configfile: "config_data.yaml"

rule all:
    input:
        "input/scRNA-Healthy-Hematopoiesis.SCE.rds",
        "input/scATAC-Healthy-Hematopoiesis.SCE.rds",
        "input/Homo_sapiens.GRCh37.87.gtf.gz",
	"input/hg19.chrom.sizes"

rule download_scRNA:
    output:
        "input/scRNA-Healthy-Hematopoiesis.SCE.rds"
    params:
        url=config['scRNAFile']
    shell:
        """
        wget -O {output} {params.url} 
        """

rule download_scATAC:
    output:
        "input/scATAC-Healthy-Hematopoiesis.SCE.rds"
    params:
        url=config['scATACFile']
    shell:
        """
        wget -O {output} {params.url} 
        """

rule download_GTF:
    output:
        "input/Homo_sapiens.GRCh37.87.gtf.gz"
    params:
        url=config['gtfFile']
    shell:
        """
        wget -O {output} {params.url}
        """

rule download_sizes:
    output:
        "input/hg19.chrom.sizes"
    params:
        url=config['chromSizesFile']
    shell:
        """
        wget -O {output} {params.url}
        """

