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New module: bamtools/convert (#1219)

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* 📦 NEW: Add bamtools/convert module

* 👌 IMPROVE: Update output channel name, Add tests for each output format

* 👌 IMPROVE: Add error test

* 🐛 FIX: Remove custom tags

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
This commit is contained in:
Sébastien Guizard 2022-01-28 09:58:25 +00:00 committed by GitHub
parent f3a405e4f2
commit 080320765c
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38
modules/bamtools/convert/main.nf Normal file
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@ -0,0 +1,38 @@
process BAMTOOLS_CONVERT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
m = args =~ /-format ([a-z]+)/
ext = m[0][1]
"""
bamtools \\
convert \\
$args \\
-in $bam \\
-out ${prefix}.${ext}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
END_VERSIONS
"""
}

52
modules/bamtools/convert/meta.yml Normal file
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name: bamtools_convert
description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
keywords:
- bamtools
- bamtools/convert
- bam
- convert
- bed
- fasta
- fastq
- json
- pileup
- sam
- yaml
tools:
- bamtools:
description: C++ API & command-line toolkit for working with BAM data
homepage: http://github.com/pezmaster31/bamtools
documentation: https://github.com/pezmaster31/bamtools/wiki
tool_dev_url: http://github.com/pezmaster31/bamtools
doi: ""
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"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
## TODO nf-core: Delete / customise this example output
- out:
type: file
description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}"
authors:
- "@sguizard"

4
tests/config/pytest_modules.yml
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@ -46,6 +46,10 @@ bamaligncleaner:
- modules/bamaligncleaner/**
- tests/modules/bamaligncleaner/**
bamtools/convert:
- modules/bamtools/convert/**
- tests/modules/bamtools/convert/**
bamtools/split:
- modules/bamtools/split/**
- tests/modules/bamtools/split/**

104
tests/modules/bamtools/convert/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML } from '../../../../modules/bamtools/convert/main.nf'
workflow test_bamtools_convert_ext_error {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_EXT_ERROR ( input )
}
workflow test_bamtools_convert_noext_error {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_NOEXT_ERROR ( input )
}
workflow test_bamtools_convert_bed {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_BED ( input )
}
workflow test_bamtools_convert_fasta {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_FASTA ( input )
}
workflow test_bamtools_convert_fastq {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_FASTQ ( input )
}
workflow test_bamtools_convert_json {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_JSON ( input )
}
workflow test_bamtools_convert_pileup {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_PILEUP ( input )
}
workflow test_bamtools_convert_sam {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_SAM ( input )
}
workflow test_bamtools_convert_yaml {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_YAML ( input )
}

41
tests/modules/bamtools/convert/nextflow.config Normal file
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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: BAMTOOLS_CONVERT_EXT_ERROR {
ext.args = "-format vcf"
}
withName: BAMTOOLS_CONVERT_NOEXT_ERROR {
ext.args = ""
}
withName: BAMTOOLS_CONVERT_BED {
ext.args = "-format bed"
}
withName: BAMTOOLS_CONVERT_FASTA {
ext.args = "-format fasta"
}
withName: BAMTOOLS_CONVERT_FASTQ {
ext.args = "-format fastq"
}
withName: BAMTOOLS_CONVERT_JSON {
ext.args = "-format json"
}
withName: BAMTOOLS_CONVERT_PILEUP {
ext.args = "-format pileup"
}
withName: BAMTOOLS_CONVERT_SAM {
ext.args = "-format sam"
}
withName: BAMTOOLS_CONVERT_YAML {
ext.args = "-format yaml"
}
}

90
tests/modules/bamtools/convert/test.yml Normal file
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@ -0,0 +1,90 @@
- name: bamtools convert test_bamtools_convert_ext_error
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_ext_error -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
exit_code: 1
- name: bamtools convert test_bamtools_convert_noext_error
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_noext_error -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
exit_code: 1
- name: bamtools convert test_bamtools_convert_bed
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_bed -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.bed
md5sum: 4e34cc15bf31e700f5f3a9f8fffb6c81
- path: output/bamtools/versions.yml
md5sum: eb7a144b8a97965d3482f6f96b8a8243
- name: bamtools convert test_bamtools_convert_fasta
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fasta -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.fasta
md5sum: 52aeacf78571862b7e97c7d44ac8f827
- path: output/bamtools/versions.yml
md5sum: 42d19a2b2b07f05edb82b34369dfd754
- name: bamtools convert test_bamtools_convert_fastq
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fastq -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.fastq
md5sum: e591c48daad2c56638e5d6f21f1f71c5
- path: output/bamtools/versions.yml
md5sum: 13f0bf8a3e1f8f527f96dabaa5c8051e
- name: bamtools convert test_bamtools_convert_json
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_json -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.json
md5sum: 04afed696f9f14da85a460353645d1f5
- path: output/bamtools/versions.yml
md5sum: 33d633dbd6209cb93c9b071f8c0ed3b3
- name: bamtools convert test_bamtools_convert_pileup
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_pileup -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.pileup
md5sum: e5a3cb4a3e1bf980a575fafce6a2826f
- path: output/bamtools/versions.yml
md5sum: fd3ad0edd1e085b1a002e0593d1d5814
- name: bamtools convert test_bamtools_convert_sam
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_sam -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.sam
md5sum: 61ab3d0de16a9da8b651f9c692e19d5e
- path: output/bamtools/versions.yml
md5sum: 4be470ce3cc0143ae5ae415b612a4965
- name: bamtools convert test_bamtools_convert_yaml
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_yaml -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.yaml
md5sum: 68b56f198da036fef33e150eb773dc3b
- path: output/bamtools/versions.yml
md5sum: 1116abc088c5edf11bee393961c18b3e