--- a +++ b/modules/local/bedtools/random/main.nf @@ -0,0 +1,48 @@ +process BEDTOOLS_RANDOM_SAMPLING { + tag "${meta.id}" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--h13024bc_3': + 'biocontainers/bedtools:2.31.1--h13024bc_3' }" + + input: + tuple val(meta), path(genome_file) + tuple val(number_sequences), val(length_sequences) + + output: + tuple val(meta), path "*.bed", emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + bedtools random \\ + -l $length_sequences \\ + -n $number_sequences \\ + -g $genome_file \\ + $args \\ + > ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version |& sed '1!d ; s/bedtools v//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version |& sed '1!d ; s/bedtools v//') + END_VERSIONS + """ +}