* update options * update test
@ -24,6 +24,7 @@ process GENMOD_COMPOUND {
genmod \\
compound \\
$args \\
--processes ${task.cpus} \\
--outfile ${prefix}_compound.vcf \\
$input_vcf
@ -30,6 +30,7 @@ process GENMOD_MODELS {
$pen_file \\
$family_file \\
--outfile ${prefix}_models.vcf \\
@ -10,7 +10,6 @@ process GENMOD_SCORE {
input:
tuple val(meta), path(input_vcf)
path (fam)
path (reduced_penetrance)
path (score_config)
output:
@ -24,13 +23,11 @@ process GENMOD_SCORE {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def family_file = fam ? "--family_file ${fam}" : ""
def pen_file = reduced_penetrance ? "--reduced_penetrance ${reduced_penetrance}" : ""
def config_file = score_config ? "--score_config ${score_config}" : ""
"""
score \\
$config_file \\
--outfile ${prefix}_score.vcf \\
@ -21,10 +21,6 @@ input:
type: file
description: vcf file
pattern: "*.{vcf}"
- reduced_penetrance:
description: file with gene ids that have reduced penetrance
pattern: "*.{tsv}"
- family_file:
description: ped file
@ -13,10 +13,10 @@ config = file(params.test_data['homo_sapiens']['illumina']['rank_model'], checkI
workflow test_genmod_score {
GENMOD_SCORE ( input, fam, [], config)
GENMOD_SCORE ( input, fam, config)
}
workflow test_genmod_score_stub {