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

nf-core

Can anyone recommend a pathogen identification pipeline that works on windows (with Docker Desktop)?

Windows is going to be extremely hard for any bioinformatics workflow. Do you have WSL set up?

And what sort of pathogen identification?

I do have WSL. Mostly blood samples, MinION sequencing, we usually do De Novo sequencing and blastn, looking for bacteria or viral presence

You might be interested in talking with <@U04JKRB6UUR> :slightly_smiling_face:

You could either check my pipeline <https://github.com/genomic-medicine-sweden/metaval|gms/metaval> or <https://github.com/nf-core/viralmetagenome|nf-core/viralmetagenome>

We can talk more details after lunch if you are interested.