process SAMTOOLS_MPILEUP { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(input), path(intervals) path fasta output: tuple val(meta), path("*.mpileup"), emit: mpileup 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 intervals = intervals ? "-l ${intervals}" : "" """ samtools mpileup \\ --fasta-ref $fasta \\ --output ${prefix}.mpileup \\ $args \\ $input cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }