SciDAP enables you to reproduce experiments, share the data and results, choose your collaborators and organize your working environment.
To enable Common Workflow Language (CWL) on a workstation or dedicated hardware it was integrated into Airflow. Full airflow documentation available on http://pythonhosted.org/airflow/.
- Airflow
git clone https://github.com/SciDAP/airflow.git
cd airflow
sudo python setup.py install
- SciDAP airflow modules
git clone https://github.com/SciDAP/scidap.git
cd modules
sudo python setup.py install
from scidap.cwldag import CWLDAG
...
default_args = {
'owner': owner,
'start_date': start_day,
'email': [email],
'email_on_failure': False,
'email_on_retry': False,
'end_date': end_day,
'on_failure_callback': fail_callback
}
...
dag = CWLDAG(
dag_id=dag_id,
cwl_workflow="workflows/scidap/bam-genomecov-bigwig.cwl",
schedule_interval=timedelta(days=1),
default_args=default_args)
dag.create()CWL Airflow examples: https://github.com/SciDAP/workflows