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https://github.com/MillironX/nf-core_modules.git
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eb9178970f
* add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/summary * remove md5sum check for bismark_summary_report.html it contains a timestamp * fix tests * update meta.yml * remove mysterious index files
38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process BISMARK_SUMMARY {
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
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} else {
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container "quay.io/biocontainers/bismark:0.23.0--0"
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}
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input:
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path(bam)
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path(align_report)
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path(dedup_report)
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path(splitting_report)
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path(mbias)
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output:
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path("*{html,txt}") , emit: summary
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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"""
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bismark2summary
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echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
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"""
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}
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