From 06790eb4437577e307351e61f852d72321ebb85d Mon Sep 17 00:00:00 2001
From: Jonathan Gesell <jonathan.gesell@utsouthwestern.edu>
Date: Thu, 30 Jan 2020 11:03:00 -0600
Subject: [PATCH] Update .gitlab-ci.yml, removed variable IDs.
---
.gitlab-ci.yml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d6f9e17..5152934 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -58,7 +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=${sortedBam} O=${repRID}.deduped.bam M=${repRID}.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=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
- pytest -m dedupData
integration_se:
--
GitLab