Add gatk4/estimatelibrarycomplexity (#965)

* Add gatk4/estimatelibrarycomplxity

* forgot to add yml

* Fix placeholder
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FriederikeHanssen 2021-10-28 17:49:27 +02:00 committed by GitHub
parent 9402595711
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//
// 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()
}
//
// Extract name of module from process name using $task.process
//
def getProcessName(task_process) {
return task_process.tokenize(':')[-1]
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
// Do not publish versions.yml unless running from pytest workflow
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
return null
}
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
}
path = path instanceof String ? path : ''
path_list.add(path)
}
}
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GATK4_ESTIMATELIBRARYCOMPLEXITY {
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::gatk4=4.2.2.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.2.0--hdfd78af_1"
} else {
container "quay.io/biocontainers/gatk4:4.2.2.0--hdfd78af_1"
}
input:
tuple val(meta), path(cram)
path(fasta)
path(fai)
path(dict)
output:
tuple val(meta), path('*.metrics'), emit: metrics
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def crams = cram.collect(){ x -> "-I ".concat(x.toString()) }.join(" ")
def avail_mem = 3
if (!task.memory) {
log.info '[GATK EstimateLibraryComplexity] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk EstimateLibraryComplexity \
${crams} \
-O ${prefix}.metrics \
--REFERENCE_SEQUENCE ${fasta} \
--VALIDATION_STRINGENCY SILENT \
--TMP_DIR . $options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

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name: gatk4_estimatelibrarycomplexity
description: Estimates the numbers of unique molecules in a sequencing library.
keywords:
- gatk4
- gatk4_estimatelibrarycomplexity
- duplication_metrics
- reporting
tools:
- gatk4:
description: Genome Analysis Toolkit (GATK4)
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us
tool_dev_url: https://github.com/broadinstitute/gatk
doi: "10.1158/1538-7445.AM2017-3590"
licence: ['Apache-2.0']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- cram:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- metrics:
type: file
description: File containing metrics on the input files
pattern: "*.{metrics}"
authors:
- "@FriederikeHanssen"

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@ -430,6 +430,10 @@ gatk4/createsomaticpanelofnormals:
- modules/gatk4/createsomaticpanelofnormals/** - modules/gatk4/createsomaticpanelofnormals/**
- tests/modules/gatk4/createsomaticpanelofnormals/** - tests/modules/gatk4/createsomaticpanelofnormals/**
gatk4/estimatelibrarycomplexity:
- modules/gatk4/estimatelibrarycomplexity/**
- tests/modules/gatk4/estimatelibrarycomplexity/**
gatk4/fastqtosam: gatk4/fastqtosam:
- modules/gatk4/fastqtosam/** - modules/gatk4/fastqtosam/**
- tests/modules/gatk4/fastqtosam/** - tests/modules/gatk4/fastqtosam/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../../modules/gatk4/estimatelibrarycomplexity/main.nf' addParams( options: [:] )
workflow test_gatk4_estimatelibrarycomplexity {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
GATK4_ESTIMATELIBRARYCOMPLEXITY ( input, fasta, fai, dict )
}

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- name: gatk4 estimatelibrarycomplexity test_gatk4_estimatelibrarycomplexity
command: nextflow run tests/modules/gatk4/estimatelibrarycomplexity -entry test_gatk4_estimatelibrarycomplexity -c tests/config/nextflow.config
tags:
- gatk4/estimatelibrarycomplexity
- gatk4
files:
- path: output/gatk4/test.metrics