From db1f8f5eb892a0f8384a9935ce886984eac8a82b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 17 Mar 2021 13:41:02 +0100
Subject: [PATCH] g2gtools: remove .gz from fa.gz
---
src/nf_modules/g2gtools/main.nf | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/g2gtools/main.nf b/src/nf_modules/g2gtools/main.nf
index c26185f4..d1266cf6 100644
--- a/src/nf_modules/g2gtools/main.nf
+++ b/src/nf_modules/g2gtools/main.nf
@@ -10,7 +10,7 @@ process vci_build {
tuple val(file_id), path(vcf)
tuple val(ref_id), path(fasta)
output:
- tuple val(file_id), path("*.vci.gz"), path("*.tbi"), emit: vci
+ tuple val(file_id), path("*.vci"), path("*.tbi"), emit: vci
tuple val(file_id), path("*_report.txt"), emit: report
script:
input_vcf = ""
@@ -36,7 +36,7 @@ process incorporate_snp {
tuple val(file_id), path(vci), path(tbi)
tuple val(ref_id), path(fasta)
output:
- tuple val(file_id), path("${file_id}_snp.fa.gz"), path("${vci}"), path("${tbi}"), emit: fasta
+ tuple val(file_id), path("${file_id}_snp.fa"), path("${vci}"), path("${tbi}"), emit: fasta
tuple val(file_id), path("*_report.txt"), emit: report
script:
"""
@@ -44,7 +44,7 @@ g2gtools patch \
-p ${task.cpus} \
-i ${fasta} \
-c ${vci} \
- -o ${file_id}_snp.fa.gz 2> ${file_id}_g2gtools_path_report.txt
+ -o ${file_id}_snp.fa 2> ${file_id}_g2gtools_path_report.txt
"""
}
@@ -56,7 +56,7 @@ process incorporate_indel {
input:
tuple val(file_id), path(fasta), path(vci), path(tbi)
output:
- tuple val(file_id), path("${file_id}_snp_indel.fa.gz"), path("${vci}"), path("${tbi}"), emit: fasta
+ tuple val(file_id), path("${file_id}_snp_indel.fa"), path("${vci}"), path("${tbi}"), emit: fasta
tuple val(file_id), path("*_report.txt"), emit: report
script:
"""
@@ -64,7 +64,7 @@ g2gtools transform \
-p ${task.cpus} \
-i ${fasta} \
-c ${vci} \
- -o ${file_id}_snp_indel.fa.gz 2> ${file_id}_g2gtools_transform_report.txt
+ -o ${file_id}_snp_indel.fa 2> ${file_id}_g2gtools_transform_report.txt
"""
}
--
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