plugins defaults for file names

[stolarczyk]

Currently our plugins produce files with the following default names:

• looper.write_sample_yaml: {sample.name}.yaml
• looper.write_submission_yaml: {sample.name}_submission.yaml

should we change the first one to {sample.name}_sample.yaml to make the naming convention consistent?

[nsheff]

I actually don't mind it the way it is, since that's the old behavior.

what's the CWL plugin's version? {sample.name}_cwl.yaml ?

[stolarczyk]

what's the CWL plugin's version? {sample.name}_cwl.yaml ?

yes

[nsheff]

I think I'd leave it, on the grounds of backwards compatibility. but if you want to change it I guess I'm ok with it.

[stolarczyk]

following the conclusions in #307, I'll change the defaults to make names consistent:

• looper.write_sample_yaml: {sample.name}_sample.yaml
• looper.write_sample_yaml_cwl: {sample.name}_sample_cwl.yaml
• looper.write_submission_yaml: {sample.name}_submission.yaml

[nsheff]

what about the project-included variant of the basic function? should that be a parameter instead of a separate function? if separate, it should have a separate output.

[stolarczyk]

Oh yeah I forgot about this one. It's a separate plugin now. So it should have a separate output and separate key to parametrize it.