# Default taxonomy directory can be defined here
TaxonomyDir:/Users/martins/Documents/Projects/MARTi/taxonomy/taxonomy_6Jul20
MinKNOWRunDirectory:/Users/martins/Documents/Projects/MARTi/marti_input
MARTiSampleDirectory:/Users/martins/Documents/Projects/MARTi/marti_output
Port:3000
https:false
Key:
Certificate:

# Blast processes can be defined in here and then settings can be simply copied to new config files

BlastProcess
    Name:nt
    Program:megablast
    Database:/Users/leggettr/Documents/Databases/nt_30Jan2020_v5/nt
    MaxE:0.001
    MaxTargetSeqs:25
    BlastThreads:2
    UseToClassify

BlastProcess
    Name:ref_prok_rep
    Program:megablast
    Database:/Users/leggettr/Documents/Databases/ref_prok_rep_genomes_29Jul21/ref_prok_rep_genomes
    MaxE:0.001
    MaxTargetSeqs:25
    BlastThreads:2
    UseToClassify

BlastProcess
    Name:zymo_mock
    Program:megablast
    Database:/Users/martins/Documents/Projects/MARTi/databases/zymo_mock/zymo_refs_sam.fasta
    MaxE:0.001
    MaxTargetSeqs:25
    BlastThreads:2
    UseToClassify

BlastProcess
    Name:card
    Program:blastn
    Database:/Users/martins/Documents/Projects/MARTi/databases/CARD_3.1.1_Download_10Mar21/nucleotide_fasta_protein_homolog_model.fasta
    MaxE:0.001
    MaxTargetSeqs:100
    BlastThreads:2

CentrifugeProcess
    Name:metagenomic
    Database:/Users/leggettr/Documents/Databases/centrifuge/202311_meta/
    CentrifugeThreads:4
    MinHitLen:25
    UseToClassify

Kraken2Process
    Name:pluspf-8
    Database:/Users/leggettr/Documents/Databases/kraken2/k2_pluspf_08gb_20230314_db/
    Kraken2Threads:4
    UseToClassify

