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

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process DRAGMAP_ALIGN {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.14 conda-forge::pigz=2.3.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:f7aad9060cde739c95685fc5ff6d6f7e3ec629c8-0':
'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:f7aad9060cde739c95685fc5ff6d6f7e3ec629c8-0' }"
input:
tuple val(meta), path(reads)
path hashmap
val sort_bam
output:
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path('*.log'), emit: log
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def samtools_command = sort_bam ? 'sort' : 'view'
if (meta.single_end) {
"""
dragen-os \\
-r $hashmap \\
-1 $reads \\
--num-threads $task.cpus \\
$args \\
2> ${prefix}.dragmap.log \\
| samtools $samtools_command -@ $task.cpus $args2 -o ${prefix}.bam -
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dragmap: \$(echo \$(dragen-os --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
} else {
"""
dragen-os \\
-r $hashmap \\
-1 ${reads[0]} \\
-2 ${reads[1]} \\
--num-threads $task.cpus \\
$args \\
2> ${prefix}.dragmap.log \\
| samtools $samtools_command -@ $task.cpus $args2 -o ${prefix}.bam -
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dragmap: \$(echo \$(dragen-os --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
}
}