COSMO tidy

[robsyme]

Hi COSMO team

I'm interested in the COSMO pipeline and found it a little difficult to understand from the workflow alone. I did some tidy and cleanup to bring the pipeline more in line with Nextflow community standards. The inside workings of the pipeline remains unchanged. The changes I made include:

• Converting the workflow to the DSL2 syntax.
• Using the outputs of the preprocessing step in both subsequent processes so that the two methods can run in parallel if the computing environment can accommodate it.
• Including a nextflow.schema file so that the parameters can be selected with the Nextflow Tower web interface if required.
• I've pulled out the R scripts from inside the container and included them in the workflow so that they can be included in version control.
• I modified the R scripts to make them executable and also combined them into a single executable and added formal parameters and command line argument parsing. You can use run bin/cosmo --help to see the options in the cosmo script.
• Included a test profile that runs the example dataset. This dataset may be still too large for CI/CD testing, but at least allows for quick testing by users.
• Documentation updates to reflect any change to parameters.

Please let me know if I've missed anything or if you'd like me to make any amendments or extra inclusions. Congratulations on the workflow!

[zhiaos]

Hi Robert,

Thanks very much for the contributions. It's great that it is now compatible with DSL2.

Zhiao

[robsyme]

It is a pleasure having an opportunity to help!

If you would like, consider adding your names to the "author" field in the manifest section of nextflow.config.