From 362879d39fea44247921edd930e95eedec6e1df9 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 16:02:35 -0600
Subject: [PATCH] Fix seqtk version extraction
---
.gitlab-ci.yml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6f7e7c4..d13cc0d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -194,7 +194,8 @@ downsampleData:
- merge_requests
- schedules
script:
- - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk 2>&1 > /dev/null | grep -o Version.* > version_seqtk.txt
+ - 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 sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
- pytest -m downsampleData
artifacts:
--
GitLab