Updating config file

[danejo3]

The purpose of this PR is to update the config file as discussed in #56 to enable hybrid assembly and grid support #61.

In this PR, users will need to follow a strict config file format that they must provide.

Large improvements were made to enable hybrid and grid support.

• Removed unnecessary or redundant code.
• Refactored and organized code.
• Provided multiple sanity checks for the user's config file.

Example of the new config file:

{
    "samples": {
        "sample1": {
            "paired": [
                [
                    "yeat/tests/data/short_reads_1.fastq.gz",
                    "yeat/tests/data/short_reads_2.fastq.gz"
                ]
            ]
        },
        "sample2": {
            "paired": [
                [
                    "yeat/tests/data/Animal_289_R1.fq.gz",
                    "yeat/tests/data/Animal_289_R2.fq.gz"
                ]
            ]
        },
        "sample3": {
            "pacbio-hifi": [
                "yeat/tests/data/ecoli.fastq.gz"
            ]
        },
        "sample4": {
            "nano-hq": [
                "yeat/tests/data/ecolk12mg1655_R10_3_guppy_345_HAC.fastq.gz"
            ]
        }
    },
    "assemblies": {
        "spades-default": {
            "algorithm": "spades",
            "extra_args": "",
            "samples": [
                "sample1",
                "sample2"
            ],
            "mode": "paired"
        },
        "hicanu": {
            "algorithm": "canu",
            "extra_args": "genomeSize=4.8m",
            "samples": [
                "sample3"
            ],
            "mode": "pacbio"
        },
        "flye_ONT": {
            "algorithm": "flye",
            "extra_args": "",
            "samples": [
                "sample4"
            ],
            "mode": "oxford"
        }
    }
}

[danejo3]

@standage This PR is ready for review!

I'm honestly not sure where you should start. I've made a lot of changes; however, most of the changes were reorganizing and throwing out unnecessary code.

Main things:

• I split up the 3 main class objects (AssemblyConfig, Sample, and Assembly) into their own individual files.
• I changed the class object instantiation in the snakemake workflow instead of doing it before and doing a bunch of crazy roundabout ways to pass their data into the snakemake workflow.
• I added a lot of checks to ensure that the user provided the correct config format.

Once this PR is merged, integration for grid support and hybrid will be pretty straight forward.

One of the biggest changes is instead of calling multiple snakemake jobs, we have consolidated it down to 1.

Example, Previously, We would have a paired run, then single run, then pacbio run, etc.., then bandage. Before a workflow could run, the current one has to finish first.

Now, in one go, config -- to --> various final outputs created by YEAT