process MAPDAMAGE2 { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0' : 'quay.io/biocontainers/mapdamage2:2.2.1--pyr40_0' }" input: tuple val(meta), path(bam) path(fasta) output: tuple val(meta), path("results_*/Runtime_log.txt") ,emit: runtime_log tuple val(meta), path("results_*/Fragmisincorporation_plot.pdf"), optional: true ,emit: fragmisincorporation_plot tuple val(meta), path("results_*/Length_plot.pdf"), optional: true ,emit: length_plot tuple val(meta), path("results_*/misincorporation.txt"), optional: true ,emit: misincorporation tuple val(meta), path("results_*/lgdistribution.txt"), optional: true ,emit: lgdistribution tuple val(meta), path("results_*/dnacomp.txt"), optional: true ,emit: dnacomp tuple val(meta), path("results_*/Stats_out_MCMC_hist.pdf"), optional: true ,emit: stats_out_mcmc_hist tuple val(meta), path("results_*/Stats_out_MCMC_iter.csv"), optional: true ,emit: stats_out_mcmc_iter tuple val(meta), path("results_*/Stats_out_MCMC_trace.pdf"), optional: true ,emit: stats_out_mcmc_trace tuple val(meta), path("results_*/Stats_out_MCMC_iter_summ_stat.csv"), optional: true ,emit: stats_out_mcmc_iter_summ_stat tuple val(meta), path("results_*/Stats_out_MCMC_post_pred.pdf"), optional: true ,emit: stats_out_mcmc_post_pred tuple val(meta), path("results_*/Stats_out_MCMC_correct_prob.csv"), optional: true ,emit: stats_out_mcmc_correct_prob tuple val(meta), path("results_*/dnacomp_genome.csv"), optional: true ,emit: dnacomp_genome tuple val(meta), path("results_*/rescaled.bam"), optional: true ,emit: rescaled tuple val(meta), path("results_*/5pCtoT_freq.txt"), optional: true ,emit: pctot_freq tuple val(meta), path("results_*/3pGtoA_freq.txt"), optional: true ,emit: pgtoa_freq tuple val(meta), path("results_*/*.fasta"), optional: true ,emit: fasta tuple val(meta), path("*/"), optional: true ,emit: folder path "versions.yml",emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ mapDamage \\ $args \\ -i $bam \\ -r $fasta cat <<-END_VERSIONS > versions.yml "${task.process}": mapdamage2: \$(echo \$(mapDamage --version)) END_VERSIONS """ }