kraken2db not being mounted for singularity about bacass HOT 7 CLOSED

Hrmpf, this looks like a weird bug. unfortunately one that we didn't catch in the CI tests, as we don't test kraken on the CI. I need to merge in the latest template #34 anyways these days, so that might be something to get in the next fix release too & re-add this to CI to get it tested with a tiny kraken2 database similar to the one used by ViralRecon.

Thanks for reporting !

from bacass.

No problem! Is there a way to bypass this in the meantime? Thanks!

from bacass.

--skip_kraken2 to skip it entirely. I'm afraid not really without skipping kraken entirely for now. I'll try to do it asap but pre-christmas thats sometimes a bit hard 😓

Could be that its enough to follow the viralrecon example is most straightforward:

/*
 * PREPROCESSING: Uncompress Kraken2 database
 */
if (!params.skip_kraken2 && params.kraken2_db && !params.skip_assembly) {
    file(params.kraken2_db, checkIfExists: true)
    if (params.kraken2_db.endsWith('.tar.gz')) {
        process UNTAR_KRAKEN2_DB {
            label 'error_retry'
            if (params.save_reference) {
                publishDir "${params.outdir}/genome", mode: params.publish_dir_mode
            }

            input:
            path db from params.kraken2_db

            output:
            path "$untar" into ch_kraken2_db

            script:
            untar = db.toString() - '.tar.gz'
            """
            tar -xvf $db
            """
        }
    } else {
        ch_kraken2_db = file(params.kraken2_db)
    }
}

and then do this in the kraken2 / kraken2-long process:

input:

        path db from ch_kraken2_db

and in the script section:

 kraken2 \\
            --db $db \\

Not sure we will support direct input of gzipped kraken2 dbs, but that could be helpful as they are now available from AWS S3 buckets by the authors, so could be a nice addition.

from bacass.

Fairly easy change - wanna give it a go and I review?
That would then fix dev and give us the possibility to get things fixed on dev for you to test ;-)

from bacass.

Let me have a go

from bacass.

should I add the --save_reference option? or should we always skip it?

from bacass.

Not required I think in this case...

from bacass.