nf-core_modules/modules/bismark/align/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BISMARK_ALIGN {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
} else {
container "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 prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def fastq = meta.single_end ? reads : "-1 ${reads[0]} -2 ${reads[1]}"
"""
bismark \\
$fastq \\
$options.args \\
--genome $index \\
--bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
END_VERSIONS
"""
}