diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 9043d72cccd6bb5ca21f9219f30e9b068ddeb5ad..bf9231c282edbd6fa25042aac9e9a9c8f9cd8f81 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,5 +1,5 @@ before_script: - - module add python/3.6.1-2-anaconda + - module add python/3.6.4-anaconda - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1 - module load singularity/3.0.2 - module load nextflow/19.09.0 @@ -23,7 +23,7 @@ getData: script: - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt - unzip ./test_data/bagit/Replicate_16-1ZX4 - - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4 TEST + - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' bash ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4 TEST - pytest -m getData parseMetadata: diff --git a/workflow/tests/test_getData.py b/workflow/tests/test_getData.py index 36d0b22155fc5ef860497bf887dc595ca368c6ad..f84a30ff9fcd33ef7ce27328742d346f10c6f68f 100644 --- a/workflow/tests/test_getData.py +++ b/workflow/tests/test_getData.py @@ -11,4 +11,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.getData def test_getData(): assert os.path.exists(os.path.join(test_output_path, 'Replicate_16-1ZX4/bagit.txt')) - assert os.path.exists(os.path.join(test_output_path, '16-1ZX4.R1.fastq.gz')) \ No newline at end of file + assert os.path.exists(os.path.join(test_output_path, 'Study_Q-Y4H0/data/assets/Study/Q-Y4H0/Experiment/Q-Y4BY/Replicate/Q-Y5F8/hMARIS_SIX2+_RiboDep#1.gene.rpkm.txt')) \ No newline at end of file