A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Fix for the input deletion with Krakenuniq/build:
<https://github.com/nf-core/modules/pull/11607>

Left I a comment, not sure about the `cp -rL` command

You're right. I forgot how large they are. I should remove the `L`,

currently testing the stability of `taxDB` though

Yep. this file isn't stable. Why though. It's worrying that if the `taxDB` is lost you won't get the same file back.

:awesome:  welcome to metagenomics :awesome:

I don't remember now off the top of my head exactly what was in `taxDB` but it could be something along the lines of the way the database gets built hashs or kmers or something are not determinisitc, resulting in some genomes not being represented (too similar to another, and the tax assignment goes to something else).

Alternatively could also be an ordering thing

I don't see any option for a seed or anything. I'll add it to unstableOutputs for now, but I'm going to see if I can find the reason first before committing.

```$ diff tmp/taxDB*
554370a554371,554375
&gt; 3711096       2605600 Lactuca sp. T79983-1    species
&gt; 3711095       83607   Arctostaphylos moranii  species
&gt; 3711094       3573060 Kopsiopsis sp. T79982-1 species
&gt; 3711093       13817   Adiantum gingkoides     species
&gt; 3711092       13817   Adiantum cf. flabellulatum      species
584576a584582
&gt; 3573060       2072959 unclassified Kopsiopsis no rank
637733c637739
&lt; 3420004       2593666 Fusarium sp. LD-2025a   species
---
&gt; 3420004       569360  Fusarium kistleri       species```
:anguished:  :cry:

That's the diff between this morning and now. So change in species and labels

What's `KRAKENUNIQ_DOWNLOAD` pulling from? I see there's no testdata_base_path

<https://github.com/fbreitwieser/krakenuniq#database-building>

But changing between this morning and now seems a bit odd

(going out again now, will check again later)