From d7b22a9f6469d208c4263180e226c50b04d788ba Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 25 Aug 2020 11:41:02 -0500
Subject: [PATCH] Add CI test for inputBag override
---
.gitlab-ci.yml | 15 +++++++++++++++
1 file changed, 15 insertions(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ab68733..4589f16 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -11,6 +11,7 @@ stages:
- unit
- integration
- consistency
+ - override
getBag:
stage: unit
@@ -191,4 +192,18 @@ consistency:
- assignedPE.txt
- assignedExpectSE.txt
- assignedExpectPE.txt
+ expire_in: 7 days
+
+inputBag:
+ stage: override
+ script:
+ - hostname
+ - ulimit -a
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --inputBagForce test_data/bagit/Replicate_Q-Y5F6.zip --ci true
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
+ artifacts:
+ name: "$CI_JOB_NAME"
+ when: always
+ paths:
+ - inputBagOverride_PE_multiqc_data.json
expire_in: 7 days
\ No newline at end of file
--
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