mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
|
process BISCUIT_ALIGN {
|
||
|
|
tag "$meta.id"
|
||
|
|
label 'process_high'
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null)
|
||
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||
|
|
'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
|
||
|
|
'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(reads)
|
||
|
|
path index
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.bam"), emit: bam
|
||
|
|
path "versions.yml" , emit: versions
|
||
|
|
|
||
|
|
when:
|
||
|
|
task.ext.when == null || task.ext.when
|
||
|
|
|
||
|
|
script:
|
||
|
|
def args = task.ext.args ?: ''
|
||
|
|
def args2 = task.ext.args2 ?: ''
|
||
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||
|
|
def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.9),1)
|
||
|
|
def samtools_cpus = task.cpus-biscuit_cpus
|
||
|
|
"""
|
||
|
|
INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
|
||
|
|
|
||
|
|
biscuit align \\
|
||
|
|
$args \\
|
||
|
|
-@ $biscuit_cpus \\
|
||
|
|
\$INDEX \\
|
||
|
|
$reads \\
|
||
|
|
| samtools sort $args2 --threads $samtools_cpus -o ${prefix}.bam -
|
||
|
|
|
||
|
|
|
||
|
|
cat <<-END_VERSIONS > versions.yml
|
||
|
|
"${task.process}":
|
||
|
|
biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
|
||
|
|
samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
|
||
|
|
END_VERSIONS
|
||
|
|
"""
|
||
|
|
}
|