From 4b16d9e37cd42ad8d659f530581be0a9d9a8d92b Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 9 Nov 2020 21:04:26 -0600
Subject: [PATCH] try version again.
---
.gitlab-ci.yml | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 49660b0..ce00100 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -180,10 +180,9 @@ 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
- - 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
-
+ - 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 --version &> version_markdups.txt
artifacts:
name: "$CI_JOB_NAME"
when: always
--
GitLab