nf-core_modules/modules/bowtie/align/main.nf

63 lines
2.4 KiB
Text
Raw Normal View History

2020-12-08 11:57:00 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
2020-12-08 11:57:00 +00:00
params.options = [:]
options = initOptions(params.options)
2020-12-08 11:57:00 +00:00
process BOWTIE_ALIGN {
tag "$meta.id"
label 'process_high'
publishDir "${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']) }
2020-12-08 11:57:00 +00:00
2021-02-16 23:58:23 +00:00
conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.11' : null)
2020-12-17 06:33:44 +00:00
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
2020-12-17 09:24:48 +00:00
container 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
2020-12-17 06:33:44 +00:00
} else {
2020-12-17 09:24:48 +00:00
container 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
2020-12-17 06:33:44 +00:00
}
2020-12-08 11:57:00 +00:00
input:
tuple val(meta), path(reads)
path index
2020-12-17 09:24:48 +00:00
2020-12-08 11:57:00 +00:00
output:
2020-12-17 09:24:48 +00:00
tuple val(meta), path('*.bam'), emit: bam
tuple val(meta), path('*.out'), emit: log
path "versions.yml" , emit: versions
2020-12-18 08:14:40 +00:00
tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
2020-12-08 11:57:00 +00:00
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
2020-12-18 08:20:35 +00:00
def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : ''
2020-12-16 10:02:58 +00:00
def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
2020-12-08 11:57:00 +00:00
"""
INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
bowtie \\
--threads $task.cpus \\
2020-12-16 10:02:58 +00:00
--sam \\
-x \$INDEX \\
-q \\
2020-12-17 09:24:48 +00:00
$unaligned \\
2020-12-16 10:02:58 +00:00
$options.args \\
$endedness \\
2020-12-17 09:24:48 +00:00
2> ${prefix}.out \\
| samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
2020-12-18 08:14:40 +00:00
if [ -f ${prefix}.unmapped.fastq ]; then
gzip ${prefix}.unmapped.fastq
fi
if [ -f ${prefix}.unmapped_1.fastq ]; then
gzip ${prefix}.unmapped_1.fastq
gzip ${prefix}.unmapped_2.fastq
fi
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
2020-12-08 11:57:00 +00:00
"""
}