develop snakemake pipeline

[sansamcl]

• outline pipeline in snakemake file
• setup scripts folder
• add blacklist and RT windows files
• make test data
• write draft of README with individual steps written
• write and test commands for fastq trimming
• write and test commands for alignment
• write and test commands for filtering bam files
• write and test commands for making count tables
• run pipeline on full samples from Siefert et al
• write vignette for Siefert et al sample test
• add code for calculating log2FC and Z Scores
• write description
• describe test data and write test data vignette
• provide more complete description of individual steps, including inputs, outputs, and parameters
• add descriptions to sample table columns in README