nf-core_modules/modules/picard/cleansam/main.nf
Sateesh 927dbfed04
Picard cleansam (#1306)
* add picard-cleansam

* add picard/cleansam

* update test yml with output

* picard 2.26.10 -> 2.26.9

* add output to test yml

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 19:17:58 -07:00

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Text

process PICARD_CLEANSAM {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
input:
tuple val(meta), path(sam)
output:
tuple val(meta), path("*.sam"), emit: sam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def STRINGENCY = task.ext.stringency ?: "STRICT"
def avail_mem = 3
if (!task.memory) {
log.info '[Picard CleanSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
picard \\
-Xmx${avail_mem}g \\
CleanSam \\
${args} \\
-I ${sam} \\
-O ${prefix}.sam \\
--VALIDATION_STRINGENCY ${STRINGENCY}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(picard CleanSam --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}