From 2ab086d225f0159cee9585962db0f52df5dcefa4 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 8 Mar 2020 17:34:20 -0500
Subject: [PATCH] Fix docker handle in unit test

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ff78339..12a6ef5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -80,8 +80,8 @@ makeBigWig:
 makeFeatureCounts:
   stage: unit
   script:
-  - singularity run 'docker://bicf/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/bicf/subread2:2.0.0' Rscript calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
+  - 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
   - pytest -m makeFeatureCounts
 
 fastqc:
-- 
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