nf-core_modules/modules/controlfreec/makegraph/main.nf
FriederikeHanssen 28e5211b35
add makegraph script (#1452)
* add makegraph script

* allow renaming of output files

* allow renaming of output files
2022-03-25 20:49:08 +01:00

40 lines
1.3 KiB
Text

process CONTROLFREEC_MAKEGRAPH {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
input:
tuple val(meta), path(ratio), path(baf)
output:
tuple val(meta), path("*_BAF.png") , emit: png_baf
tuple val(meta), path("*_ratio.log2.png"), emit: png_ratio_log2
tuple val(meta), path("*_ratio.png") , emit: png_ratio
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def baf = baf ?: ""
"""
cat /usr/local/bin/makeGraph.R | R --slave --args ${args} ${ratio} ${baf}
mv *_BAF.txt.png ${prefix}_BAF.png
mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
mv *_ratio.txt.png ${prefix}_ratio.png
cat <<-END_VERSIONS > versions.yml
"${task.process}":
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
}