User parameters? - Githubissues

AlexanderLabWHOI / eukrhythmic

A metatranscriptomic pipeline optimized for the study of microeukaryotes.

MIT License

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User parameters? #17

Closed halexand closed 1 year ago

halexand commented 4 years ago

[x] Identify user parameters for clustering that we might want to make user-specifiable. (e.g. secondary clustering with cd-hit)
[x] Add kmer selection for different assemblers (e.g. Trinity, TransAbyss, etc.)
[x] Transdecoder length cutoff?

halexand commented 4 years ago

Do we want an advanced config file?

akrinos commented 4 years ago

Added user parameters for TransDecoder length and the secondary clustering with cd-hit. All of these are managed centrally through the scripts/importworkspace.py module, which is now called from each individual module to ensure that every module has a shared workspace. We can also now correct things like typos in the assembler name if we want, now that this process is centralized.