diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 478d49574438ef27e74a002c380d15761600e0f2..7537d250836af8bf64b4e945c0936c57046a3b4d 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 708ca049476874328cf1041faeb689ad38dd7788..57bc30dfed523968bfa2fd0d078f10f25b5a6be9 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>