nf-core_modules/modules/pairtools/flip/main.nf
2022-02-04 09:53:32 +01:00

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process PAIRTOOLS_FLIP {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' :
'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }"
input:
tuple val(meta), path(sam)
path chromsizes
output:
tuple val(meta), path("*.flip.gz"), emit: flip
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}"
"""
pairtools \\
flip \\
-c $chromsizes \\
$args \\
-o ${prefix}.flip.gz \\
$sam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
END_VERSIONS
"""
}