Merge pull request #245 from phue/bismark_deduplicate

add bismark/deduplicate + tests
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Harshil Patel 2021-02-23 21:08:24 +00:00 committed by GitHub
commit 5287fe5f95
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7 changed files with 200 additions and 0 deletions

4
.github/filters.yml vendored
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@ -54,6 +54,10 @@ bedtools_sort:
- software/bedtools/sort/** - software/bedtools/sort/**
- tests/software/bedtools/sort/** - tests/software/bedtools/sort/**
bismark_deduplicate:
- software/bismark/deduplicate/**
- tests/software/bismark/deduplicate/**
bismark_genome_preparation: bismark_genome_preparation:
- software/bismark/genome_preparation/** - software/bismark/genome_preparation/**
- tests/software/bismark/genome_preparation/** - tests/software/bismark/genome_preparation/**

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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 +1,41 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BISMARK_DEDUPLICATE {
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), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bismark==0.23.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
} else {
container "quay.io/biocontainers/bismark:0.23.0--0"
}
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.deduplicated.bam") , emit: bam
tuple val(meta), path("*.deduplication_report.txt"), emit: report
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def seqtype = meta.single_end ? '-s' : '-p'
"""
deduplicate_bismark \\
$options.args \\
$seqtype \\
--bam $bam
echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
"""
}

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@ -0,0 +1,72 @@
name: bismark_deduplicate
description: |
Removes alignments to the same position in the genome
from the Bismark mapping output.
keywords:
- bismark
- 3-letter genome
- map
- methylation
- 5mC
- methylseq
- bisulphite
- bam
tools:
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
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:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file containing read alignments
pattern: "*.{bam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Deduplicated output BAM file containing read alignments
pattern: "*.{deduplicated.bam}"
- report:
type: file
description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@phue"

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
workflow test_bismark_deduplicate {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/bismark/Ecoli_10K_methylated_R1_bismark_bt2_pe.bam", checkIfExists: true) ] ]
BISMARK_DEDUPLICATE ( input )
}

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- name: Run bismark deduplicate test workflow
command: nextflow run ./tests/software/bismark/deduplicate -entry test_bismark_deduplicate -c tests/config/nextflow.config
tags:
- bismark
- bismark_deduplicate
files:
- path: output/bismark/Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.bam
md5sum: 35794f413740d9097010e8411f03b785
- path: output/bismark/Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplication_report.txt
md5sum: 125b01ad4f1784a77b7802667d4bfee7