Bugfix/metafusion script error exiting behavior

[anoronh4]

Closes #116

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the mskcc/forte branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[anoronh4]

I could have added a test here for metafusion only, but I think a better option will be to add a test for the fusion merging and annotation workflow in another PR.

[pintoa1-mskcc]

I dont know explicitly how test works (L75 and L126 in metafusion_forte.sh).

Asssuming the line is just a trycatch like condition it should be fine so long as we are still outputting the files the grep conditions are running

[anoronh4]

I dont know explicitly how test works (L75 and L126 in metafusion_forte.sh).

Asssuming the line is just a trycatch like condition it should be fine so long as we are still outputting the files the grep conditions are running

@pintoa1-mskcc So the reason i added this is because grep will have a non-zero exit code if 0 matches are found in the input file. The changes are a way to bypass any exit code of 1 ($? = 1). i think this can happen, for example, if the input cff doesn't have any "problematic" chromosomes, or if there are no ReadThrough calls. I'm not sure what other errors we could be ignoring that would be a problem.