nf-core_modules/software/delly/call/main.nf
Mei Wu 3f4eccbf0f
Delly/call (#565)
* testing works but need to fix paths and add exclude list

* edited meta file and removed TODOs

* left over TODOs

* test passed, final push

* resolving initial comments

* Update software/delly/call/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-06 12:54:14 +01:00

44 lines
1.4 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process DELLY_CALL {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::delly=0.8.7" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/delly:0.8.7--he03298f_1"
} else {
container "quay.io/biocontainers/delly:0.8.7--he03298f_1"
}
input:
tuple val(meta), path(bam), path(bai)
path fasta
path fai
output:
tuple val(meta), path("*.bcf"), emit: bcf
tuple val(meta), path("*.csi"), emit: csi
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
delly \\
call \\
$options.args \\
-o ${prefix}.bcf \\
-g $fasta \\
$bam \\
echo \$(delly --version 2>&1) | sed 's/^.*Delly //; s/Using.*\$//' > ${software}.version.txt
"""
}