nf-core_modules/software/minimap2/align/main.nf

44 lines
1.4 KiB
Text
Raw Normal View History

2021-02-04 19:42:08 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
2021-02-04 19:42:08 +00:00
process MINIMAP2_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), publish_id:meta.id) }
2021-02-16 23:58:23 +00:00
conda (params.enable_conda ? "bioconda::minimap2=2.17" : null)
2021-02-04 19:42:08 +00:00
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/minimap2:2.17--hed695b0_3"
} else {
container "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
}
input:
tuple val(meta), path(reads)
path reference
output:
tuple val(meta), path("*.paf"), emit: paf
2021-02-05 17:35:11 +00:00
path "*.version.txt", emit: version
2021-02-04 19:42:08 +00:00
script:
def software = getSoftwareName(task.process)
2021-02-05 17:35:11 +00:00
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
2021-02-05 17:41:36 +00:00
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
2021-02-05 17:35:11 +00:00
"""
minimap2 \\
$options.args \\
-t $task.cpus \\
$reference \\
$input_reads \\
> ${prefix}.paf
echo \$(minimap2 --version 2>&1) > ${software}.version.txt
"""
2021-02-04 19:45:39 +00:00
}