Adjust input run.yaml format

Require pairs of accessions for exp/control samples instead of experiment accession Create run_parser class to return list of run classes, and list of genome classes.

Adding the sample format here for future reference

run.yaml

genomes:

• assembly:
  • chrom.sizes: "/path/to/chrom/file"

runs:

• align: [bwa | bowtie2]
• assembly: "assembly"
• peak: [gem|ccat|peakranger|spp|macs2]
• idr: [true|false]
• file_type: [fastq|bam]
• control1: "accession"
• signal1: "accession"