bacteria_example.yaml

general:
    protein_xref: '~/database/protein.sqlite'
CDS:
    prodigal:
        params: '-f gff'
        priority: 100
        threads: 1
rho_independent_terminator:
    transtermhp:
        params: '-p $TRANSTERMHP'
        # '--all-context'  # output all predicted terminators instead of legitimate ones
        priority: 99
        threads: 1
ncRNA:
    # cmscan:
    #     params: ''
    #     priority: 50
    #     threads: 1
    #     db: '/Users/zech/Dropbox/git/micronota/micronota/data/rfam.cm'
    #     output: 'cmscan'
CRISPR:
    minced:
        params: ''
        priority: 50
        threads: 1
tRNA:
    aragorn:
        params: '-w'
        priority: 50
        threads: 1
tandem_repeats:
    tandem_repeats_finder:
        params: ''
        priority: 50
        threads: 1
        output: 'tandem_repeats_finder'
rRNA:
    rnammer:
        params: '-m lsu,ssu,tsu'
    # cmscan_rRNA:
    #     params: ''
    #     priority: 50
    #     threads: 1
    #     db: '/Users/zech/database/Rfam/v12.2/bacteria.cm'
protein:
    diamond_uniref90:
        params: '--index-chunks 1 --id 90 --subject-cover 80 --query-cover 80 --max-target-seqs 3'
        priority: 50
        threads: 1
        db: '/Users/zech/Dropbox/git/micronota/micronota/data/uniref90.dmnd'
        input: 'prodigal.faa'
        output: 'diamond_uniref90.faa'
    diamond_uniref50:
        params: '--index-chunks 1 --id 50 --subject-cover 80 --query-cover 80 --max-target-seqs 3'
        priority: 50
        threads: 1
        db: '/Users/zech/Dropbox/git/micronota/micronota/data/uniref50.dmnd'
        input: 'diamond_uniref90.faa'
        output: 'diamond_uniref50.faa'

    # hmmscan_tigrfam:
    #     params: '−−cug_nc'
    #     priority: 60
    #     threads: 1
    #     db: '~/database/TIGRFAM/tigrfam.hmm'
    #     input: ''
    #     output: ''
    # hmmscan_tigrfam:
    #     params: '−−cug_ga'
    #     priority: 60
    #     threads: 1
    #     db: '~/database/TIGRFAM/tigrfam.hmm'
    #     input: ''
    #     output: ''