From 2a74ce1fa06e6fdab0d21eb98b344f754308d2a3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 17 Mar 2021 13:10:33 +0100
Subject: [PATCH] g2gtools: rename fasta output to fa.gz
---
src/nf_modules/g2gtools/main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/g2gtools/main.nf b/src/nf_modules/g2gtools/main.nf
index 3898c8c0..d0b66248 100644
--- a/src/nf_modules/g2gtools/main.nf
+++ b/src/nf_modules/g2gtools/main.nf
@@ -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("${file_id}_snp.fasta"), path("${vci}"), path("${tbi}"), emit: fasta
+ tuple val(file_id), path("${file_id}_snp.fa.gz"), 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.fasta 2> ${file_id}_g2gtools_path_report.txt
+ -o ${file_id}_snp.fa.gz > ${file_id}_g2gtools_path_report.txt
"""
}
@@ -56,7 +56,7 @@ process incorporate_indel {
input:
tuple val(file_id), path(fasta), path(vci), path(tbi)
output:
- tuple val(file_id), path("${file_id}_snp_indel.fasta"), path("${vci}"), path("${tbi}"), emit: fasta
+ tuple val(file_id), path("${file_id}_snp_indel.fa.gz"), path("${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.fasta 2> ${file_id}_g2gtools_transform_report.txt
+ -o ${file_id}_snp_indel.fa.gz 2> ${file_id}_g2gtools_transform_report.txt
"""
}
--
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