From 4882cf04fe9006704fc0061231f7b500dbe2729a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 14 Jan 2020 11:56:13 -0600
Subject: [PATCH] Add CI for trimData
---
.gitlab-ci.yml | 14 +++++++++++++-
1 file changed, 13 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 84af1dd..24cd799 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,4 +18,16 @@ getData:
script:
- ln -sf `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- unzip ./test_data/bagit/Replicate_16-1ZX4
- - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4
\ No newline at end of file
+ - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4
+
+trimData_se:
+ tage: unit
+ script:
+ - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi
+ - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename 16-1ZX4 -j ${ncore} ./test_data/fastq/16-1ZX4.R1.fastq.gz
+
+ trimData_pe:
+ tage: unit
+ script:
+ - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi
+ - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA -j ${ncore} ./test_data/fastq/Q-Y5JA.R1.fastq.gz ./test_data/fastq/Q-Y5JA.R2.fastq.gz
\ No newline at end of file
--
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