PR for sequenzautils/bam2seqz (#395)

* added files

* edited files

* removed file

* README.md edited

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
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Ravneet Bhuller 2021-04-01 06:08:27 +01:00 committed by GitHub
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9 changed files with 199 additions and 8 deletions

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@ -540,4 +540,6 @@ nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf
> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
> files + singularity containers + institutional configs + modules in one go for you, to make this process easier.
# New test data created for the module- sequenzautils/bam2seqz
The new test data is an output from another module- sequenzautils/bcwiggle- (which uses sarscov2 genome fasta file as an input).
-->

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@ -0,0 +1,60 @@
/*
* -----------------------------------------------------
* 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 +1,45 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SEQUENZAUTILS_BAM2SEQZ {
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::sequenza-utils=3.0.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2"
} else {
container "quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2"
}
input:
tuple val(meta), path(normalbam), path(tumourbam)
path fasta
path wigfile
output:
tuple val(meta), path("*.seqz.gz"), emit: seqz
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
sequenza-utils \\
bam2seqz \\
$options.args \\
-n $normalbam \\
-t $tumourbam \\
--fasta $fasta \\
-gc $wigfile \\
-o ${prefix}.seqz.gz
echo \$(sequenzautils --version 2>&1) | sed 's/^.*sequenzautils //; s/Using.*\$//' > ${software}.version.txt
"""
}

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@ -0,0 +1,50 @@
name: sequenzautils_bam2seqz
description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
keywords:
- bam2seqz
tools:
- sequenzautils:
description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.
homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html
documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html
doi: 10.1093/annonc/mdu479
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- normalbam:
type: file
description: BAM file from the reference/normal sample
pattern: "*.{bam}"
- tumourbam:
type: file
description: BAM file from the tumour sample
pattern: "*.{bam}"
- fasta:
type: file
description: Reference FASTA file
pattern: "*.{fasta}"
- wigfile:
type: file
description: GC content wiggle file
pattern: "*.{wig.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- seqz:
type: file
description: Seqz file
pattern: "*.{seqz.gz}"
authors:
- "@kaurravneet4123"

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@ -206,9 +206,6 @@ gatk4_createsequencedictionary:
- software/gatk4/createsequencedictionary/**
- tests/software/gatk4/createsequencedictionary/**
gatk4_markduplicates:
- software/gatk4/markduplicates/**
- tests/software/gatk4/markduplicates/**
gatk4_fastqtosam:
- software/gatk4/fastqtosam/**
- tests/software/gatk4/fastqtosam/**
@ -217,6 +214,10 @@ gatk4_haplotypecaller:
- software/gatk4/haplotypecaller/**
- tests/software/gatk4/haplotypecaller/**
gatk4_markduplicates:
- software/gatk4/markduplicates/**
- tests/software/gatk4/markduplicates/**
gatk4_mergebamalignment:
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**
@ -308,14 +309,14 @@ mosdepth:
- software/mosdepth/**
- tests/software/mosdepth/**
msisensor_scan:
- software/msisensor/scan/**
- tests/software/msisensor/scan/**
msisensor_msi:
- software/msisensor/msi/**
- tests/software/msisensor/msi/**
msisensor_scan:
- software/msisensor/scan/**
- tests/software/msisensor/scan/**
multiqc:
- software/fastqc/**
- software/multiqc/**
@ -429,6 +430,10 @@ sequenza_wiggle:
- software/sequenza/wiggle/**
- tests/software/sequenza/wiggle/**
sequenzautils_bam2seqz:
- software/sequenzautils/bam2seqz/**
- tests/software/sequenzautils/bam2seqz/**
sequenzautils_gcwiggle:
- software/sequenzautils/gcwiggle/**
- tests/software/sequenzautils/gcwiggle/**

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@ -22,6 +22,8 @@ params {
kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
test_wig_gz = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
}
'illumina' {
test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"

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@ -0,0 +1,20 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../software/sequenzautils/bam2seqz/main.nf' addParams( options: [:] )
workflow test_sequenzautils_bam2seqz {
tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
input = [ [ id:'test' ], // meta map
tumourbam,
normalbam
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
wigfile = file(params.test_data['sarscov2']['genome']['test_wig_gz'], checkIfExists: true)
SEQUENZAUTILS_BAM2SEQZ ( input, fasta, wigfile )
}

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@ -0,0 +1,7 @@
- name: sequenzautils bam2seqz
command: nextflow run ./tests/software/sequenzautils/bam2seqz -entry test_sequenzautils_bam2seqz -c tests/config/nextflow.config
tags:
- sequenzautils
- sequenzautils_bam2seqz
files:
- path: output/sequenzautils/test.seqz.gz