diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index d69be394ea94320e9b79161d898937693b79dcd2..5e7404188c1168aac622e48bbbe1914393217f2c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -16,30 +16,25 @@ variables: default: tags: - #- vm # Pass jobs to the VM runner - - astrocyte # Pass jobs to the astrocyte runner + - vm # Pass jobs to the VM runner + #- astrocyte # Pass jobs to the astrocyte runner before_script: - # - export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH" # Necessary to run on VM + - export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH" # Necessary to run on VM download-test-data: # Download the test data if missing stage: download - rules: - - exists: - - "test_data/Brain_Tumor_3p_LT_fastqs" - when: never - - when: always script: - cd test_data - - ./fetch_Brain_Tumor_3p_LT.sh - - echo "Download complete." + - if [ ! -d "test_data/Brain_Tumor_3p_LT_fastqs" ]; then ./fetch_Brain_Tumor_3p_LT.sh; fi artifacts: paths: - test_data/ expire_in: 2 days -test-cr-count: # Test cellranger count on the test data +test-cr-count: # Run cellranger count on the test data stage: test script: - #- nextflow run workflow/main.nf --reference=/home/strand_admin/ref/refdata-gex-GRCh38-2020-A # Necessary to run on VM - - module load nextflow/22.04.5 - - nextflow run workflow/main.nf \ No newline at end of file + - nextflow run workflow/main.nf --reference=/home/strand_admin/ref/refdata-gex-GRCh38-2020-A # Necessary to run on VM + #- module load nextflow/22.04.5 # Necessary to run on astrocyte + - nextflow run workflow/main.nf + - nextflow clean -keep-logs