Add variantbam (#618)

* template created for variantbam (#616)

* Add bcftools reheader (#585) (#608)

* local tests and linting passing (#585)

* fix: picard filtersamreads input (#610)

* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

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

* fix test

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

* Added module arriba (#611)

* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

* Added module arriba

* Changes in test configs

* Added module Arriba for fusion detection

* Fixed review comments

* Added an output option for discarded fusions

* Resolved some conflits

* conflicts

* Apply suggestions from code review

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

* added test for new header

* enhance module fastp: add `save_merged` (#598) (#614)

* enhance module fastp: add `save_merged` (#598)

* removed md5sum checks from log and json

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>

* fixed autogenerated biocontainter links

* variantbam module passing all tests/lints (#616)

* Added an optional output junction channel in STAR (#621)

* Added an optional output channel for chimeric junctions

* Fix in test.yml

* Apply suggestions from code review

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

* removed qcreport output

fixes #616

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
This commit is contained in:
Johnathan D 2021-07-26 19:07:29 +01:00 committed by GitHub
parent df909015b6
commit a21cc95c69
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6 changed files with 179 additions and 0 deletions

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//
// 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"
}
}
}

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
def VERSION = '1.4.4a'
process VARIANTBAM {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5"
} else {
container "quay.io/biocontainers/variantbam:1.4.4a--h7d7f7ad_5"
}
input:
tuple val(meta), path(bam)
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}"
"""
variant \\
$bam \\
-o ${prefix}.bam \\
$options.args
echo $VERSION > ${software}.version.txt
"""
}

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name: variantbam
description: Filtering, downsampling and profiling alignments in BAM/CRAM formats
keywords:
- filter
- bam
- subsample
- downsample
- downsample bam
- subsample bam
tools:
- variantbam:
description: Filtering and profiling of next-generational sequencing data using region-specific rules
homepage: https://github.com/walaj/VariantBam
documentation: https://github.com/walaj/VariantBam#table-of-contents
tool_dev_url: https://github.com/walaj/VariantBam
doi: 10.1093/bioinformatics/btw111
licence: ['Apache2']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
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: Filtered or downsampled BAM file
pattern: "*.{bam}"
authors:
- "@bjohnnyd"

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@ -831,6 +831,10 @@ untar:
- modules/untar/** - modules/untar/**
- tests/modules/untar/** - tests/modules/untar/**
variantbam:
- modules/variantbam/**
- tests/modules/variantbam/**
vcftools: vcftools:
- modules/vcftools/** - modules/vcftools/**
- tests/modules/vcftools/** - tests/modules/vcftools/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { VARIANTBAM } from '../../../modules/variantbam/main.nf' addParams( options: [args: '-m 1'] )
workflow test_variantbam {
input = [ [ id:'test', single_end:false ],
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
VARIANTBAM ( input )
}

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- name: variantbam test_variantbam
command: nextflow run tests/modules/variantbam -entry test_variantbam -c tests/config/nextflow.config
tags:
- variantbam
files:
- path: output/variantbam/test.bam
md5sum: fc08f065475d60b3b06ee32920564d4b