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ccmbioinfo / MetaFusion-Clinical

BSD 3-Clause Clear License
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Metafusion.clinical.sh not accounting for options in file naming. #2

Open pintoa1-mskcc opened 2 months ago

pintoa1-mskcc commented 2 months ago

There are a few times within the Metafusion.clinical.sh script where if an option isnt specified, the name of the file is still updated and results in an empty file and failure for the rest of the run

  1. https://github.com/ccmbioinfo/MetaFusion-Clinical/blob/f29363c812f59e436aa4f5a62d0292b31d263b6b/scripts/MetaFusion.clinical.sh#L162
  2. https://github.com/ccmbioinfo/MetaFusion-Clinical/blob/f29363c812f59e436aa4f5a62d0292b31d263b6b/scripts/MetaFusion.clinical.sh#L169
  3. https://github.com/ccmbioinfo/MetaFusion-Clinical/blob/f29363c812f59e436aa4f5a62d0292b31d263b6b/scripts/MetaFusion.clinical.sh#L181
  4. etc etc...
mapostolides commented 2 months ago

Is this a breaking bug, or can you still use the tool by specifying the flag? Which specific flag are you referring to?

pintoa1-mskcc commented 1 month ago

Not including per sample, pfam or fusion annotator breaks the function, as well as in the locations listed. I commented out those sections to allow it to run, but i saw this occurring in multiple locations where the cluster filename was specified outside the if statement of the flag. Any "optional" flag shouldnt have the cluster name being updated outside the if statement