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Code Issues Releases Packages Activity

Module new version reporting fixes (#753)

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* 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 2021-09-28 11:51:19 +02:00 committed by GitHub
parent 3c5492b4a3
commit e971f538a9
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GPG key ID: 4AEE18F83AFDEB23
16 changed files with 23 additions and 19 deletions
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2
modules/iqtree/main.nf
View file

@ -41,7 +41,7 @@ process IQTREE {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(iqtree -version 2>&1 | sed 's/^IQ-TREE multicore version \\([0-9\\.]*\\) .*\$/\\1/')
${getSoftwareName(task.process)}: \$(echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version //;s/ .*//')
END_VERSIONS
"""
}

2
modules/picard/markduplicates/main.nf
View file

@ -47,7 +47,7 @@ process PICARD_MARKDUPLICATES {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(picard MarkDuplicates --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
${getSoftwareName(task.process)}: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}

4
modules/picard/mergesamfiles/main.nf
View file

@ -45,7 +45,7 @@ process PICARD_MERGESAMFILES {
OUTPUT=${prefix}.bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(picard MergeSamFiles --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
${getSoftwareName(task.process)}: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
} else {
@ -53,7 +53,7 @@ process PICARD_MERGESAMFILES {
ln -s ${bam_files[0]} ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(picard MergeSamFiles --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
${getSoftwareName(task.process)}: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}

2
modules/plink/vcf/main.nf
View file

@ -41,7 +41,7 @@ process PLINK_VCF {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
plink: \$( plink --version 2>&1 | sed 's/^PLINK //' | sed 's/..-bit.*//' )
plink: \$(echo \$(plink --version 2>&1) | sed 's/^PLINK v//' | sed 's/..-bit.*//' )
END_VERSIONS
"""
}

2
modules/prokka/main.nf
View file

@ -53,7 +53,7 @@ process PROKKA {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(prokka --version 2>&1 | sed 's/^.*prokka //')
${getSoftwareName(task.process)}: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
END_VERSIONS
"""
}

2
modules/pydamage/analyze/main.nf
View file

@ -37,7 +37,7 @@ process PYDAMAGE_ANALYZE {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(pydamage --version 2>&1 | sed -e 's/pydamage, version //g')
${getSoftwareName(task.process)}: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g')
END_VERSIONS
"""
}

2
modules/pydamage/filter/main.nf
View file

@ -37,7 +37,7 @@ process PYDAMAGE_FILTER {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(pydamage --version 2>&1 | sed -e 's/pydamage, version //g')
${getSoftwareName(task.process)}: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g')
END_VERSIONS
"""
}

2
modules/snpeff/main.nf
View file

@ -54,7 +54,7 @@ process SNPEFF {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(snpEff -version 2>&1)
${getSoftwareName(task.process)}: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
END_VERSIONS
"""
}

2
modules/vcftools/main.nf
View file

@ -126,7 +126,7 @@ process VCFTOOLS {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(vcftools --version 2>&1 | sed 's/^.*vcftools //; s/Using.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
END_VERSIONS
"""
}

2
tests/modules/iqtree/test.yml
View file

@ -1,4 +1,4 @@
- name: iqtree
- name: iqtree test workflow
command: nextflow run ./tests/modules/iqtree -entry test_iqtree -c tests/config/nextflow.config
tags:
- iqtree

2
tests/modules/picard/filtersamreads/test.yml
View file

@ -8,7 +8,7 @@
md5sum: b44a6ca04811a9470c7813c3c9465fd5
- name: picard filtersamreads_readlist
- name: picard filtersamreads readlist
command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c tests/config/nextflow.config
tags:
- picard

3
tests/modules/picard/markduplicates/main.nf
View file

@ -3,6 +3,7 @@
nextflow.enable.dsl = 2
include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [:] )
include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [args : '--ASSUME_SORT_ORDER queryname' ] )
workflow test_picard_markduplicates_sorted_bam {
input = [ [ id:'test', single_end:false ], // meta map
@ -17,5 +18,5 @@ workflow test_picard_markduplicates_unsorted_bam {
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
PICARD_MARKDUPLICATES ( input )
PICARD_MARKDUPLICATES_UNSORTED ( input )
}

10
tests/modules/picard/markduplicates/test.yml
View file

@ -1,4 +1,4 @@
- name: picard markduplicates on sorted bam
- name: picard markduplicates sorted bam
command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
tags:
- picard
@ -7,9 +7,13 @@
- path: ./output/picard/test.MarkDuplicates.metrics.txt
- path: ./output/picard/test.bam
md5sum: b520ccdc3a9edf3c6a314983752881f2
- name: picard markduplicates on unsorted bam
- name: picard markduplicates unsorted bam
command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
tags:
- picard
- picard/markduplicates
exit_code: 1
files:
- path: ./output/picard/test.MarkDuplicates.metrics.txt
- path: ./output/picard/test.bam
md5sum: 46a6fc76048ba801d328f869ac9db020

1
tests/modules/picard/mergesamfiles/test.yml
View file

@ -5,4 +5,3 @@
- picard/mergesamfiles
files:
- path: ./output/picard/test.bam
md5sum: 82bb91735aff82eae4f0b631114e9e15

2
tests/modules/pydamage/analyze/test.yml
View file

@ -1,4 +1,4 @@
- name: test_pydamage_analyze
- name: pydamage analyze test workflow
command: nextflow run tests/modules/pydamage/analyze -entry test_pydamage -c tests/config/nextflow.config
tags:
- pydamage

2
tests/modules/pydamage/filter/test.yml
View file

@ -1,4 +1,4 @@
- name: test_pydamage_filter
- name: pydamage filter test workflow
command: nextflow run tests/modules/pydamage/filter -entry test_pydamage -c tests/config/nextflow.config
tags:
- pydamage