From 7dbcab2b91ba3df88f5f865bbd490b1f11bd3475 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 6 May 2021 13:16:35 +0200
Subject: [PATCH] nf_modules: add beagle
---
src/nf_modules/beagle/main.nf | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
create mode 100644 src/nf_modules/beagle/main.nf
diff --git a/src/nf_modules/beagle/main.nf b/src/nf_modules/beagle/main.nf
new file mode 100644
index 00000000..bc0a54b2
--- /dev/null
+++ b/src/nf_modules/beagle/main.nf
@@ -0,0 +1,23 @@
+version = "5.1_24Aug19.3e8--hdfd78af_1"
+container_url = "quay.io/biocontainers/beagle::${version}"
+
+params.phasing = ""
+process phasing {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(vcf)
+ tuple val(ref_id), path(ref_vcf)
+
+ output:
+ tuple val(file_id), path("*.bam*"), emit: bam
+
+ script:
+"""
+beagle nthread=${task.cpus} \
+ gtgl=${vcf} \
+ ref=${ref_vcf}
+"""
+}
--
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