From 01dac1f90a497db483819338269188aa2fb7f49c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 18 Jul 2019 17:24:59 +0200
Subject: [PATCH] fastqdump.nf: force tmp file to be in the right place
---
src/nf_modules/sratoolkit/fastqdump.nf | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/nf_modules/sratoolkit/fastqdump.nf b/src/nf_modules/sratoolkit/fastqdump.nf
index 3dde5964..6ba77271 100644
--- a/src/nf_modules/sratoolkit/fastqdump.nf
+++ b/src/nf_modules/sratoolkit/fastqdump.nf
@@ -33,6 +33,7 @@ process fastq_dump {
script:
"""
+HOME=\$(pwd) # ensure that fastq dump tmp file are in the right place
#for test only 10000 reads are downloading with the option -N 10000 -X 20000
fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" -N 10000 -X 20000 ${file_id}
if [ -f ${file_id}_1.fastq ]
--
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