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partition

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Ramprasad Neethiraj 2022-05-03 14:26:34 +02:00
parent 7cc47f6ba6
commit 829c15c98b
2 changed files with 7 additions and 3 deletions
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7
modules/cnvpytor/partition/main.nf
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@ -9,6 +9,7 @@ process CNVPYTOR_PARTITION {
input: input:
tuple val(meta), path(pytor) tuple val(meta), path(pytor)
val bin_sizes
output: output:
tuple val(meta), path("${pytor.baseName}.pytor"), emit: pytor tuple val(meta), path("${pytor.baseName}.pytor"), emit: pytor
@ -18,15 +19,15 @@ process CNVPYTOR_PARTITION {
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
script: script:
def args = task.ext.args ?: '' def bins = bin_sizes ?: '1000'
""" """
cnvpytor \\ cnvpytor \\
-root $pytor \\ -root $pytor \\
-partition $args -partition $bins
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${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
""" """

3
modules/cnvpytor/partition/meta.yml
View file

@ -22,6 +22,9 @@ input:
type: file type: file
description: pytor file containing read depth data description: pytor file containing read depth data
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: