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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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Update Output Docs for Collapsed Abundance Tables #671

Closed danclaytondev closed 11 months ago

danclaytondev commented 11 months ago

Hi,

This PR is a minor output documentation update.

Recently I was confused why the qiime output relative abundance tsvs only went to level 6, not level 7 when the reference database we are using includes level 7. In the parameter schema, it shows that the level is controlled by --tax_agglom_max which defaults to 6, so hopefully the output docs better reflect the situation with this change.

I agree that level 6 is a sensible default, I am not proposing to change that, just the output docs! :)

To verify the changed documentation, I believe this is the code that collapses the taxa for absolute abundance counts, and relative abundance counts.

d4straub commented 11 months ago

Hi there, looks good to me, why did you close the PR?