From 43153b59557382b1a515558dbb8f782048f897e1 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 16:05:25 -0600
Subject: [PATCH] Try to ignore err from seqtk version extraction
---
.gitlab-ci.yml | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d13cc0d..0a6fe3b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -194,8 +194,7 @@ downsampleData:
- merge_requests
- schedules
script:
- - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk 2> temp.txt
- - cat temp.txt | grep -o Version.* > version_seqtk.txt
+ - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
- singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
- pytest -m downsampleData
artifacts:
--
GitLab