
rule all:
    input: 
        "fastqc_SE/fastqc.done", "fastqc_PE/fastqc.done"

rule fastqc_PE:
    input:
        "test_R1_.fastq", "test_R2_.fastq"
    output:
        done = "fastqc_PE/fastqc.done"
    params:
        options= " -nogroup ",
        working_directory= "fastqc_PE" 
    threads: 2
    log:
        "fastqc_PE/fastqc.log"
    wrapper:
        "main/wrappers/fastqc"

rule fastqc_SE:
    input:
        "test_R1_.fastq"
    output:
        done = "fastqc_SE/fastqc.done"
    params:
        options= " -nogroup ",
        working_directory= "fastqc_SE" 
    threads: 2
    log:
        "fastqc_SE/fastqc.log"
    wrapper:
        "main/wrappers/fastqc"


