From 22455a05469832c6af2934af93496da6c1efc1d1 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 28 Jun 2021 09:49:43 +0200
Subject: [PATCH] gatk4: rename _out option for gvcf
---
src/nf_modules/gatk4/main.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index ac8c879c..ced6f77e 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -154,13 +154,13 @@ process apply_base_recalibration {
}
/*******************************************************************/
-
+params.variant_calling_gvcf_out = ""
process call_variants_per_sample {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
- if (params.variant_calling_out != "") {
- publishDir "results/${params.variant_calling_out}", mode: 'copy'
+ if (params.variant_calling_gvcf_out != "") {
+ publishDir "results/${params.variant_calling_gvcf_out}", mode: 'copy'
}
input:
--
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