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callcnv module

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Ramprasad Neethiraj 2022-05-03 14:20:05 +02:00
parent 9a9f3e97de
commit 2990dc8357
2 changed files with 14 additions and 11 deletions
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12
modules/cnvpytor/callcnvs/main.nf
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@ -9,9 +9,10 @@ process CNVPYTOR_CALLCNVS {
input: input:
tuple val(meta), path(pytor) tuple val(meta), path(pytor)
val bin_sizes
output: output:
tuple val(meta), path("*.tsv"), emit: cnvs tuple val(meta), path("${pytor.baseName}.pytor") , emit: pytor
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -23,22 +24,21 @@ process CNVPYTOR_CALLCNVS {
""" """
cnvpytor \\ cnvpytor \\
-root $pytor \\ -root $pytor \\
-call $args > ${prefix}.tsv -call $bin_sizes
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
stub: stub:
def prefix = task.ext.prefix ?: "${meta.id}"
""" """
touch ${prefix}.tsv touch ${pytor.baseName}.pytor
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
} }

11
modules/cnvpytor/callcnvs/meta.yml
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@ -17,8 +17,11 @@ input:
e.g. [ id:'test'] e.g. [ id:'test']
- pytor: - pytor:
type: file type: file
description: cnvpytor root file description: pytor file containing partitions of read depth histograms using mean-shift method
pattern: "*.{pytor}" pattern: "*.{pytor}"
- bin_sizes:
type: string
description: list of binsizes separated by space e.g. "1000 10000" and "1000"
output: output:
- meta: - meta:
@ -26,10 +29,10 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test' ] e.g. [ id:'test' ]
- cnvs: - pytor:
type: file type: file
description: file containing identified copy numer variations description: pytor files containing cnv calls
pattern: "*.{tsv}" pattern: "*.{pytor}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions