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Merge pull request #1694 from SusiJo/cnvkit/reference

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Add prefix to cnvkit/reference
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SusiJo 2022-05-24 15:11:06 +02:00 committed by GitHub
commit 60793adea2
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2 changed files with 4 additions and 2 deletions
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4
modules/cnvkit/reference/main.nf
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@ -21,13 +21,15 @@ process CNVKIT_REFERENCE {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: targets.BaseName
""" """
cnvkit.py \\ cnvkit.py \\
reference \\ reference \\
--fasta $fasta \\ --fasta $fasta \\
--targets $targets \\ --targets $targets \\
--antitargets $antitargets \\ --antitargets $antitargets \\
--output reference.cnn \\ --output ${prefix}.reference.cnn \\
$args $args
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

2
tests/modules/cnvkit/reference/test.yml
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@ -4,5 +4,5 @@
- cnvkit/reference - cnvkit/reference
- cnvkit - cnvkit
files: files:
- path: output/cnvkit/reference.cnn - path: output/cnvkit/multi_intervals.reference.cnn
md5sum: 7c4a7902f5ab101b1f9d6038d331b3d9 md5sum: 7c4a7902f5ab101b1f9d6038d331b3d9