process BISMARK_ALIGN { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : 'quay.io/biocontainers/bismark:0.23.0--0' }" input: tuple val(meta), path(reads) path index output: tuple val(meta), path("*bam") , emit: bam tuple val(meta), path("*report.txt"), emit: report tuple val(meta), path("*fq.gz") , optional:true, emit: unmapped path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def fastq = meta.single_end ? reads : "-1 ${reads[0]} -2 ${reads[1]}" """ bismark \\ $fastq \\ $args \\ --genome $index \\ --bam cat <<-END_VERSIONS > versions.yml "${task.process}": bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ }