artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
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inclusion of gzip import in guppyplex target #17

Closed sagrudd closed 4 years ago

sagrudd commented 4 years ago

We have users with gzipped fastq from guppy base-calling; this import fixes the workflow and will accommodate the aggregation of gzipped fastq files

sagrudd commented 4 years ago

Trivial update included - in the code for iterating through fastq entries in guppyplex there was a slice to exclude the last fastq file within the list (am I missing something clever here?) - this means that if working with e.g. SRA / ENA monolithic datasets that the pipeline fails because the read collection will only ever be 0 reads in length

nickloman commented 4 years ago

Thanks - merged, although artic guppyplex would not be the way to deal with monolithic datasets.