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AlexanderLabWHOI / eukrhythmic

A metatranscriptomic pipeline optimized for the study of microeukaryotes.
MIT License
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Optimizing the automated pairing of forward and reverse reads #10

Closed halexand closed 4 years ago

halexand commented 4 years ago

Ideally, we might avoid asking the user to specify both in the input files or config files-- but file naming formats vary quite a bit.

We should look around and try to figure out if there is a good way to do this. @akrinos

halexand commented 4 years ago

EukHeist reads in both a sample grouping file and an ena table that has PE reads listed next to each other. Again... this is sub optimal and has format requirements.

halexand commented 4 years ago

(This whole thing makes me wonder how long until we no longer use paired end reads...)

akrinos commented 4 years ago

Current solution is to check the number of files present in the input directory matching the FastqFile column in the sample data folder, and to run PE with two files, SE with 1 file, throw error if >2, etc.