nf-core_modules/modules/pints/caller/main.nf

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process PINTS_CALLER {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pypints:1.1.6--pyh5e36f6f_1' :
'quay.io/biocontainers/pypints:1.1.6--pyh5e36f6f_1' }"
input:
tuple val(meta), path(bams)
output:
tuple val(meta), path("*_divergent_peaks.bed") , emit: divergent_TREs
tuple val(meta), path("*_bidirectional_peaks.bed") , emit: bidirectional_TREs
tuple val(meta), path("*_unidirectional_peaks.bed"), emit: unidirectional_TREs
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
// TODO handle bigwigs
// def input_type = ("${input[0]}".endsWith(".bam")) ? "--bam-file $input" :
// ("$input".contains(".bw")) ? "--bw-pl ${input[0]} --bw-mn ${input[1]}" :
// error "Please use bam or BigWig files"
"""
pints_caller \\
--bam-file $bams \\
--save-to . \\
--file-prefix $prefix \\
--thread $task.cpus \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(python --version | sed 's/Python //g')
pints: \$(pints_caller --version)
END_VERSIONS
"""
}