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New module: genrich (#877)

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* Add genrich module

* Rearrange genrich module from genrich/genrich to genrich

* Remove copy/paste code

* Fix meta.yml

* Implement save_duplicates independently of -r opt
This commit is contained in:
Jose Espinosa-Carrasco 2021-10-22 12:22:02 +02:00 committed by GitHub
parent 4ed5e4eff3
commit 32f6191aca
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78
modules/genrich/functions.nf Normal file
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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// Do not publish versions.yml unless running from pytest workflow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"
}
}

69
modules/genrich/main.nf Normal file
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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GENRICH {
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::genrich=0.6.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1"
} else {
container "quay.io/biocontainers/genrich:0.6.1--h5bf99c6_1"
}
input:
tuple val(meta), path(treatment_bam)
path control_bam
path blacklist_bed
output:
tuple val(meta), path("*narrowPeak") , emit: peaks
tuple val(meta), path("*pvalues.bedGraph"), optional:true, emit: bedgraph_pvalues
tuple val(meta), path("*pileup.bedGraph") , optional:true, emit: bedgraph_pileup
tuple val(meta), path("*intervals.bed") , optional:true, emit: bed_intervals
tuple val(meta), path("*duplicates.txt") , optional:true, emit: duplicates
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def control = params.control_bam ? "-c $control_bam" : ''
def pvalues = params.pvalues ? "-f ${prefix}.pvalues.bedGraph" : ""
def pileup = params.pileup ? "-k ${prefix}.pileup.bedGraph" : ""
def bed = params.bed ? "-b ${prefix}.intervals.bed" : ""
def blacklist = params.blacklist_bed ? "-E $blacklist_bed" : ""
def duplicates = ""
if (params.save_duplicates) {
if (options.args.contains('-r')) {
duplicates = "-R ${prefix}.duplicates.txt"
} else {
log.info '[Genrich] Duplicates can only be saved if they are filtered, defaulting to -r option (Remove PCR duplicates).'
duplicates = "-r -R ${prefix}.duplicates.txt"
}
}
"""
Genrich \\
-t $treatment_bam \\
$options.args \\
$control \\
$blacklist \\
-o ${prefix}.narrowPeak \\
$pvalues \\
$pileup \\
$bed \\
$duplicates \\
$blacklist \\
$control
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(Genrich --version 2>&1) | sed 's/^Genrich, version //; s/ .*\$//')
END_VERSIONS
"""
}

71
modules/genrich/meta.yml Normal file
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name: genrich
description: Peak-calling for ChIP-seq and ATAC-seq enrichment experiments
keywords:
- peak-calling
- ChIP-seq
- ATAC-seq
tools:
- genrich:
description: |
Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).
It analyzes alignment files generated following the assay and produces a file
detailing peaks of significant enrichment.
homepage: https://github.com/jsh58/Genrich
documentation: https://github.com/jsh58/Genrich#readme
tool_dev_url: https://github.com/jsh58/Genrich
doi: ""
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- treatment_bam:
type: file
description: Coordinate sorted BAM/SAM file from treatment sample
pattern: "*.{bam,sam}"
- control_bam:
type: file
description: Coordinate sorted BAM/SAM file from control sample
pattern: "*.{bam,sam}"
- blacklist_bed:
type: file
description: Bed file containing genomic intervals to exclude from the analysis
pattern: "*.{bed}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- peaks:
type: file
description: Output file is in ENCODE narrowPeak format
pattern: "*.{narrowPeak}"
- bedgraph_pvalues:
type: file
description: bedGraph file containing p/q values
pattern: "*.{pvalues.bedGraph}"
- bedgraph_pileup:
type: file
description: bedGraph file containing pileups and p-values
pattern: "*.{pileup.bedGraph}"
- bed_intervals:
type: file
description: Bed file containing annotated intervals
pattern: "*.{intervals.bed}"
- duplicates:
type: file
description: Text output file containing intervals corresponding to PCR duplicates
pattern: "*.{intervals.txt}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@JoseEspinosa"

4
tests/config/pytest_modules.yml
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@ -466,6 +466,10 @@ genmap/mappability:
- modules/genmap/mappability/**
- tests/modules/genmap/mappability/**
genrich:
- modules/genrich/**
- tests/modules/genrich/**
gffread:
- modules/gffread/**
- tests/modules/gffread/**

2
tests/config/test_data.config
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@ -123,6 +123,7 @@ params {
'illumina' {
test_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"
test_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam"
test_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam"
test_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai"
test_paired_end_markduplicates_sorted_referencesn_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt"
@ -137,6 +138,7 @@ params {
test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"

44
tests/modules/genrich/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GENRICH } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:false, save_duplicates:false, options: ["args": "-p 0.1"] )
include { GENRICH as GENRICH_BLACKLIST } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:true, save_duplicates:false, options: ["args": "-p 0.1"] )
include { GENRICH as GENRICH_ALL_OUTPUTS } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: true, pileup:true, bed:true, blacklist_bed:false, save_duplicates:true, options: ["args": "-r -p 0.1"] )
include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:false, save_duplicates:false, options: ["args": "-j -p 0.1"] )
workflow test_genrich {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ ]
blacklist = [ ]
GENRICH ( input, control, blacklist )
}
workflow test_genrich_ctrl {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
blacklist = [ ]
GENRICH ( input, control, blacklist )
}
workflow test_genrich_all_outputs {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
blacklist = [ ]
GENRICH_ALL_OUTPUTS ( input, control, blacklist )
}
workflow test_genrich_atacseq {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
blacklist = [ ]
GENRICH_ATACSEQ ( input, control, blacklist )
}

39
tests/modules/genrich/test.yml Normal file
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- name: genrich test_genrich
command: nextflow run tests/modules/genrich -entry test_genrich -c tests/config/nextflow.config
tags:
- genrich
files:
- path: output/genrich/test.narrowPeak
md5sum: 6afabdd3f691c7c84c66ff8a23984681
- name: genrich test_genrich_ctrl
command: nextflow run tests/modules/genrich -entry test_genrich_ctrl -c tests/config/nextflow.config
tags:
- genrich
files:
- path: output/genrich/test.narrowPeak
md5sum: 6afabdd3f691c7c84c66ff8a23984681
- name: genrich test_genrich_all_outputs
command: nextflow run tests/modules/genrich -entry test_genrich_all_outputs -c tests/config/nextflow.config
tags:
- genrich
files:
- path: output/genrich/test.duplicates.txt
md5sum: a92893f905fd8b3751bc6a960fbfe7ba
- path: output/genrich/test.intervals.bed
md5sum: 52edf47e6641c0cc03f9cca7324f7eaa
- path: output/genrich/test.narrowPeak
md5sum: e45eb7d000387975050c2e85c164e5be
- path: output/genrich/test.pileup.bedGraph
md5sum: e4f7fa664cd4ed2cf3a1a3a9eb415e71
- path: output/genrich/test.pvalues.bedGraph
md5sum: 564859953704983393d4b7d6317060cd
- name: genrich test_genrich_atacseq
command: nextflow run tests/modules/genrich -entry test_genrich_atacseq -c tests/config/nextflow.config
tags:
- genrich
files:
- path: output/genrich/test.narrowPeak
md5sum: ddea556b820f8be3695ffdf6c6f70aff