CWL workflow for epitope prediction

What does this workflow do?

• Label and input feature generation for epitope prediction model
• Train and test epitope prediction model, which is based on OPUS-TASS and multitask-PPI-prediction model.

Overview of workflow components:

• ro_full_wf/: a RO of a (test) workflow run
• tools/: CommandLineTool descriptions for each step in the workflow.
• tests/: Tests and test data for part of the steps.
• requirements.txt: Installed software on which original workflow run was enacted
• niaa_wf.cwl: Epitope prediction workflow in CWL
• niaa_abstract.cwl: Abstract workflow, originally only contained abstract Operations for the steps.
• niaa_wf_job.yml: Input parameter file for niaa_wf.cwl
• niaa_real_graph.svg: Graph of niaa_wf.cwl
• niaa_abstract_graph.svg: Graph of niaa_abstract.cwl

What (software) does it need to run?

• A CWL engine, e.g. cwltool (at this moment the only CWL runner with an implementation of CWLProv)
• Underlying software for the CWL CommandLineTools (possibly specified in SoftwareRequirement)
• Optional: Docker, Singularity or Podman (the software containers that are supported by cwltool)

How do you install it?

• Clone this repository
• Install cwltool and other required software (e.g. graphviz + software that is part of the workflow itself)

How do you use it?

• Workflow description: niaa_wf.cwl
• Parameter file: niaa_wf_job.yml
• Run the workflow: cwltool niaa_wf.cwl niaa_wf_job.yml
• To run + generate a research object: cwltool --provenance ./ro niaa_wf.cwl niaa_wf_job.yml
• To run and cache intermediate output (rerun will use cached results): cwltool --cachedir ./cache niaa_wf.cwl niaa_wf_job.yml
• Workflow plan (yellow steps = implemented, dashed = not implemented yet): niaa_abstract_graph.svg (generated from niaa_abstract.cwl)
• Generate a workflow graph: cwltool --print-dot <workflow>.cwl | dot -Tsvg > <graph>.svg

Attribution and contact details

• OPUS-TASS repository: https://github.com/thuxugang/opus_tass
• IBIVU multi-task PPI prediction model: https://github.com/ibivu/multi-task-PPI

License

• Apache-2.0

Help and support

• CWL user guide: https://www.commonwl.org/user_guide/
• CWL tool repository: https://github.com/common-workflow-library/bio-cwl-tools
• Ask CWL-related questions: https://matrix.to/#/#common-workflow-language_common-workflow-language:gitter.im
• cwltool repository: https://github.com/common-workflow-language/cwltool
• official CWL example repository: https://github.com/common-workflow-library/cwl-patterns
• custom cwl-example repository: https://github.com/RenskeW/cwl-examples

Common errors and troubleshooting

Sometimes tool descriptions work when run as separate files but give an error when connected in a workflow. Possible solutions:

• Error: "anonymous file object missing 'basename' and 'contents'? fields" --> When using default values for file inputs in the CWL tool description, change path into location. path is technically correct but gives an error when the tool is run as a step in a workflow.
• Error: no input ports found for step ... / step ... has no output X". When step gives an error when connected in a workflow even though the tool run by itself works properly, comment the DockerRequirement and SoftwareRequirement fields, save the CommandLineTool description, save the workflow document. The errors should disappear. Now you can uncomment the DockerRequirement and SoftwareRequirement fields again and save the CommandLineTool document. Repeat if error resurfaces.
• Error: I'm sorry, I couldn't load this CWL file, try again with --debug for more information. The error was: cwltool requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it. Tried nodejs, node, docker run node:slim --> Solution: run workflow with --singularity