Adding samtools_mpileup module

This commit is contained in:
JoseEspinosa 2021-01-29 17:58:42 +01:00
parent 3eedca9bb4
commit 22dcdc692d
6 changed files with 228 additions and 0 deletions

40
.github/workflows/samtools_mpileup.yml vendored Normal file
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@ -0,0 +1,40 @@
name: samtools_mpileup
on:
push:
paths:
- software/samtools/mpileup/**
- .github/workflows/samtools_mpileup.yml
- tests/software/samtools/**
pull_request:
paths:
- software/samtools/mpileup/**
- .github/workflows/samtools_mpileup.yml
- tests/software/samtools/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: pytest --tag samtools_mpileup --symlink --wt 2

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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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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process SAMTOOLS_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::samtools=1.10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
} else {
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
}
input:
tuple val(meta), path(bam)
path fasta
output:
tuple val(meta), path("*.mpileup"), emit: mpileup
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
samtools mpileup \\
--fasta-ref $fasta \\
--output ${prefix}.mpileup \\
$options.args \\
$bam
echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
"""
}

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name: samtools_mpileup
description: BAM
keywords:
- mpileup
- bam
- sam
- cram
tools:
- samtools:
description: |
SAMtools is a set of utilities for interacting with and post-processing
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
These files are generated as output by short read aligners like BWA.
homepage: http://www.htslib.org/
documentation: hhttp://www.htslib.org/doc/samtools.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: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- fasta-ref:
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 ]
- mpileup:
type: file
description: mpileup file
pattern: "*.{mpileup}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@drpatelh"
- "@joseespinosa"

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@ -8,6 +8,7 @@ include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addPa
include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] ) include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] ) include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] )
include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] ) include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] )
include { SAMTOOLS_MPILEUP } from '../../../software/samtools/mpileup/main.nf' addParams( options: [:] )
workflow test_samtools_flagstat { workflow test_samtools_flagstat {
@ -66,3 +67,14 @@ workflow test_samtools_view {
SAMTOOLS_VIEW ( input ) SAMTOOLS_VIEW ( input )
} }
workflow test_samtools_mpileup {
def input = []
def fasta = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
SAMTOOLS_MPILEUP ( input, fasta )
}

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@ -51,3 +51,12 @@
files: files:
- path: output/samtools/test.bam - path: output/samtools/test.bam
md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff
- name: Run samtools mpileup test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_mpileup -c tests/config/nextflow.config
tags:
- samtools
- samtools_mpileup
files:
- path: output/samtools/test.bam
md5sum: 95c2646fa7bd535207722008c581c81d