From b724942b6dfa1be84bca542972087b68d9eb2984 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 9 Nov 2020 20:11:58 -0600
Subject: [PATCH] remove jar version.
---
.gitlab-ci.yml | 1 -
1 file changed, 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 54e67a3..fa9a696 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -173,7 +173,6 @@ dedupData:
except:
- merge_requests
script:
- - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version &> version_markdups.txt
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools --version > version_samtools.txt
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5F6_1M.se.deduped.bam
--
GitLab