From c251a7893f58622b1b347918412e81d2c084195c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 10:16:25 +0100
Subject: [PATCH] g2gtools: add vci_build process
---
src/nf_modules/g2gtools/main.nf | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
create mode 100644 src/nf_modules/g2gtools/main.nf
diff --git a/src/nf_modules/g2gtools/main.nf b/src/nf_modules/g2gtools/main.nf
new file mode 100644
index 00000000..128e5123
--- /dev/null
+++ b/src/nf_modules/g2gtools/main.nf
@@ -0,0 +1,23 @@
+version = "0.2.8"
+container_url = "lbmc/g2gtools:${version}"
+
+process vci_build {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(vcf)
+ tuple val(ref_id), path(fasta), path(fai), path(dict)
+ output:
+ tuple val(file_id), path("*.chain"), emit: vci
+ script:
+"""
+g2gtools vcf2vci \
+ -p ${task.cpus} \
+ -f ${fasta} \
+ -i ${vcf} \
+ -s ${file_id} \
+ -o ${file_id}.vci
+"""
+}
\ No newline at end of file
--
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