nf-core_modules/modules/snapaligner/align/main.nf
Matthias De Smet 44baf85bcc
snapaligner: improve index detection (#1836)
* improve index detection

* fix escaping
2022-06-30 12:19:46 +02:00

43 lines
1.3 KiB
Text

process SNAPALIGNER_ALIGN {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
input:
tuple val(meta), path(reads)
path index
output:
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.bai"), optional: true, emit: bai
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def subcmd = meta.single_end ? "single" : "paired"
"""
INDEX=`dirname \$(find -L ./ -name "OverflowTable*")`
[ -z "\$INDEX" ] && echo "Snap index files not found" 1>&2 && exit 1
snap-aligner ${subcmd} \\
\$INDEX \\
${reads.join(" ")} \\
-o ${prefix}.bam \\
-t ${task.cpus} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/.\$//')
END_VERSIONS
"""
}