skip-kraken2 requires Kraken2 DB arg
ropolomx opened this issue · comments
Running the following command using bacass 1.1.0:
nextflow run nf-core/bacass --input bacass_short.csv -profile singularity --skip-kraken2
results in the following:
Missing Kraken2 DB arg
One would need to specify the --kraken2db argument, which is a bit counter-intuitive to the role of --skip-kraken2.
Agreed - something that should be fixed 😓
I think I found your issue. The parameter is:
--skip_kraken2 and not --skip-kraken2 :-)
If this isn't fixing the issue let me know again and reopen accordingly!