search

biowdl / tasks

A collection of reusable WDL tasks. Category:Other
https://biowdl.github.io/tasks/
MIT License
85 stars 31 forks source link

BIOWDL-524: Add parameter_meta outputs. #262

Closed JasperBoom closed 4 years ago

JasperBoom commented 4 years ago

Checklist

I have added outputs to tasks that already had a parameter_meta section. Since I don't have experience with a lot of these tools, I would like to ask for reviewers to double check the descriptions of tasks they have used previously. Let me know what I can and should improve!

This is a continuation of: https://github.com/biowdl/tasks/pull/261

JasperBoom commented 4 years ago

Hey reviewers, besides checking the outputs I have added and described. I could use some help with filling the empty output in Picard and somaticseq. Could you guys maybe suggest or add the outputs for those remaining tools? I don't have much or no experience with running them. And the manuals aren't helping very much.

JasperBoom commented 4 years ago

Secondly, I have added a file called TO-DO.md. I will take this out before merging I suppose. But it shows the files/tasks that we haven't updated to the new SLURM standard. It also shows a few files that import other files, do we still use those imports?

rhpvorderman commented 4 years ago

Miniwdl has a check function that checks for imports that are not used. You could run that and see if things show up. The unfinished tasks are not a problem. This is already a lot of progress. We can fix those tasks later when it turns out they cause problems. Our CI checks for any used tasks that are not compliant, if I am correct. Tasks that are not used are less important.

JasperBoom commented 4 years ago

Miniwdl has a check function that checks for imports that are not used. You could run that and see if things show up. The unfinished tasks are not a problem. This is already a lot of progress. We can fix those tasks later when it turns out they cause problems. Our CI checks for any used tasks that are not compliant, if I am correct. Tasks that are not used are less important.

Running the miniwdl check is a good idea, thanks! I will do that.