From 913a420cd25cb61fc53575a52e6bfc0a6edf34f2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 10 Mar 2021 17:21:48 +0100
Subject: [PATCH] gatk4: change recalibrate_snp to pair recall_table with BAM
---
src/nf_modules/gatk4/main.nf | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index c767ed70..add285f5 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -144,8 +144,7 @@ process recalibrate_snp {
tag "$file_id"
input:
- tuple val(file_id), path(snp_file), path(indel_file), path(bam), path(bam_idx)
- tuple val(table_id), path(recal_data_table)
+ tuple val(file_id), path(snp_file), path(indel_file), path(bam), path(bam_idx), path(recal_table)
tuple val(ref_id), path(fasta), path(fai), path(dict)
output:
tuple val(file_id), path("*.bam"), emit: bam
--
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