def VERSION = '1.3' // Version information not provided by tool on CLI process SEACR_CALLPEAK { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' : 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' }" input: tuple val(meta), path(bedgraph), path(ctrlbedgraph) val (threshold) output: tuple val(meta), path("*.bed"), emit: bed path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold" """ SEACR_1.3.sh \\ $bedgraph \\ $function_switch \\ $args \\ $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": seacr: $VERSION bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') END_VERSIONS """ }