From c415b31450b4e3e544c6c8482ed1cc68fbb8c340 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 9 Nov 2020 21:02:15 -0600
Subject: [PATCH] try version again.
---
.gitlab-ci.yml | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e3e052a..49660b0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -180,9 +180,10 @@ dedupData:
for i in {"chr8","chr4","chrY"}; do
echo "samtools view -b Q-Y5F6_1M.se.sorted.deduped.bam ${i} > Q-Y5F6_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.${i}.bam Q-Y5F6_1M.se.sorted.deduped.${i}.bam.bai;";
done | singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' parallel -j 20 -k
- - pytest -m dedupData
- - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates &> version_markdups.txt
+ - 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
+ - pytest -m dedupData
+
artifacts:
name: "$CI_JOB_NAME"
when: always
--
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