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 """ }