From f167d1595fdce783cc4719eacfc59deb6925ac1c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 17 Mar 2021 08:47:47 +0100
Subject: [PATCH] g2gtools: fix vci_build command
---
src/nf_modules/g2gtools/main.nf | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/g2gtools/main.nf b/src/nf_modules/g2gtools/main.nf
index ae4b108e..b50eca41 100644
--- a/src/nf_modules/g2gtools/main.nf
+++ b/src/nf_modules/g2gtools/main.nf
@@ -13,11 +13,15 @@ process vci_build {
tuple val(file_id), path("*.vci.gz"), emit: vci
tuple val(file_id), path("*_report.txt"), emit: report
script:
+ input_vcf = ""
+ for (vcf_file in vcf) {
+ input_vcf += " -i ${vcf_file}"
+ }
"""
g2gtools vcf2vci \
-p ${task.cpus} \
-f ${fasta} \
- -i ${vcf} \
+ ${input_vcf} \
-s ${file_id} \
-o ${file_id}.vci.gz 2> ${file_id}_g2gtools_vcf2vci_report.txt
"""
--
GitLab