mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
process MINIMAP2_ALIGN {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
|
|
'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path reference
|
|
val bam_format
|
|
val cigar_paf_format
|
|
val cigar_bam
|
|
|
|
output:
|
|
tuple val(meta), path("*.paf"), optional: true, emit: paf
|
|
tuple val(meta), path("*.bam"), optional: true, emit: bam
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
|
|
def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
|
|
def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
|
|
def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
|
|
"""
|
|
minimap2 \\
|
|
$args \\
|
|
-t $task.cpus \\
|
|
$reference \\
|
|
$input_reads \\
|
|
$cigar_paf \\
|
|
$set_cigar_bam \\
|
|
$bam_output
|
|
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
minimap2: \$(minimap2 --version 2>&1)
|
|
END_VERSIONS
|
|
"""
|
|
}
|