mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
c25c3fe466
* 👌 IMPROVE: Update .gitignore * 📦 Add ultra module * 👌 IMPROVE: Update test input * 👌 IMPROVE: Update and clean code - Update to last versions.yml file - Update meta.yml - Correct typos * 👌 IMPROVE: Update output channels + Rename following subtool * 👌 IMPROVE: Remove old ultre files * 👌 IMPROVE: Update of pytest_modules.yml * 👌 IMPROVE: Update test.yml * 👌 IMPROVE: Keep md5sum as much as possible * 👌 IMPROVE: Remove old ultra files * 👌 IMPROVE: Update of pytest_modules.yml * 👌 IMPROVE: Update test.yml * 👌 IMPROVE: Keep md5sum as much as possible * 🐛 Fix: add unsaved modifications * 🐛 FIX: Remove one inconstant md5sum * 🐛 FIX: Grab software name using ${getSoftwareName(task.process)} * 🐛 FIX: Remove md5sums for pickle files (not constant). * Update modules/ultra/pipeline/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/ultra/pipeline/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * 👌 IMPROVE: update output directory, update meta.yml * 👌 IMPROVE: Use modules to gunzip and sort gtf * 🐛 FIX: Set up channel correctly * 👌 IMPROVE: Remove pickles files and databases Those data might be useful in a debugging purpose. * Apply suggestions from code review * Update main.nf * 🐛 FIX: Update uLTRA to version 0.0.4.1 + remove $(pwd) * 👌 IMPROVE: Sort tags in test.yml * align order of input between main.nf and meta.yml. Add ksahlin as co-author (he did update his package to overcome the pwd-problem * Update main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process ULTRA_PIPELINE {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0"
|
|
} else {
|
|
container "quay.io/biocontainers/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path genome
|
|
path gtf
|
|
|
|
output:
|
|
tuple val(meta), path("*.sam"), emit: sam
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
uLTRA \\
|
|
pipeline \\
|
|
--t $task.cpus \\
|
|
--prefix $prefix \\
|
|
$options.args \\
|
|
$genome \\
|
|
$gtf \\
|
|
$reads \\
|
|
./
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$( uLTRA --version|sed 's/uLTRA //g' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|