From f2dd8009b14222e57f0f1ae800d095f2f7ef6bbd Mon Sep 17 00:00:00 2001
From: Jonathan Gesell <jonathan.gesell@utsouthwestern.edu>
Date: Thu, 30 Jan 2020 11:33:08 -0600
Subject: [PATCH] Corrected input and output BAM file paths.

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

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5152934..27cf3be 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -58,8 +58,8 @@ alignReads:
 dedupReads:
   stage: unit
   script:
-  - singularity run 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=Q-Y5JA.sorted.bam O=Q-Y5JA.deduped.bam M=Q-Y5JA.deduped.Metrics.txt REMOVE_DUPLICATES=true
-  - singularity run 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=16-1ZX4.sorted.bam O=16-1ZX4.deduped.bam M=16-1ZX4.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.sorted.bam O=./test_data/bam/small/Q-Y5JA.deduped.bam M=Q-Y5JA.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/16-1ZX4.sorted.bam O=./test_data/bam/small/16-1ZX4.deduped.bam M=16-1ZX4.deduped.Metrics.txt REMOVE_DUPLICATES=true
   - pytest -m dedupData
 
 integration_se:
-- 
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