From 07605c0dcc890bcbb40354cac3eee6434363e5ee Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 15 Jan 2020 10:26:57 -0600
Subject: [PATCH] Add initial integration CI test
---
.gitlab-ci.yml | 13 ++++++++++++-
1 file changed, 12 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a83427a..848918b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -8,6 +8,7 @@ before_script:
stages:
- unit
+ - integration
getBag:
stage: unit
@@ -36,4 +37,14 @@ trimData_pe:
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
- - pytest -m trimData_pe
\ No newline at end of file
+ - pytest -m trimData_pe
+
+integration_se:
+ stage: integration
+ script:
+ - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4
+
+integration_pe:
+ stage: integration
+ script:
+ - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA
\ No newline at end of file
--
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