From bb8b6af8c1d7d6ba8cd975364e24cb27e13051eb Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 3 Mar 2021 14:07:25 -0600
Subject: [PATCH] Change ci fail ambiguous species to species error
---
.gitlab-ci.yml | 4 ++--
CHANGELOG.md | 3 +++
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 478d495..7537d25 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -807,7 +807,7 @@ integration_pe:
- always
-failAmbiguousSpecies:
+failSpecies:
stage: integration
only: [merge_requests]
except:
@@ -816,7 +816,7 @@ failAmbiguousSpecies:
script:
- hostname
- ulimit -a
- - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failAmbiguousSpecies_report.html
+ - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F4 --source staging --inputBagForce ./test_data/bag/wrongSpecies/Q-Y5F6_inputBag_xxxxxxxx.zip --upload true -with-dag dag.png --dev false --ci true --track false -with-report ./failSpecies_report.html
retry:
max: 0
when:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 708ca04..57bc30d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,6 +33,7 @@
* Make compatible with XPACK-DNANEXUS
* Don't download fastq's if fastq override present
* Override fastq count to override counts
+* Change ambiguous species ci to wrong species
*Known Bugs*
* Override params (inputBag, fastq, species) aren't checked for integrity
@@ -40,6 +41,8 @@
* Check for outputBag in hatrac doesn't check for any uploaded by chaise
* CI container cache will fail if cache folder is not owned by CI runner user
* CI container cache will not error if container failed to pull
+* CI (container cache, version collection, and unit tests) will not work correctly if containers reffered to in nextflow.config aren't prefixed perfectly with: "container = "
+ * also, it is assumed that the containers are on dockerhub and don't have the "docker://" prefix
<hr>
--
GitLab