From b23c5e41c5302bd692771113dc2f70f4ed832664 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 10:33:52 +0100
Subject: [PATCH] g2gtools: add incorporate_snp and incorporate_indel processes
---
src/nf_modules/g2gtools/main.nf | 45 ++++++++++++++++++++++++++++++---
1 file changed, 42 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/g2gtools/main.nf b/src/nf_modules/g2gtools/main.nf
index 128e5123..39a1c7e6 100644
--- a/src/nf_modules/g2gtools/main.nf
+++ b/src/nf_modules/g2gtools/main.nf
@@ -8,9 +8,9 @@ process vci_build {
input:
tuple val(file_id), path(vcf)
- tuple val(ref_id), path(fasta), path(fai), path(dict)
+ tuple val(ref_id), path(fasta)
output:
- tuple val(file_id), path("*.chain"), emit: vci
+ tuple val(file_id), path("*.vci.gz"), emit: vci
script:
"""
g2gtools vcf2vci \
@@ -18,6 +18,45 @@ g2gtools vcf2vci \
-f ${fasta} \
-i ${vcf} \
-s ${file_id} \
- -o ${file_id}.vci
+ -o ${file_id}.vci.gz
+"""
+}
+
+process incorporate_snp {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(vci)
+ tuple val(ref_id), path(fasta)
+ output:
+ tuple val(file_id), path("${file_id}_snp.fasta"), path("${vci}"), emit: fasta
+ script:
+"""
+g2gtools patch \
+ -p ${task.cpus} \
+ -i ${fasta} \
+ -c ${vci} \
+ -o ${file_id}_snp.fasta
+"""
+}
+
+process incorporate_indel {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(fasta), path(vci)
+ output:
+ tuple val(file_id), path("${file_id}_snp_indel.fasta"), path("${vci}"), emit: fasta
+ script:
+"""
+g2gtools transform \
+ -p ${task.cpus} \
+ -i ${fasta} \
+ -c ${vci} \
+ -o ${file_id}_snp_indel.fasta
"""
}
\ No newline at end of file
--
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