*Not an issue just adding changes we made and also the link to the Athena cwl workflows

[carmelinacharalambous]

Hi Jethro,

I'm adding the below information here as I could not find a better place.

We have made a single change to the code here in order to save the output coverage report to specific locations and not within the folder it was currently set to save the file. You can review this change in the PR
Basically, changing out_dir to os.getcwd()

You can find the docker image created for the above Athena version here

We wrote cwl subworkflows for each python script and also one bigger cwl workflow incorporating all steps into one. We currently run all our tools/workflows in cwl hence why we created these.
The sub workflow cwls can be found here
The overall coverage_report cwl can be found here
All the latest code is on the develop branch. Also in the repos there are example yaml files for each cwl.

Let me know if you are interested in learning how we run the cwls. Also, we use the coverage report in a research setting and not in a clinical setting. Every time I mention this tool I always give credits to the East genomics team and you specifically.

Thank you and apologies for the delay in my response.
Hope everyone is well!
Kind regards,
Carmelina