Merge pull request #247 from JoseEspinosa/bcftools-mpileup

Add bcftools mpileup module
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Jose Espinosa-Carrasco 2021-02-24 09:24:43 +01:00 committed by GitHub
commit 8f4363ccb5
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6 changed files with 215 additions and 0 deletions

4
.github/filters.yml vendored
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@ -18,6 +18,10 @@ bcftools_merge:
- software/bcftools/merge/**
- tests/software/bcftools/merge/**
bcftools_mpileup:
- software/bcftools/mpileup/**
- tests/software/bcftools/mpileup/**
bcftools_stats:
- software/bcftools/stats/**
- tests/software/bcftools/stats/**

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@ -0,0 +1,61 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files
* -----------------------------------------------------
*/
/*
* Extract name of software tool from process name using $task.process
*/
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
/*
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
/*
* Tidy up and join elements of a list to return a path string
*/
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes
return paths.join('/')
}
/*
* Function to save/publish module results
*/
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}
}

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@ -0,0 +1,47 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BCFTOOLS_MPILEUP {
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::bcftools=1.11" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
} else {
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
}
input:
tuple val(meta), path(bam)
path fasta
output:
tuple val(meta), path("*.gz") , emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
tuple val(meta), path("*stats.txt"), emit: stats
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
echo "${meta.id}" > sample_name.list
bcftools mpileup \\
--fasta-ref $fasta \\
$options.args \\
$bam \\
| bcftools call --output-type v $options.args2 \\
| bcftools reheader --samples sample_name.list \\
| bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3
tabix -p vcf -f ${prefix}.vcf.gz
bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
"""
}

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@ -0,0 +1,73 @@
name: bcftools_mpileup
description: Compresses VCF files
keywords:
- variant calling
- mpileup
- VCF
tools:
- consensus:
description: |
Generates genotype likelihoods at each genomic position with coverage.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
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: Input BAM file
pattern: "*.{bam}"
- fasta:
type: file
description: FASTA reference file
pattern: "*.{fasta,fa}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF gzipped output file
pattern: "*.{vcf.gz}"
- tbi:
type: file
description: tabix index file
pattern: "*.{tbi}"
- stats:
type: file
description: Text output file containing stats
pattern: "*{stats.txt}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"

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@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BCFTOOLS_MPILEUP } from '../../../../software/bcftools/mpileup/main.nf' addParams( options: ['args2': '--no-version --ploidy 1 --multiallelic-caller',
'args3': '--no-version' ] )
workflow test_bcftools_mpileup {
def input = []
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ]]
fasta = [ file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) ]
BCFTOOLS_MPILEUP ( input, fasta )
}

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@ -0,0 +1,13 @@
- name: bcftools mpileup
command: nextflow run ./tests/software/bcftools/mpileup -entry test_bcftools_mpileup -c tests/config/nextflow.config
tags:
- bcftools
- bcftools_mpileup
files:
- path: output/bcftools/test.vcf.gz
md5sum: f25141161cb935ef7719cfb41563ffb0
- path: output/bcftools/test.vcf.gz.tbi
md5sum: 4423be9f13fa07e5eadb13b1cbe8baf7
- path: output/bcftools/test.bcftools_stats.txt
md5sum: b8d6b6927f7bf024acf11ba438b54fa0