mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
7d0ddbc8ab
* Add atlas/call * Apply suggestions from code review * Update modules/atlas/call/main.nf Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com> * Apply suggestions from code review Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
52 lines
1.6 KiB
Text
52 lines
1.6 KiB
Text
process ATLAS_CALL {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
|
|
'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam), path(bai)
|
|
path fasta
|
|
path fai
|
|
path recal
|
|
path pmd
|
|
path known_alleles
|
|
val method
|
|
|
|
output:
|
|
tuple val(meta), path("*.vcf.gz"), emit: vcf
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def recal_file = recal ? "recal=${recal}" : ""
|
|
def pmd_file = pmd ? "pmdFile=${pmd}" : ""
|
|
def known_alleles_file = known_alleles ? "pmdFile=${known_alleles}" : ""
|
|
|
|
def valid_method = ['MLE', 'Bayesian', 'allelePresence', 'randomBase', 'majorityBase']
|
|
if ( !valid_method.contains(method) ) { error "Unrecognised calling method for ATLAS_CALL. Options: MLE, Bayesian, allelePresence, randomBase, majorityBase" }
|
|
|
|
"""
|
|
atlas \\
|
|
task=call \\
|
|
bam=${bam} \\
|
|
fasta=${fasta} \\
|
|
$recal_file \\
|
|
$pmd_file \\
|
|
method=${method} \\
|
|
$args
|
|
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
atlas: \$((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //')
|
|
END_VERSIONS
|
|
"""
|
|
}
|