How to build standard databases?

[ChillarAnand]

Description of the bug

To build kraken2 database, we can directly run

$ kraken2-build --standard --threads 24 --db $DBNAME

This will build the standard database by default.

How should input file be created to create standard databases?

Command used and terminal output

$ nextflow run nf-core/createtaxdb -r dev --input i.csv --outdir k2s --dbname kraken2

Relevant files

No response

System information

No response

[jfy133]

Hi @ChillarAnand

Thanks for the question!

The primary purpose of createtaxdb is to create custom databases rather than standard databases you can download in a 'one shot'.

I don't plan to support such functionality currently, because as in your example, you just need to run a single command without requiring any input files (as the tool presumably downloads this for you), which should be simple enough without the need of a pipeline.

[jfy133]

Feel free to reopen if you have a strong case for including it.

[ChillarAnand]

I was trying to build a custom db but got stuck. So I was trying to build a standard db.

Here is a sample file as per docs.

❯ cat in.csv
sample,fastq_1,fastq_2
test,/home/anand/avilpage/BS006840.fastq,

When I run the below command it is failing with

❯ nextflow run nf-core/createtaxdb -r dev --input in.csv --outdir k2_db --dbname kraken2

...
------------------------------------------------------
ERROR ~ ERROR: Validation of 'input' file failed!

 -- Check '.nextflow.log' file for details
The following errors have been detected:

* -- Entry 1: Missing required value: fasta_dna
* -- Entry 1: Missing required value: fasta_aa
* -- Entry 1: Missing required value: id
* -- Entry 1: Missing required value: taxid
*

From the docs, I am not able to figure out the issue.