# vim: syntax=python tabstop=4 expandtab
# coding: utf-8



rule razers3_map_gold_unprep:
    input:
        "{prefix}/{reference}.fasta",
        "{prefix}/{reads}.fastq"
    output:
        "{prefix}/{reads}.{reference}.razers3_gold_unprep.bam"
    log:
        "{prefix}/{reads}.{reference}.razers3_gold_unprep.bam.log"
    params:
        config["razers3_gold_param"]
    shell:
        "command time -f 'RES:%e\\t%M\\t%P' "
        "./bin/razers3 {params} --output {output} {input} 2> {log}"
