From a9b7c8685310207d862e53f9ece5f66995548422 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 4 Aug 2020 09:48:25 -0500
Subject: [PATCH] Fix countData unit summary file name

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9cceb49..a525151 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -107,7 +107,7 @@ countData:
   script:
   - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' -o Q-Y5F6_1M.se.featureCounts -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam 
   - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.featureCounts
-  - assignedReads=$(grep -m 1 'Assigned' *.countData.summary | grep -oe '\([0-9.]*\)')
+  - assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
   - pytest -m makeFeatureCounts
 
 makeBigWig:
-- 
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