From 26d1170030ee10f98b0062e5a367fe00cdce0944 Mon Sep 17 00:00:00 2001
From: Jonathan Gesell <jonathan.gesell@utsouthwestern.edu>
Date: Fri, 7 Feb 2020 16:24:11 -0600
Subject: [PATCH] Update .gitlab-ci.yml to include makeBigWig step.

---
 .gitlab-ci.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 10b06f9..2327f2e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -64,8 +64,16 @@ alignData:
 dedupData:
   stage: unit
   script:
-  - 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_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - singularity run 'docker://bicf/gudmaprbkdedup.2.0.0' samtools sort -@ `nproc` -O BAM -o ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bai
   - pytest -m dedupData
+  
+makeBigWig
+  stage: unit
+  script:
+  - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -o ./test_data/bam/small/Q-Y5JA_1M.se.bw
+  - pytest -m makeBigWig
 
 fastqc:
   stage: unit
-- 
GitLab