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MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
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Long input filenames break the pipeline #46

Open pansapiens opened 5 years ago

pansapiens commented 5 years ago

Additional notes here: https://github.com/MonashBioinformaticsPlatform/laxy/issues/36

The particular task that broke with a ~238 character input filename was: https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe/blob/master/src/sikQC.bds#L39 - this was because the input filename is included in the task name, which ultimately generates a BDS task.*.sh script with a too-long name. taskName := should be changed to a short string that does not include any input or output filenames, this way the generated task.*.sh files should remain fairly short (and will be [almost] constant length irrespective of the input filenames).

RNAsik could also apply a pre-run test to check input file name aren't too long.

pansapiens commented 4 years ago

The biggest offender here that tends to generate failures is the getFastqcReport task. Simply renaming this to something short, like fastqc would save a lot of headaches.