flye_medaka_workflow

Assembles nanopore data with Flye, polish with medaka. Then runs MLST and BAKTA and puts all GFF files in ROARY.

nextflow run  https://github.com/oxfordmmm/flye_medaka_workflow \
        -r v0.1 \
        --inputFastq data/ \
        -resume \
        --inputmodel r1041_e82_400bps_hac_g615_model.tar.gz \
        -with-trace -profile conda,bmrc

Outputs

CSVs - seqkit contig summaries

MLST - output from MLST

assemblies - contigs from flye or spades

bakta - output from bakta annotation

roary - output from ROARY