
# Call wrappers combine PE and SE data.
# Note, that we also test the case where params.tmp_graph_name is provided or not to test the 
# default value implemented in the wrapper

rule all:
    input: "dn_PE.log", "dn_SE.log"



rule digital_normalisation_PE:
    input:
        fastq=["data_R1_.fastq.gz", "data_R2_.fastq.gz"]
    output:
        fastq=["data_R1_.dnpe.fastq", "data_R2_.dnpe.fastq"],
    log:
        "dn_PE.log"
    params:
        ksize = 20,
        cutoff = 20,
        m = 1000000000,
        options = '',
    threads: 1
    wrapper:
        "main/wrappers/digital_normalisation"



rule digital_normalisation_SE:
    input:
        fastq="data_R1_.fastq.gz"
    output:
        fastq="data_R1_.dnse.fastq",
    log:
        "dn_SE.log"
    params:
        ksize = 20,
        cutoff = 20,
        m = 1000000000,
        options = '',
        tmp_graph_name="graph.ct.se"
    threads: 1
    wrapper:
        "main/wrappers/digital_normalisation"

