diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index ad1d3a802b177400bfe4b8afee62334d1792b6d8..141fc56791d1cea908250ece29e2b32dfe6a8355 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]