From 2c60afce41128fa31861581b3ad6b24fd6dfe9f1 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 30 Jul 2020 09:48:38 -0500
Subject: [PATCH] Add fastqc commad to unit now that using singularity run

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

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7bcfc37..8f71ff4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -112,7 +112,7 @@ makeBigWig:
 fastqc:
   stage: unit
   script:
-  - singularity run 'docker://bicf/fastqc:2.0.1_indev' ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
+  - singularity run 'docker://bicf/fastqc:2.0.1_indev' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
   - pytest -m fastqc
 
 dataQC:
-- 
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