From 3ce1ddf761c5948ecd543ba107ee6b580b7280c8 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 23 Feb 2021 22:02:03 -0600
Subject: [PATCH] Use datahub as source for integration_se ci
---
.gitlab-ci.yml | 2 +-
CHANGELOG.md | 1 +
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8dd2e7a..49b09a1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -683,7 +683,7 @@ integration_se:
script:
- hostname
- ulimit -a
- - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./SE_report.html
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --refSource datahub --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./SE_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
- pytest -m completionMultiqc --filename SE_multiqc_data.json
artifacts:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index faa11d1..7553409 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@
* Change uploadOutputBag logic to change reuse hatrac file if alread exists (re-uses Output_Bag entry by reassigning Execution_Run RID) (#112)
* Add new CI py tests for override and integration
* Fix fastq file and species error status detail bub (#118)
+* Use datahub as source for references for integration_se ci
*Known Bugs*
* Override params (inputBag, fastq, species) aren't checked for integrity
--
GitLab