diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 7537d250836af8bf64b4e945c0936c57046a3b4d..ad1d3a802b177400bfe4b8afee62334d1792b6d8 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -947,31 +947,6 @@ 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]