e8daba34298e99e42942435286f9b3f0
|
||||
- path: output/index/genmap/index.rev.lf.drp
|
||||
- path: output/genmap/genmap/index.rev.lf.drp
|
||||
md5sum: 5d9107e3aeec0721553dd661d4365fef
|
||||
- path: output/index/genmap/index.rev.lf.drp.sbl
|
||||
- path: output/genmap/genmap/index.rev.lf.drp.sbl
|
||||
md5sum: f1d3ff8443297732862df21dc4e57262
|
||||
- path: output/index/genmap/index.rev.lf.drs
|
||||
- path: output/genmap/genmap/index.rev.lf.drs
|
||||
md5sum: 93b885adfe0da089cdf634904fd59f71
|
||||
- path: output/index/genmap/index.rev.lf.drv
|
||||
- path: output/genmap/genmap/index.rev.lf.drv
|
||||
md5sum: df7e795edc0a034577a9d2599fe8cfeb
|
||||
- path: output/index/genmap/index.rev.lf.drv.sbl
|
||||
- path: output/genmap/genmap/index.rev.lf.drv.sbl
|
||||
md5sum: 8dd6bb7329a71449b0a1b292b5999164
|
||||
- path: output/index/genmap/index.rev.lf.pst
|
||||
- path: output/genmap/genmap/index.rev.lf.pst
|
||||
md5sum: e8daba34298e99e42942435286f9b3f0
|
||||
- path: output/index/genmap/index.sa.ind
|
||||
- path: output/genmap/genmap/index.sa.ind
|
||||
md5sum: e21e5c7ce887cc8e3d0fa44ab1019cab
|
||||
- path: output/index/genmap/index.sa.len
|
||||
- path: output/genmap/genmap/index.sa.len
|
||||
md5sum: 5dfc20cfe8ed9892451461a8d402f51c
|
||||
- path: output/index/genmap/index.sa.val
|
||||
- path: output/genmap/genmap/index.sa.val
|
||||
md5sum: 400ee7f2fe93b2000ae3a5da5e509730
|
||||
- path: output/index/genmap/index.txt.concat
|
||||
- path: output/genmap/genmap/index.txt.concat
|
||||
md5sum: b4303962e0c176107945f3405370e6ae
|
||||
- path: output/index/genmap/index.txt.limits
|
||||
- path: output/genmap/genmap/index.txt.limits
|
||||
md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- ivar/trim
|
||||
files:
|
||||
- path: output/ivar/test.bam
|
||||
md5sum: 8705d032b28a1c3dbfe78fa762a2132f
|
||||
md5sum: 12cff17d43b1efdba8120a6bff5311e3
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@
|
|||
files:
|
||||
- path: ./output/qualimap/test/qualimapReport.html
|
||||
- path: ./output/qualimap/test/genome_results.txt
|
||||
md5sum: 00ad697dbec5141428ac8d850c13e1c5
|
||||
md5sum: 5ec87ea86ad734d512c8c76fe8eb37b1
|
||||
- path: ./output/qualimap/test/css/plus.png
|
||||
md5sum: 0125e6faa04e2cf0141a2d599d3bb220
|
||||
- path: ./output/qualimap/test/css/down-pressed.png
|
||||
|
|
|
|||
|
|
@ -2,20 +2,21 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [args: "--star"])
|
||||
include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/rsem/calculateexpression/main.nf' addParams(options: [args: "--star --star-gzipped-read-file"])
|
||||
include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [args: "--star"])
|
||||
include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/rsem/calculateexpression/main.nf' addParams(options: [args: "--star --star-gzipped-read-file"])
|
||||
|
||||
workflow test_rsem_calculateexpression {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false, strandedness: 'forward' ], // meta map
|
||||
[
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
|
||||
|
||||
input = [ [ id:'test', single_end:false, strandedness: 'forward' ], // meta map
|
||||
[file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)]
|
||||
]
|
||||
|
||||
RSEM_PREPAREREFERENCE ( fasta, gtf )
|
||||
|
||||
RSEM_CALCULATEEXPRESSION( input, RSEM_PREPAREREFERENCE.out.index )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [:])
|
||||
include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [publish_dir:'rsem'])
|
||||
|
||||
workflow test_rsem_preparereference {
|
||||
|
||||
|
|
|
|||
|
|
@ -4,19 +4,19 @@
|
|||
- rsem
|
||||
- rsem/preparereference
|
||||
files:
|
||||
- path: output/index/rsem/genome.chrlist
|
||||
- path: output/rsem/rsem/genome.chrlist
|
||||
md5sum: b190587cae0531f3cf25552d8aa674db
|
||||
- path: output/index/rsem/genome.fasta
|
||||
- path: output/rsem/rsem/genome.fasta
|
||||
md5sum: f315020d899597c1b57e5fe9f60f4c3e
|
||||
- path: output/index/rsem/genome.grp
|
||||
- path: output/rsem/rsem/genome.grp
|
||||
md5sum: c2848a8b6d495956c11ec53efc1de67e
|
||||
- path: output/index/rsem/genome.idx.fa
|
||||
- path: output/rsem/rsem/genome.idx.fa
|
||||
md5sum: 050c521a2719c2ae48267c1e65218f29
|
||||
- path: output/index/rsem/genome.n2g.idx.fa
|
||||
- path: output/rsem/rsem/genome.n2g.idx.fa
|
||||
md5sum: 050c521a2719c2ae48267c1e65218f29
|
||||
- path: output/index/rsem/genome.seq
|
||||
- path: output/rsem/rsem/genome.seq
|
||||
md5sum: 94da0c6b88c33e63c9a052a11f4f57c1
|
||||
- path: output/index/rsem/genome.ti
|
||||
- path: output/rsem/rsem/genome.ti
|
||||
md5sum: c9e4ae8d4d13a504eec2acf1b8589a66
|
||||
- path: output/index/rsem/genome.transcripts.fa
|
||||
- path: output/rsem/rsem/genome.transcripts.fa
|
||||
md5sum: 050c521a2719c2ae48267c1e65218f29
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [:] )
|
||||
include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [publish_dir:'star'] )
|
||||
|
||||
workflow test_star_genomegenerate {
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
|
|||
|
|
@ -4,34 +4,34 @@
|
|||
- star/genomegenerate
|
||||
- star
|
||||
files:
|
||||
- path: output/index/star/Genome
|
||||
- path: output/star/star/Genome
|
||||
md5sum: a654229fbca6071dcb6b01ce7df704da
|
||||
- path: output/index/star/Log.out
|
||||
- path: output/index/star/SA
|
||||
- path: output/star/star/Log.out
|
||||
- path: output/star/star/SA
|
||||
md5sum: 8c3edc46697b72c9e92440d4cf43506c
|
||||
- path: output/index/star/SAindex
|
||||
- path: output/star/star/SAindex
|
||||
md5sum: d0fbf2789ee1e9f60c352ba3655d9de4
|
||||
- path: output/index/star/chrLength.txt
|
||||
- path: output/star/star/chrLength.txt
|
||||
md5sum: c81f40f27e72606d7d07097c1d56a5b5
|
||||
- path: output/index/star/chrName.txt
|
||||
- path: output/star/star/chrName.txt
|
||||
md5sum: 5ae68a67b70976ee95342a7451cb5af1
|
||||
- path: output/index/star/chrNameLength.txt
|
||||
- path: output/star/star/chrNameLength.txt
|
||||
md5sum: b190587cae0531f3cf25552d8aa674db
|
||||
- path: output/index/star/chrStart.txt
|
||||
- path: output/star/star/chrStart.txt
|
||||
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
|
||||
- path: output/index/star/exonGeTrInfo.tab
|
||||
- path: output/star/star/exonGeTrInfo.tab
|
||||
md5sum: d04497f69d6ef889efd4d34fe63edcc4
|
||||
- path: output/index/star/exonInfo.tab
|
||||
- path: output/star/star/exonInfo.tab
|
||||
md5sum: 0d560290fab688b7268d88d5494bf9fe
|
||||
- path: output/index/star/geneInfo.tab
|
||||
- path: output/star/star/geneInfo.tab
|
||||
md5sum: 8b608537307443ffaee4927d2b428805
|
||||
- path: output/index/star/genomeParameters.txt
|
||||
- path: output/star/star/genomeParameters.txt
|
||||
md5sum: 5a1ec027e575c3d7c1851e6b80fb8c5d
|
||||
- path: output/index/star/sjdbInfo.txt
|
||||
- path: output/star/star/sjdbInfo.txt
|
||||
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
|
||||
- path: output/index/star/sjdbList.fromGTF.out.tab
|
||||
- path: output/star/star/sjdbList.fromGTF.out.tab
|
||||
md5sum: 8760c33e966dad0b39f440301ebbdee4
|
||||
- path: output/index/star/sjdbList.out.tab
|
||||
- path: output/star/star/sjdbList.out.tab
|
||||
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
|
||||
- path: output/index/star/transcriptInfo.tab
|
||||
- path: output/star/star/transcriptInfo.tab
|
||||
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
|
||||
|
|
|
|||
|
|
@ -2,37 +2,45 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { STRINGTIE as STRINGTIE_FORWARD } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward' ] )
|
||||
include { STRINGTIE as STRINGTIE_REVERSE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
|
||||
include { STRINGTIE_MERGE as STRINGTIE_FORWARD_MERGE} from '../../../../modules/stringtie/merge/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward_merge'] )
|
||||
include { STRINGTIE_MERGE as STRINGTIE_REVERSE_MERGE} from '../../../../modules/stringtie/merge/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse_merge'] )
|
||||
include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [:] )
|
||||
include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf' addParams( options: [:] )
|
||||
|
||||
/*
|
||||
* Test with forward strandedness
|
||||
*/
|
||||
workflow test_stringtie_forward_merge {
|
||||
input = [ [ id:'test', strandedness:'forward' ], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
|
||||
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
|
||||
|
||||
STRINGTIE_FORWARD ( input, annotation_gtf )
|
||||
STRINGTIE_FORWARD.out.transcript_gtf
|
||||
.map { it -> it[1] }
|
||||
.set { stringtie_gtf }
|
||||
STRINGTIE_FORWARD_MERGE ( stringtie_gtf, annotation_gtf )
|
||||
input = [
|
||||
[ id:'test', strandedness:'forward' ], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
]
|
||||
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
|
||||
|
||||
STRINGTIE ( input, annotation_gtf )
|
||||
STRINGTIE
|
||||
.out
|
||||
.transcript_gtf
|
||||
.map { it -> it[1] }
|
||||
.set { stringtie_gtf }
|
||||
|
||||
STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
|
||||
}
|
||||
|
||||
/*
|
||||
* Test with reverse strandedness
|
||||
*/
|
||||
workflow test_stringtie_reverse_merge {
|
||||
input = [ [ id:'test', strandedness:'reverse' ], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
]
|
||||
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
|
||||
|
||||
STRINGTIE_REVERSE ( input, annotation_gtf )
|
||||
STRINGTIE_REVERSE.out.transcript_gtf
|
||||
.map { it -> it[1] }
|
||||
.set { stringtie_gtf }
|
||||
STRINGTIE_REVERSE_MERGE ( stringtie_gtf, annotation_gtf )
|
||||
input = [
|
||||
[ id:'test', strandedness:'reverse' ], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
]
|
||||
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
|
||||
|
||||
STRINGTIE ( input, annotation_gtf )
|
||||
STRINGTIE
|
||||
.out
|
||||
.transcript_gtf
|
||||
.map { it -> it[1] }
|
||||
.set { stringtie_gtf }
|
||||
|
||||
STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,22 +1,22 @@
|
|||
- name: stringtie forward-strand merge
|
||||
- name: stringtie merge forward-strand
|
||||
command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_forward_merge -c tests/config/nextflow.config
|
||||
tags:
|
||||
- stringtie
|
||||
- stringtie/merge
|
||||
files:
|
||||
- path: ./output/test_stringtie_forward_merge/stringtie.merged.gtf
|
||||
- path: ./output/stringtie/stringtie.merged.gtf
|
||||
contains:
|
||||
- 'stringtie'
|
||||
- 'merge'
|
||||
- 'chr22'
|
||||
|
||||
- name: stringtie reverse-strand merge
|
||||
- name: stringtie merge reverse-strand
|
||||
command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_reverse_merge -c tests/config/nextflow.config
|
||||
tags:
|
||||
- stringtie
|
||||
- stringtie/merge
|
||||
files:
|
||||
- path: ./output/test_stringtie_reverse_merge/stringtie.merged.gtf
|
||||
- path: ./output/stringtie/stringtie.merged.gtf
|
||||
contains:
|
||||
- 'stringtie'
|
||||
- 'merge'
|
||||
|
|
|
|||
|
|
@ -2,27 +2,29 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { STRINGTIE as STRINGTIE_FORWARD } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward' ] )
|
||||
include { STRINGTIE as STRINGTIE_REVERSE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
|
||||
|
||||
include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [:] )
|
||||
//
|
||||
// Test with forward strandedness
|
||||
//
|
||||
workflow test_stringtie_forward {
|
||||
input = [ [ id:'test', strandedness:'forward' ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
|
||||
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
|
||||
input = [
|
||||
[ id:'test', strandedness:'forward' ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
]
|
||||
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
|
||||
|
||||
STRINGTIE_FORWARD ( input, annotation_gtf )
|
||||
STRINGTIE ( input, annotation_gtf )
|
||||
}
|
||||
|
||||
//
|
||||
// Test with reverse strandedness
|
||||
//
|
||||
workflow test_stringtie_reverse {
|
||||
input = [ [ id:'test', strandedness:'reverse' ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
|
||||
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
|
||||
input = [
|
||||
[ id:'test', strandedness:'reverse' ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
]
|
||||
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
|
||||
|
||||
STRINGTIE_REVERSE ( input, annotation_gtf )
|
||||
STRINGTIE ( input, annotation_gtf )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,43 +1,43 @@
|
|||
- name: test_stringtie_forward
|
||||
- name: stringtie stringtie forward
|
||||
command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config
|
||||
tags:
|
||||
- stringtie
|
||||
- stringtie/stringtie
|
||||
files:
|
||||
- path: ./output/test_stringtie_forward/test.transcripts.gtf
|
||||
- path: ./output/test_stringtie_forward/test.gene.abundance.txt
|
||||
- path: ./output/stringtie/test.transcripts.gtf
|
||||
- path: ./output/stringtie/test.gene.abundance.txt
|
||||
md5sum: 7d8bce7f2a922e367cedccae7267c22e
|
||||
- path: ./output/test_stringtie_forward/test.coverage.gtf
|
||||
- path: ./output/stringtie/test.coverage.gtf
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: ./output/test_stringtie_forward/test.ballgown/e_data.ctab
|
||||
- path: ./output/stringtie/test.ballgown/e_data.ctab
|
||||
md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
|
||||
- path: ./output/test_stringtie_forward/test.ballgown/i_data.ctab
|
||||
- path: ./output/stringtie/test.ballgown/i_data.ctab
|
||||
md5sum: be3abe09740603213f83d50dcf81427f
|
||||
- path: ./output/test_stringtie_forward/test.ballgown/t_data.ctab
|
||||
- path: ./output/stringtie/test.ballgown/t_data.ctab
|
||||
md5sum: 3b66c065da73ae0dd41cc332eff6a818
|
||||
- path: ./output/test_stringtie_forward/test.ballgown/i2t.ctab
|
||||
- path: ./output/stringtie/test.ballgown/i2t.ctab
|
||||
md5sum: 8a117c8aa4334b4c2d4711932b006fb4
|
||||
- path: ./output/test_stringtie_forward/test.ballgown/e2t.ctab
|
||||
- path: ./output/stringtie/test.ballgown/e2t.ctab
|
||||
md5sum: e981c0038295ae54b63cedb1083f1540
|
||||
|
||||
- name: test_stringtie_reverse
|
||||
- name: stringtie stringtie reverse
|
||||
command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config
|
||||
tags:
|
||||
- stringtie
|
||||
- stringtie/stringtie
|
||||
files:
|
||||
- path: ./output/test_stringtie_reverse/test.transcripts.gtf
|
||||
- path: ./output/test_stringtie_reverse/test.gene.abundance.txt
|
||||
- path: ./output/stringtie/test.transcripts.gtf
|
||||
- path: ./output/stringtie/test.gene.abundance.txt
|
||||
md5sum: 7385b870b955dae2c2ab78a70cf05cce
|
||||
- path: ./output/test_stringtie_reverse/test.coverage.gtf
|
||||
- path: ./output/stringtie/test.coverage.gtf
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: ./output/test_stringtie_reverse/test.ballgown/e_data.ctab
|
||||
- path: ./output/stringtie/test.ballgown/e_data.ctab
|
||||
md5sum: 879b6696029d19c4737b562e9d149218
|
||||
- path: ./output/test_stringtie_reverse/test.ballgown/i_data.ctab
|
||||
- path: ./output/stringtie/test.ballgown/i_data.ctab
|
||||
md5sum: be3abe09740603213f83d50dcf81427f
|
||||
- path: ./output/test_stringtie_reverse/test.ballgown/t_data.ctab
|
||||
- path: ./output/stringtie/test.ballgown/t_data.ctab
|
||||
md5sum: 3b66c065da73ae0dd41cc332eff6a818
|
||||
- path: ./output/test_stringtie_reverse/test.ballgown/i2t.ctab
|
||||
- path: ./output/stringtie/test.ballgown/i2t.ctab
|
||||
md5sum: 8a117c8aa4334b4c2d4711932b006fb4
|
||||
- path: ./output/test_stringtie_reverse/test.ballgown/e2t.ctab
|
||||
- path: ./output/stringtie/test.ballgown/e2t.ctab
|
||||
md5sum: e981c0038295ae54b63cedb1083f1540
|
||||
|
|
|
|||
Loading…
Reference in a new issue