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https://github.com/MillironX/nf-core_modules.git
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commit
889fced870
6 changed files with 165 additions and 0 deletions
4
.github/filters.yml
vendored
4
.github/filters.yml
vendored
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@ -104,6 +104,10 @@ gffread:
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- software/gffread/**
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- tests/software/gffread/**
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gunzip:
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- software/gunzip/**
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- tests/software/gunzip/**
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minimap2_align:
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- software/minimap2/align/**
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- tests/software/minimap2/align/**
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59
software/gunzip/functions.nf
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59
software/gunzip/functions.nf
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@ -0,0 +1,59 @@
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/*
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* -----------------------------------------------------
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* Utility functions used in nf-core DSL2 module files
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* -----------------------------------------------------
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*/
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/*
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* Extract name of software tool from process name using $task.process
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*/
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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/*
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* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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*/
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.publish_by_id = args.publish_by_id ?: false
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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/*
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* Tidy up and join elements of a list to return a path string
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*/
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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/*
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* Function to save/publish module results
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*/
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def saveFiles(Map args) {
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if (!args.filename.endsWith('.version.txt')) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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if (ioptions.publish_by_id) {
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path_list.add(args.publish_id)
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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}
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34
software/gunzip/main.nf
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34
software/gunzip/main.nf
Normal file
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@ -0,0 +1,34 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process GUNZIP {
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tag "$archive"
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
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} else {
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container "biocontainers/biocontainers:v1.2.0_cv1"
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}
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input:
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path archive
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output:
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path "$gunzip", emit: gunzip
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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gunzip = archive.toString() - '.gz'
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"""
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gunzip -f $options.args $archive
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echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//' > ${software}.version.txt
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"""
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}
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48
software/gunzip/meta.yml
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48
software/gunzip/meta.yml
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@ -0,0 +1,48 @@
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name: gunzip
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description: Compresses and decompresses files.
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keywords:
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- gunzip
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- compression
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tools:
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- gunzip:
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description: |
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gzip is a file format and a software application used for file compression and decompression.
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documentation: https://www.gnu.org/software/gzip/manual/gzip.html
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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input:
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- archive:
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type: file
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description: File to be compressed/uncompressed
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pattern: "*.*"
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output:
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- gunzip:
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type: file
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description: Compressed/uncompressed file
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pattern: "*.*"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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13
tests/software/gunzip/main.nf
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13
tests/software/gunzip/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GUNZIP } from '../../../software/gunzip/main.nf' addParams( options: [:] )
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workflow test_gunzip {
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def input = []
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input = [ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ]
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GUNZIP ( input )
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}
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7
tests/software/gunzip/test.yml
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7
tests/software/gunzip/test.yml
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- name: gunzip
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command: nextflow run ./tests/software/gunzip -entry test_gunzip -c tests/config/nextflow.config
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tags:
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- gunzip
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files:
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- path: output/gunzip/test.vcf
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md5sum: 9b291062f1a43aee8e890901324a5616
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