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bio-raum / FooDMe2

A nextflow pipeline for the identification of species from mixed samples based on mitochondrial amplicons
https://bio-raum.github.io/FooDMe2/
GNU General Public License v3.0
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💡 [REQUEST] - Add read count to XLS table #67

Closed marchoeppner closed 3 weeks ago

marchoeppner commented 1 month ago

Is your feature request related to a problem?

Too lazy to dig up actual read counts to evaluate sample/call quality ;)

Describe the solution you'd like

We need to extract and add the actual read counts per taxonomic assignment and sample to the Excel table (also recommended in L 00.00-184). The excel table is based on the composition file, which is currently lacking that information - i.e. needs to be added for this to work.

Description

See solution.

Additional context

No response

gregdenay commented 1 month ago

I support this. We should also add the % of assigned reads in addition to % of all reads.

marchoeppner commented 1 month ago

Added in commit dcfe7ff

Could you clarify what you were thinking re: % assigned reads?

gregdenay commented 4 weeks ago

The % amount but with the unassigned reads removed from total. The rational is that unassigned reads are usually problematic and should be removed as a QC step. This is considering that the DB ist "complete" though.