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

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
process BBMAP_ALIGN {
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::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0"
} else {
container "quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0"
}
input:
tuple val(meta), path(fastq)
path ref
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: version
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script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"
// Set the db variable to reflect the three possible types of reference input: 1) directory
// named 'ref', 2) directory named something else (containg a 'ref' subdir) or 3) a sequence
// file in fasta format
if ( ref.isDirectory() ) {
if ( ref ==~ /(.\/)?ref\/?/ ) {
db = ''
} else {
db = "path=${ref}"
}
} else {
db = "ref=${ref}"
}
"""
bbmap.sh \\
$db \\
$input \\
out=${prefix}.bam \\
$options.args \\
threads=$task.cpus \\
-Xmx${task.memory.toGiga()}g
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(bbversion.sh)
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
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"""
}