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Add stub star align genomegenerate (#1948)

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* correct md5sum for updated star/samtools

* merge changes in align test.yml

* update md5sum for star genomegenerate

* update md5sum for star align
This commit is contained in:
Annick Renevey 2022-08-09 09:42:19 +02:00 committed by GitHub
parent ac1c6ad710
commit cd22a76c78
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4 changed files with 91 additions and 0 deletions
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24
modules/star/align/main.nf
View file

@ -70,4 +70,28 @@ process STAR_ALIGN {
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}Xd.out.bam
touch ${prefix}.Log.final.out
touch ${prefix}.Log.out
touch ${prefix}.Log.progress.out
touch ${prefix}.sortedByCoord.out.bam
touch ${prefix}.toTranscriptome.out.bam
touch ${prefix}.Aligned.unsort.out.bam
touch ${prefix}.unmapped_1.fastq.gz
touch ${prefix}.unmapped_2.fastq.gz
touch ${prefix}.tab
touch ${prefix}.Chimeric.out.junction
touch ${prefix}.out.sam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
star: \$(STAR --version | sed -e "s/STAR_//g")
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
}

28
modules/star/genomegenerate/main.nf
View file

@ -65,4 +65,32 @@ process STAR_GENOMEGENERATE {
END_VERSIONS
"""
}
stub:
"""
mkdir star
touch star/Genome
touch star/Log.out
touch star/SA
touch star/SAindex
touch star/chrLength.txt
touch star/chrName.txt
touch star/chrNameLength.txt
touch star/chrStart.txt
touch star/exonGeTrInfo.tab
touch star/exonInfo.tab
touch star/geneInfo.tab
touch star/genomeParameters.txt
touch star/sjdbInfo.txt
touch star/sjdbList.fromGTF.out.tab
touch star/sjdbList.out.tab
touch star/transcriptInfo.tab
cat <<-END_VERSIONS > versions.yml
"${task.process}":
star: \$(STAR --version | sed -e "s/STAR_//g")
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
}

16
tests/modules/star/align/test.yml
View file

@ -175,3 +175,19 @@
- path: output/star/test.Log.out
- path: output/star/test.Log.progress.out
- path: output/star/test.SJ.out.tab
- name: star align test_star_alignment_single_end stub
command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config -stub-run
tags:
- star/align
- star
files:
- path: output/star/test.Aligned.unsort.out.bam
- path: output/star/test.Log.final.out
- path: output/star/test.Log.out
- path: output/star/test.Log.progress.out
- path: output/star/test.Chimeric.out.junction
- path: output/star/test.unmapped_1.fastq.gz
- path: output/star/test.unmapped_2.fastq.gz
- path: output/star/test.tab
- path: output/star/test.out.sam

23
tests/modules/star/genomegenerate/test.yml
View file

@ -35,3 +35,26 @@
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- name: star genomegenerate test_star_genomegenerate stub
command: nextflow run ./tests/modules/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/star/genomegenerate/nextflow.config -stub-run
tags:
- star
- star/genomegenerate
files:
- path: output/star/star/Genome
- path: output/star/star/Log.out
- path: output/star/star/SA
- path: output/star/star/SAindex
- path: output/star/star/chrLength.txt
- path: output/star/star/chrName.txt
- path: output/star/star/chrNameLength.txt
- path: output/star/star/chrStart.txt
- path: output/star/star/exonGeTrInfo.tab
- path: output/star/star/exonInfo.tab
- path: output/star/star/geneInfo.tab
- path: output/star/star/genomeParameters.txt
- path: output/star/star/sjdbInfo.txt
- path: output/star/star/sjdbList.fromGTF.out.tab
- path: output/star/star/sjdbList.out.tab
- path: output/star/star/transcriptInfo.tab