From 7db849c4b2a3b075e407a5ffe0c0a47151adf41f Mon Sep 17 00:00:00 2001
From: Jonathan Gesell <jonathan.gesell@utsouthwestern.edu>
Date: Fri, 27 Mar 2020 10:25:46 -0500
Subject: [PATCH] Update .gitlab-ci.yml
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8b211e8..adf71b8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -69,7 +69,7 @@ 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
+ - 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;\";
done | parallel -j `nproc` -k"
- pytest -m dedupData
--
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