mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 04:18:17 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
40 lines
1.3 KiB
Text
40 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process BISMARK_SUMMARY {
|
|
label 'process_low'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
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:
|
|
path(bam)
|
|
path(align_report)
|
|
path(dedup_report)
|
|
path(splitting_report)
|
|
path(mbias)
|
|
|
|
output:
|
|
path "*report.{html,txt}", emit: summary
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
"""
|
|
bismark2summary
|
|
|
|
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
|
|
"""
|
|
}
|