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add stub for cat/fastq (#1943)

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* add stub for cat/fastq

* prettier linting
This commit is contained in:
Annick Renevey 2022-08-09 09:18:37 +02:00 committed by GitHub
parent 5644df8d43
commit b034029b59
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2 changed files with 63 additions and 0 deletions
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29
modules/cat/fastq/main.nf
View file

@ -48,4 +48,33 @@ process CAT_FASTQ {
"""
}
}
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def readList = reads.collect{ it.toString() }
if (meta.single_end) {
if (readList.size > 1) {
"""
touch ${prefix}.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
}
} else {
if (readList.size > 2) {
"""
touch ${prefix}_1.merged.fastq.gz
touch ${prefix}_2.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
}
}
}

34
tests/modules/cat/fastq/test.yml
View file

@ -37,3 +37,37 @@
md5sum: 63f817db7a29a03eb538104495556f66
- path: ./output/cat/test_2.merged.fastq.gz
md5sum: fe9f266f43a6fc3dcab690a18419a56e
- name: cat fastq single-end stub
command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
tags:
- cat
- cat/fastq
files:
- path: ./output/cat/test.merged.fastq.gz
- name: cat fastq fastqc_paired_end stub
command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
tags:
- cat
- cat/fastq
files:
- path: ./output/cat/test_2.merged.fastq.gz
- path: ./output/cat/test_1.merged.fastq.gz
- name: cat fastq single-end-same-name stub
command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
tags:
- cat
- cat/fastq
files:
- path: ./output/cat/test.merged.fastq.gz
- name: cat fastq fastqc_paired_end_same_name stub
command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
tags:
- cat
- cat/fastq
files:
- path: ./output/cat/test_1.merged.fastq.gz
- path: ./output/cat/test_2.merged.fastq.gz