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

nf-core

Dear all, im trying to run the bacass pipline, however i get this error: Not a valid path value: ‘kmerfinder_db/viral’ for the --kmerfinderdb argument. Im not sure how to go on from this since i downloaded the database from the link given in the description and it is in the directory mentioned above. Any help is appreciated!

Hello, kmerfinder `bacteria` database is harcoded in this pipeline because is a bacterial assembly pipeline, sorry :disappointed:.

do you think its still reasonable to use your pipline for viral data? i didnt find a similar one (de novo assembly) for viral data.

what about <https://nf-co.re/viralrecon/2.6.0/|nf-core/viralrecon> :thinking_face: ?   It includes a de novo assembly strategy.