mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
6d3d8306e1
* Fitst attempt at mapdamage2 * Add new module mapdamage2 * Removed __pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc * Modify main.nf and meta.yml * Modify main.nf and meta.yml * Modify main.nf and meta.yml * Modify meta.yml * Update pytest_modules.yml * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * edit the meta.yml and main.nf after reviews * Update meta.yml * Update meta.yml Co-authored-by: AIbrahim <AIbrahim@apate.hki-jena.de> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
58 lines
3.2 KiB
Text
58 lines
3.2 KiB
Text
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process MAPDAMAGE2 {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0"
|
|
} else {
|
|
container "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 prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
mapDamage \\
|
|
$options.args \\
|
|
-i $bam \\
|
|
-r $fasta
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(mapDamage --version))
|
|
END_VERSIONS
|
|
"""
|
|
}
|