mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
53 lines
1.4 KiB
Text
53 lines
1.4 KiB
Text
def VERSION_HAP = '0.3.14'
|
|
def VERSION_PRE = '0.3.14'
|
|
|
|
process HAPPY {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0':
|
|
'quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(truth_vcf), path(query_vcf), path(bed)
|
|
tuple path(fasta), path(fasta_fai)
|
|
|
|
output:
|
|
tuple val(meta), path('*.csv'), path('*.json') , emit: metrics
|
|
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}"
|
|
|
|
"""
|
|
pre.py \\
|
|
$args \\
|
|
-R $bed \\
|
|
--reference $fasta \\
|
|
--threads $task.cpus \\
|
|
$query_vcf \\
|
|
${prefix}_preprocessed.vcf.gz
|
|
|
|
hap.py \\
|
|
$truth_vcf \\
|
|
${prefix}_preprocessed.vcf.gz \\
|
|
$args2 \\
|
|
--reference $fasta \\
|
|
--threads $task.cpus \\
|
|
-R $bed \\
|
|
-o $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
hap.py: $VERSION_HAP
|
|
pre.py: $VERSION_PRE
|
|
END_VERSIONS
|
|
"""
|
|
}
|