From 2735b0c4877c2f393b2d673353c80168ce6f3a03 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 3 Feb 2020 22:08:46 -0600
Subject: [PATCH] Write fastqc output in current dir for ci

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

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 41afb3f..5a4263a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -70,7 +70,7 @@ dedupData:
 fastqc:
   stage: unit
   script:
-  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz
+  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz .
   - pytest -m fastqc
 
 integration_se:
-- 
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