mirror of
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52 lines
2.9 KiB
Text
52 lines
2.9 KiB
Text
process MAPDAMAGE2 {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0' :
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'quay.io/biocontainers/mapdamage2:2.2.1--pyr40_0' }"
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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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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mapDamage \\
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$args \\
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-i $bam \\
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-r $fasta
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mapdamage2: \$(echo \$(mapDamage --version))
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END_VERSIONS
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"""
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}
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