mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
52 lines
2.9 KiB
Text
52 lines
2.9 KiB
Text
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
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
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
|
|
"""
|
|
}
|