How to handle failed fusion runs?

[e-t-k]

Currently (as of ERCC branch being merged):

if the fusion step fails (for both regular and ERCC), fab will continue on with subsequent steps (jfkm pizzly variants) and subsequent samples.

At the end of the run, if any fusion steps failed, fab will print for each sample that failed fusion:

ERROR: Sample (whatever) did not generate fusion results.

@klearned suggests:

what if in the fusion results folder, an error.txt file was created that contained that message: ERROR: Sample (whatever) did not generate fusion results.

My thoughts are:

• Right now if there's no fusion results, it does not make the fusion results folder at all. I don't like the idea of putting in a folder just to have an error.txt file.
• However, it should definitely print the 'missing fusion' error message to the errors.txt file that fab generates in the pipelines work dir when running, and it doesn't currently do that.

[klearned]

@e-t-k I didn't realize the folder wouldn't get created at all if fusion fails. I think that is actually ideal! Thanks!