rule all:
    input:"a/a.sorted.bam"

rule bwa_build:
    input:
        reference="index/genome.fasta"
    output:
        bwa_bwt="index/genome.fasta.bwt",
        fai="index/genome.fasta.fai"
    log:
        "reference/build.log"
    params:
        options="",
        index_algorithm='is'
    threads: 2
    wrapper:
        "main/wrappers/bwa/build"


rule bwa_align:
    input:
        fastq=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
        bwa_bwt="index/genome.fasta.bwt",
        fai="index/genome.fasta.fai",
        reference="index/genome.fasta"
    output:
        sorted="{sample}/{sample}.sorted.bam"
    log:
        "{sample}/{sample}.log"
    params:
        options="-T 30 -M",
        tmp_directory="./tmp"
    threads: 2
    wrapper:
        "main/wrappers/bwa/align"

