nf-core_modules/software/bismark/methylationextractor/main.nf
Harshil Patel dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423)
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
2021-04-09 17:23:56 +01:00

48 lines
1.7 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BISMARK_METHYLATIONEXTRACTOR {
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(bam)
path index
output:
tuple val(meta), path("*.bedGraph.gz") , emit: bedgraph
tuple val(meta), path("*.txt.gz") , emit: methylation_calls
tuple val(meta), path("*.cov.gz") , emit: coverage
tuple val(meta), path("*_splitting_report.txt"), emit: report
tuple val(meta), path("*.M-bias.txt") , emit: mbias
path "*.version.txt" , emit: version
script:
def seqtype = meta.single_end ? '-s' : '-p'
def software = getSoftwareName(task.process)
"""
bismark_methylation_extractor \\
--bedGraph \\
--counts \\
--gzip \\
--report \\
$seqtype \\
$options.args \\
$bam
echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
"""
}