From 2ee9ebdceda7daf5740cb5b04756b0b14cb3d2b8 Mon Sep 17 00:00:00 2001
From: Jonathan Gesell <jonathan.gesell@utsouthwestern.edu>
Date: Fri, 27 Mar 2020 09:17:26 -0500
Subject: [PATCH] Update .gitlab-ci.yml to include splitting the BAM and BAI
files.
---
.gitlab-ci.yml | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 83783dd..a2889e0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -69,6 +69,10 @@ dedupData:
- 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 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 Q-Y5JA_1M.se.sorted.deduped.bam.bai
+ - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' "
+ for i in {chr1,chr2,chr8}; do
+ echo \"samtools view -b Q-Y5JA_1M.se.sorted.deduped.bam ${i} > Q-Y5JA_1M.se.sorted.deduped.${i}.bam; samtools index -@ \`nproc\` -b Q-Y5JA_1M.se.sorted.deduped.${i}.bam Q-Y5JA_1M.se.sorted.deduped.${i}.bam.bai\" | parallel -j `nproc` -k
+ "
- pytest -m dedupData
makeBigWig:
--
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