diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index a42a1acee4959566f6bdb027532004e25a5b469a..8084d969f1808a6893d9e7c894eb0aeadfa52a9f 100755 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -4,34 +4,24 @@ before_script: - module load nextflow/0.31.1_Ignite - mkdir test_data/v2s2r100k - mkdir test_data/v3s2r100k - - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v2s2r100k/* test_data/v2s2r100k/ - - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/* test_data/v3s2r100k/ + - 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 - - integration + - run astrocyte_check: stage: astrocyte script: - astrocyte_cli check ../cellranger_count -simple_cr2v2ref1.2.0: - stage: integration +simple_mu.cr2v2ref1.2.0: + stage: run script: - - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1' + - 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 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1' -simple_cr2v2ref3.0.0: - stage: integration +simple_hu.cr3v3ref3.0.0: + stage: run script: - - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '2.1.1' - -simple_cr3v2ref3.0.0: - stage: integration - script: - - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '3.0.2' - -simple_cr3v3ref3.0.0: - stage: integration - script: - - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v3s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v3s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2' + - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'