contamination-nf

Nextflow pipeline for checking contamination problems with reads among other tasks

Install

git clone [email protected]:biocorecrg/contamination-nf.git --recurse-submodules

Run:

Modify params.config accordingly or copy it and replace it in the command-line below.

# Running KRAKEN2
nextflow run -bg --config params.config main.nf &> log

Different subworkflows:

• build
• bracken

TODO

• Allow adding custom FASTAs (now in build.sh)

Links

• Kraken2 manual
• Bracken manual