before_script: - module add python/3.6.1-2-anaconda - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1 - module load nextflow/0.31.0 - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/ stages: - unit - astrocyte - single - multiple - skip user_configuration: stage: unit script: - pytest -m unit --cov=./workflow/scripts bash_tests: stage: unit script: - module load singularity/3.0.2 - module load deeptools/2.5.0.1 - singularity run docker://bats/bats:v1.1.0 --tap workflow/tests/plot_profile.bats astrocyte: stage: astrocyte script: - module load astrocyte/0.1.0 - module unload nextflow - cd .. - astrocyte_cli validate chipseq_analysis artifacts: expire_in: 2 days single_end_mouse: stage: single only: - master script: - nextflow run workflow/main.nf --astrocyte true -resume - pytest -m singleend paired_end_human: stage: single only: - branches except: - master script: - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume - pytest -m pairedend single_end_diff: stage: multiple only: - branches except: - master script: - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false -resume - pytest -m singleend - pytest -m singlediff paired_end_diff: only: - master stage: multiple script: - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume - pytest -m pairedend - pytest -m paireddiff single_end_skip: stage: skip only: - master script: - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false -resume - pytest -m singleskip_true