PR for lofreq/indelqual module (#539)

* first commit

* edited functions.nf

* edited functions.nf

* version line updated

* Update software/lofreq/indelqual/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/lofreq/indelqual/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/lofreq/indelqual/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/lofreq/indelqual/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/lofreq/indelqual/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/lofreq/indelqual/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* updated files

* updated file

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Ravneet Bhuller 2021-07-05 10:17:57 +01:00 committed by GitHub
parent 2395734492
commit cd8bacc90a
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
6 changed files with 180 additions and 0 deletions

View file

@ -0,0 +1,68 @@
//
// Utility functions used in nf-core DSL2 module files
//
//
// Extract name of software tool from process name using $task.process
//
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${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"
}
}
}

View file

@ -0,0 +1,40 @@
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process LOFREQ_INDELQUAL {
tag "$meta.id"
label 'process_low'
publishDir "${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::lofreq=2.1.5" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4"
} else {
container "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
}
input:
tuple val(meta), path(bam)
path fasta
output:
tuple val(meta), path("*.bam"), emit: bam
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
lofreq indelqual \\
$options.args \\
-f $fasta \\
-o ${prefix}.bam \\
$bam
echo \$(lofreq version 2>&1) | sed 's/^.*lofreq //; s/Using.*\$//' > ${software}.version.txt
"""
}

View file

@ -0,0 +1,44 @@
name: lofreq_indelqual
description: Inserts indel qualities in a BAM file
keywords:
- bam
- indel
- qualities
tools:
- lofreq:
description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file
homepage: https://csb5.github.io/lofreq/
doi: "10.1093/nar/gks918"
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file
pattern: "*.{bam}"
- fasta:
type: file
description: Reference genome FASTA file
pattern: "*.{fasta}"
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}"
- bam:
type: file
description: BAM file with indel qualities inserted into it
pattern: "*.{bam}"
authors:
- "@kaurravneet4123"

View file

@ -422,6 +422,10 @@ last/train:
- software/last/train/** - software/last/train/**
- tests/software/last/train/** - tests/software/last/train/**
lofreq/indelqual:
- software/lofreq/indelqual/**
- tests/software/lofreq/indelqual/**
mash/sketch: mash/sketch:
- software/mash/sketch/** - software/mash/sketch/**
- tests/software/mash/sketch/** - tests/software/mash/sketch/**

View file

@ -0,0 +1,16 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { LOFREQ_INDELQUAL } from '../../../../software/lofreq/indelqual/main.nf' addParams( options: [ 'args': '--dindel', 'suffix':'.indelqual'] )
workflow test_lofreq_indelqual {
input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
LOFREQ_INDELQUAL ( input, fasta )
}

View file

@ -0,0 +1,8 @@
- name: lofreq indelqual
command: nextflow run ./tests/software/lofreq/indelqual -entry test_lofreq_indelqual -c tests/config/nextflow.config
tags:
- lofreq
- lofreq/indelqual
files:
- path: output/lofreq/test.indelqual.bam
md5sum: 18de975638c2633069bfe1a41ebc5ff7