From 91a9ea5f5faef4258215fcd90ae10108dcbfbfc0 Mon Sep 17 00:00:00 2001
From: Jonathan Gesell <jonathan.gesell@utsouthwestern.edu>
Date: Thu, 30 Jan 2020 11:59:56 -0600
Subject: [PATCH] RE-specified the output directory.

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

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1c99db7..edff724 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -58,8 +58,8 @@ alignReads:
 dedupReads:
   stage: unit
   script:
-  - singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.pe.sorted.bam O=./test_data/bam/small/Q-Y5JA_1M.pe.deduped.bam M=Q-Y5JA_1M.pe.deduped.Metrics.txt REMOVE_DUPLICATES=true
-  - singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.pe.sorted.bam O=Q-Y5JA_1M.pe.deduped.bam M=Q-Y5JA_1M.pe.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
   - pytest -m dedupData
 
 integration_se:
-- 
GitLab