From b36bb08eff0c85128d0e66bb5ad1210f93e21738 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 8 Mar 2020 17:40:17 -0500
Subject: [PATCH] Fix path of script for unit test

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 12a6ef5..9483d1b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -81,7 +81,7 @@ makeFeatureCounts:
   stage: unit
   script:
   - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -R SAM -p -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -T `nproc` -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam 
-  - singularity run 'docker://bicf/subread2:2.0.0' Rscript calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
+  - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
   - pytest -m makeFeatureCounts
 
 fastqc:
-- 
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