Snakefile_basic

configfile:
    "config.json"

SAMPLES, = glob_wildcards(config['data']+"/{id}_L001_R1_001.fastq.gz")

rule move:
    input:
        bam = expand("{sample}.final.bam", sample=SAMPLES),
        bai = expand("{sample}.final.bai", sample=SAMPLES)
    params:
        output = config['data']+"/Alignment"
    shell:
        """
        mkdir -p {params.output}
        mv {input} {params.output}
        """

rule align_sort:
    input:
        config['data']+"/{sample}_L001_R1_001.fastq.gz",
        config['data']+"/{sample}_L001_R2_001.fastq.gz"
    output:
        temp("{sample}.mapped.bam")
    params:
        rg = "@RG\\tID:{sample}\\tPL:ILLUMINA\\tSM:{sample}",
        ref = config['genome']
    conda:
        "envs.yaml"
    shell:
        "bwa mem -R '{params.rg}' -M {params.ref} {input} | samtools sort -o {output} -"

rule mark_duplicates:
    input:
        "{sample}.mapped.bam"
    output:
        bam = "{sample}.final.bam",
        bai = "{sample}.final.bai",
        metrics = temp("{sample}_dedup_metricx.txt")
    conda:
        "envs.yaml"
    shell:
        "picard MarkDuplicates I={input} O={output.bam} M={output.metrics} CREATE_INDEX=true"