Installation and running

All CWL files from this repository are compatible with any workflow management system or runner that implements CWL v1.0 standard (see the complete list here). As an example, we will use the reference CWL implementation - cwltool. For installation instructions refer to the Install section of the official manual or just run

pip install cwltool   # this will install the latest version from Pypi

Please note, for better portability and reproducibility all the tools used in our workflows are containerized, thus a properly configured Docker is required.

A general example of running any workflow with cwltool is shown below.

1. Create a template job definition file.

   cwltool --make-template workflow.cwl > job.yaml
   

2. Open job.yaml file in a text editor, update the values of the provided inputs, and save changes.

3. Run the workflow with the updated job definition file.

   cwltool workflow.cwl job.yaml
   

For sc-rna-analyze-wf.cwl and sc-multiome-analyze-wf.cwl workflows running examples refer to Single-cell RNA Sequencing Analysis and Single-cell Multiome ATAC-Seq and RNA-Seq Analysis correspondingly.