Merge pull request #157 from JoseEspinosa/gunzip

Add gunzip module
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Harshil Patel 2021-02-09 10:40:46 +00:00 committed by GitHub
commit 889fced870
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6 changed files with 165 additions and 0 deletions

4
.github/filters.yml vendored
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@ -104,6 +104,10 @@ gffread:
- software/gffread/**
- tests/software/gffread/**
gunzip:
- software/gunzip/**
- tests/software/gunzip/**
minimap2_align:
- software/minimap2/align/**
- tests/software/minimap2/align/**

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@ -0,0 +1,59 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files
* -----------------------------------------------------
*/
/*
* Extract name of software tool from process name using $task.process
*/
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
/*
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
/*
* Tidy up and join elements of a list to return a path string
*/
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
/*
* Function to save/publish module results
*/
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}
}

34
software/gunzip/main.nf Normal file
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@ -0,0 +1,34 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process GUNZIP {
tag "$archive"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
} else {
container "biocontainers/biocontainers:v1.2.0_cv1"
}
input:
path archive
output:
path "$gunzip", emit: gunzip
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
gunzip = archive.toString() - '.gz'
"""
gunzip -f $options.args $archive
echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//' > ${software}.version.txt
"""
}

48
software/gunzip/meta.yml Normal file
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@ -0,0 +1,48 @@
name: gunzip
description: Compresses and decompresses files.
keywords:
- gunzip
- compression
tools:
- gunzip:
description: |
gzip is a file format and a software application used for file compression and decompression.
documentation: https://www.gnu.org/software/gzip/manual/gzip.html
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- archive:
type: file
description: File to be compressed/uncompressed
pattern: "*.*"
output:
- gunzip:
type: file
description: Compressed/uncompressed file
pattern: "*.*"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"

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@ -0,0 +1,13 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GUNZIP } from '../../../software/gunzip/main.nf' addParams( options: [:] )
workflow test_gunzip {
def input = []
input = [ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ]
GUNZIP ( input )
}

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@ -0,0 +1,7 @@
- name: gunzip
command: nextflow run ./tests/software/gunzip -entry test_gunzip -c tests/config/nextflow.config
tags:
- gunzip
files:
- path: output/gunzip/test.vcf
md5sum: 9b291062f1a43aee8e890901324a5616