diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 1e339716c435f74c0cf4d60eb083499f81e3ae5a..93407885c80700abd3b706ef82ee533129905cc3 100755 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -2,29 +2,37 @@ before_script: - module load astrocyte - module load python/3.6.1-2-anaconda - module load nextflow/0.31.1_Ignite + - mkdir test_data/hu.v2s1r1k - mkdir test_data/mu.v2s2r10k - mkdir test_data/hu.v3s2r10k + - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v2s1r1k/ - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v2s2r10k/* test_data/mu.v2s2r10k/ - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/ stages: - astrocyte - - run + - simple + - detailed astrocyte_check: stage: astrocyte script: - astrocyte_cli check ../cellranger_count +run_hu.cr3v2ref3.0.0: + stage: simple + script: + - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2' + run_mu.cr2v2ref1.2.0: - stage: run + stage: detailed except: - tags script: - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/design.csv" --genome 'mm10-1.2.0' --kitVersion 'two' --version '2.1.1' run_hu.cr3v3ref3.0.0: - stage: run + stage: detailed except: - tags script: