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nf-core

Hello guys, i have a made a new PR for centrifuger/build, could you please check it whenever you have time :slightly_smiling_face:

I left some more comments, but good porogress!

But before you continue I want to wrap my head around exactly what centrifuger-build expects as input... as I think I didn't understand it fully yestday when eadying the docs

reading again now:

```Required:
	-r FILE: reference sequence file (can use multiple -r to specify more than one input file)
		or
	-l FILE: list of reference sequence file stored in &lt;file&gt;, one file per row
	--taxonomy-tree FILE: taxonomy tree, i.e., nodes.dmp file
	--name-table FILE: name table, i.e., names.dmp file
Optional:
	--conversion-table FILE: seqID to taxID conversion file
		When not set, expect -l option and the -l file should have two columns as "file taxID"```
My understanding _now_ is that you have only two options:

• `-r` plus `--conversion-table`
• `-l` in `file taxID`, format
Is that correct?

I.e., you can't give `-r` alone, and you can't give `-l` alone?

Thank you! Yeah it was also confusing for me at first .  I agree, i am understanding the options you described.

• `-r` plus `--conversion-table`
         OR `-l` in `file taxID`, format

(arriving at train station, will have a think and look again when in teh office)

but technichally you can give -l alone, with just the file TaxID format

If this means we always need one or the other, then I guess we need a check that if niether conversion table nor conversion table is given, then it should error?

neither conversion or file you mean? It will give an error if are not provided, you mean explicit give an error "like provide either of one"?

<https://docs-v2--nf-core-docs.netlify.app/docs/specifications/components/modules/naming-conventions#command-file-output-naming>

1. -r + taoxnomy + names
2. -r + taoxnomy + names + conversion table
3. -l + taxonomy + names + conversion table
We DO NOT want to support

2. -l + taxonomy + names (because this requires the weird variant of the `-l` file which will be more complicated to make)

image.png

3rd option works (without taxID inside the -l file)

1st does not, requires  conversion file. So we have either 2 or 3