process RSEQC_INNERDISTANCE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" input: tuple val(meta), path(bam) path bed output: tuple val(meta), path("*distance.txt"), optional:true, emit: distance tuple val(meta), path("*freq.txt") , optional:true, emit: freq tuple val(meta), path("*mean.txt") , optional:true, emit: mean tuple val(meta), path("*.pdf") , optional:true, emit: pdf tuple val(meta), path("*.r") , optional:true, emit: rscript path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" if (!meta.single_end) { """ inner_distance.py \\ -i $bam \\ -r $bed \\ -o $prefix \\ $args \\ > stdout.txt head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt cat <<-END_VERSIONS > versions.yml "${task.process}": rseqc: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g") END_VERSIONS """ } else { """ cat <<-END_VERSIONS > versions.yml "${task.process}": rseqc: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g") END_VERSIONS """ } }