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nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://nf-co.re/taxprofiler
MIT License
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Split up longread- and short-read parameters in databases #226

Closed jfy133 closed 5 months ago

jfy133 commented 1 year ago

Description of feature

We should somehow allow specifying different profiling parameters depending on whether a database is for short-read or long-read use.

e.g. for bracken, a database of 400bp of short read read length doesn't make sense to run with nanopore data.

Could have a column in the database sheet specifying whether a database is for short- or long-read (or both?), and then only samples for e.g. illumina goes is combined with the short-reads, and samples for e.g. annopore goes with long-read databases

sofstam commented 11 months ago

Add extra columns to databases.csv and update the meta to make sure that binding is correct for short-read and long-read.

LilyAnderssonLee commented 5 months ago

Fixed in the PR https://github.com/nf-core/taxprofiler/pull/466