mirror of
https://github.com/MillironX/nf-core_modules.git
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59 lines
3.2 KiB
Text
59 lines
3.2 KiB
Text
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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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process MAPDAMAGE2 {
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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::mapdamage2=2.2.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0"
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} else {
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container "quay.io/biocontainers/mapdamage2:2.2.1--pyr40_0"
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}
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input:
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tuple val(meta), path(bam)
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path(fasta)
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output:
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tuple val(meta), path("results_*/Runtime_log.txt") ,emit: runtime_log
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tuple val(meta), path("results_*/Fragmisincorporation_plot.pdf"), optional: true ,emit: fragmisincorporation_plot
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tuple val(meta), path("results_*/Length_plot.pdf"), optional: true ,emit: length_plot
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tuple val(meta), path("results_*/misincorporation.txt"), optional: true ,emit: misincorporation
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tuple val(meta), path("results_*/lgdistribution.txt"), optional: true ,emit: lgdistribution
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tuple val(meta), path("results_*/dnacomp.txt"), optional: true ,emit: dnacomp
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tuple val(meta), path("results_*/Stats_out_MCMC_hist.pdf"), optional: true ,emit: stats_out_mcmc_hist
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tuple val(meta), path("results_*/Stats_out_MCMC_iter.csv"), optional: true ,emit: stats_out_mcmc_iter
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tuple val(meta), path("results_*/Stats_out_MCMC_trace.pdf"), optional: true ,emit: stats_out_mcmc_trace
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tuple val(meta), path("results_*/Stats_out_MCMC_iter_summ_stat.csv"), optional: true ,emit: stats_out_mcmc_iter_summ_stat
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tuple val(meta), path("results_*/Stats_out_MCMC_post_pred.pdf"), optional: true ,emit: stats_out_mcmc_post_pred
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tuple val(meta), path("results_*/Stats_out_MCMC_correct_prob.csv"), optional: true ,emit: stats_out_mcmc_correct_prob
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tuple val(meta), path("results_*/dnacomp_genome.csv"), optional: true ,emit: dnacomp_genome
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tuple val(meta), path("results_*/rescaled.bam"), optional: true ,emit: rescaled
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tuple val(meta), path("results_*/5pCtoT_freq.txt"), optional: true ,emit: pctot_freq
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tuple val(meta), path("results_*/3pGtoA_freq.txt"), optional: true ,emit: pgtoa_freq
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tuple val(meta), path("results_*/*.fasta"), optional: true ,emit: fasta
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tuple val(meta), path("*/"), optional: true ,emit: folder
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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}" : "${meta.id}"
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"""
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mapDamage \\
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$options.args \\
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-i $bam \\
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-r $fasta
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(mapDamage --version))
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END_VERSIONS
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"""
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}
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