From e79377567d6a2d9d2042791352a4b07abaf02c0a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 22 Apr 2020 13:59:38 -0500
Subject: [PATCH] Move parseMetadata unit ci if statements to single line
---
.gitlab-ci.yml | 10 ++--------
1 file changed, 2 insertions(+), 8 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index acb9bec..907fd30 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -40,17 +40,11 @@ inferMetadata:
script:
- >
align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5JA_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%'))
- if [[ ${align} == "" ]]
- then
- exit 1
- fi
+ if [[ ${align} == "" ]]; then exit 1; fi
- >
singularity run 'docker://bicf/rseqc3.0:2.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam" 1>> Q-Y5JA_1M.se.inferMetadata.log
ended=`singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/inferMeta.sh endness Q-Y5JA_1M.se.inferMetadata.log`
- if [[ ${ended} == "" ]]
- then
- exit 1
- fi
+ if [[ ${ended} == "" ]]; then exit 1; fi
- pytest -m inferMetadata
getRef:
--
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