From 1310010d520c8e54e81a23e8fbe998781f0c4bcf Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 22 Apr 2020 13:53:12 -0500
Subject: [PATCH] Fix inferMetadata unit
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e4a3c10..acb9bec 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -46,7 +46,7 @@ inferMetadata:
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=`bash inferMeta.sh endness 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
--
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