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https://github.com/MillironX/nf-core_modules.git
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4d89d6b2f0
* hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Updated seacr callpeak to include a control threshold * Whitespace Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
47 lines
1.8 KiB
Text
47 lines
1.8 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = '1.3'
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process SEACR_CALLPEAK {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0"
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} else {
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container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0'
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}
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input:
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tuple val(meta), path(bedgraph), path(ctrlbedgraph)
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val (threshold)
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output:
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tuple val(meta), path("*.bed"), emit: bed
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold"
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"""
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SEACR_1.3.sh \\
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$bedgraph \\
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$function_switch \\
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$options.args \\
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$prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo $VERSION)
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bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
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r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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