From 5eae8fe15774a5c65b4d92d2ecd537816f86389c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 28 Jun 2021 09:49:00 +0200
Subject: [PATCH] gatk4: add gvcf to variant_calling_out
---
src/nf_modules/gatk4/main.nf | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 1d166613..ac8c879c 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -159,6 +159,10 @@ 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'
+ }
+
input:
tuple val(file_id), path(bam), path(bam_idx)
tuple val(ref_id), path(fasta), path(fai), path(dict)
--
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