From 8ce8b56efc8a604b3b5c0178dac675c4c07ce94d Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Fri, 27 Mar 2020 13:52:54 -0500
Subject: [PATCH] Updated inferMetadata testing script
---
.gitlab-ci.yml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index efc6ece..a1c2c25 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -89,7 +89,8 @@ fastqc:
inferMetadata:
stage: unit
script:
- - singularity run 'docker://bicf/rseqc3.0:2.0.0' tin.py -i ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed
+ - for i in {"chrNC_000001.11","chrNC_000002.12","chrNC_000019.10"}; do
+ echo " tin.py -i tin.py -i /test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5JA_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\"" | singularity run 'docker://bicf/rseqc3.0:2.0.0' parallel -j `nproc` -k > Q-Y5JA_1M.se.sorted.deduped.tin.xls
- pytest -m inferMetadata
integration_se:
--
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