added gatk4 revertsam

This commit is contained in:
kevinmenden 2021-02-22 15:21:39 +01:00
parent efd60d94ee
commit 3fee38ee2d
6 changed files with 116 additions and 25 deletions

4
.github/filters.yml vendored
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@ -136,6 +136,10 @@ gatk4_bedtointervallist:
- software/gatk4/bedtointervallist/** - software/gatk4/bedtointervallist/**
- tests/software/gatk4/bedtointervallist/** - tests/software/gatk4/bedtointervallist/**
gatk4_revertsam:
- software/gatk4/revertsam/**
- tests/software/gatk4/revertsam/**
gatk4_samtofastq: gatk4_samtofastq:
- software/gatk4/samtofastq/** - software/gatk4/samtofastq/**
- tests/software/gatk4/samtofastq/** - tests/software/gatk4/samtofastq/**

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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"
}
}
}

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@ -0,0 +1,39 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process GATK4_REVERTSAM {
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), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
} else {
container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
}
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path('*.bam') , emit: bam
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
"""
gatk RevertSam \\
I=$bam \\
O=${prefix}.reverted.bam \\
$options.args
gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
"""
}

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@ -40,21 +40,14 @@ input:
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test'] e.g. [ id:'test']
- bam: - bam:
type: list
description: Two or more VCF files
pattern: "*.{vcf,vcf.gz}"
- ref_dict:
type: file type: file
description: Optional Sequence Dictionary as input description: The input bam/sam file
pattern: "*.dict" pattern: "*.{bam,sam}"
- use_ref_dict:
type: boolean
description: Specify whether or not to use a given reference dictionary
output: output:
- vcf: - bam:
type: file type: file
description: merged vcf file description: The reverted bam/sam file
pattern: "*.vcf.gz" pattern: "*.reverted.bam"
- version: - version:
type: file type: file
description: File containing software version description: File containing software version

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@ -2,17 +2,13 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] ) include { GATK4_REVERTSAM } from '../../../../software/gatk4/revertsam/main.nf' addParams( options: [:] )
workflow test_gatk4_mergevcfs { workflow test_gatk4_revertsam {
def input = [] def input = []
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true), file("${launchDir}/tests/data/bam/sarscov2_aln.bam", checkIfExists: true) ]
file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true) ] ]
ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true) GATK4_REVERTSAM( input )
GATK4_MERGEVCFS ( input, ref_dict, false )
} }

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@ -1,8 +1,8 @@
- name: gatk4 mergevcfs - name: gatk4 revertsam
command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config command: nextflow run ./tests/software/gatk4/revertsam -entry test_gatk4_revertsam -c tests/config/nextflow.config
tags: tags:
- gatk4 - gatk4
- gatk4_mergevcfs - gatk4_revertsam
files: files:
- path: output/gatk4/test.merged.vcf.gz - path: output/gatk4/test.reverted.bam
md5sum: f25850b7bd4d362b5ea67d4453e9df55 md5sum: 6de199f7a0577e2a3fe7b3a9cb4ae25d