rule hmmscan_profile:
    input:
        fasta="test-protein.fa",
        profile="test-profile.hmm.h3f",
    output:
        # only one of these is required
        tblout="test-prot-tbl.txt", # save parseable table of per-sequence hits to file <f>
        domtblout="test-prot-domtbl.txt", # save parseable table of per-domain hits to file <f>
        pfamtblout="test-prot-pfamtbl.txt", # save table of hits and domains to file, in Pfam format <f>
        outfile="test-prot-out.txt", # Direct the main human-readable output to a file <f> instead of the default stdout.
    log:
        "logs/hmmscan.log"
    params:
        evalue_threshold=0.00001,
        # if bitscore threshold provided, hmmscan will use that instead
        #score_threshold=50,
        extra="",
    threads: 4
    wrapper:
        "main/wrappers/hmmer/hmmscan"
