archaea_example.yaml

bacteria:
    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: '-S arc -m lsu,ssu,tsu'
        # cmscan_rRNA:
        #     params: ''
        #     priority: 50
        #     threads: 1
        #     db: '/Users/zech/database/Rfam/v12.2/archaea.cm'
    protein:
        metadata: '/Users/zech/database/protein.sqlite'
        diamond_uniref90:
            params: '--index-chunks 1 --query-cover 80 -k 3'
            priority: 50
            threads: 1
            db: '/Users/zech/Dropbox/git/micronota/micronota/data/uniref90.dmnd'
            input: 'prodigal.faa'
            output: 'diamond_uniref90'
        diamond_uniref50:
            params: '--index-chunks 1 --query-cover 80 -k 3'
            priority: 50
            threads: 1
            db: '/Users/zech/Dropbox/git/micronota/micronota/data/uniref50.dmnd'
            input: 'diamond_uniref90.faa'
            output: 'diamond_uniref50'

        # 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: ''

eukarya:
    cmscan_rRNA:
        params: ''
        priority: 50
        threads: 1
        db: '/Users/zech/database/rfam/v12.2/eukarya.cm'