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Split up longread- and short-read parameters in databases #226

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jfy133 opened this issue Jan 31, 2023 · 2 comments
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Split up longread- and short-read parameters in databases #226

jfy133 opened this issue Jan 31, 2023 · 2 comments
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enhancement Improvement for existing functionality

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@jfy133
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jfy133 commented Jan 31, 2023

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

@jfy133 jfy133 added the enhancement Improvement for existing functionality label Jan 31, 2023
@jfy133 jfy133 added this to the 1.1 milestone Jan 31, 2023
@LilyAnderssonLee LilyAnderssonLee self-assigned this Aug 14, 2023
@sofstam
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sofstam commented Oct 16, 2023

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

@LilyAnderssonLee
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Fixed in the PR #466

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