From 0b1a56ba4fd9f4b7a78841fc4e5b21f325f5e7a6 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 3 Mar 2021 17:30:09 -0600
Subject: [PATCH] Remove species error ci
---
.gitlab-ci.yml | 40 +++++++++++++++++++++++++---------------
1 file changed, 25 insertions(+), 15 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ad1d3a8..141fc56 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -807,21 +807,6 @@ integration_pe:
- always
-failSpecies:
- stage: integration
- only: [merge_requests]
- except:
- variables:
- - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
- script:
- - hostname
- - ulimit -a
- - 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:
- - always
-
failTrunkation:
stage: integration
only: [merge_requests]
@@ -947,6 +932,31 @@ override_fastq:
when:
- always
+override_species:
+ stage: integration
+ only: [merge_requests]
+ except:
+ variables:
+ - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+ script:
+ - hostname
+ - ulimit -a
+ - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EW --source staging --speciesForce 'Homo sapiens' --upload true --dev false --ci true --track false -with-report ./speciesOverride_report.html
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_multiqc_data.json \;
+ - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./speciesOverride_multiqc.html \;
+ - pytest -m completionMultiqc --filename speciesOverride_multiqc_data.json
+ artifacts:
+ name: "$CI_JOB_NAME"
+ when: always
+ paths:
+ - speciesOverride_multiqc_data.json
+ - speciesOverride_multiqc.html
+ expire_in: 7 days
+ retry:
+ max: 0
+ when:
+ - always
+
override_stranded:
stage: integration
only: [merge_requests]
--
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