priorities

[aryarm]

We should probably do these issues in this order. But since @zrcjessica needed quick changes to the pipeline, I tried to address a few of the issues whilst disregarding the order of this list.

• Test dataset create a small, test dataset and a testing suite #73
• BAM file input allow BAM files as input to the WASP subworkflow #71 (@aryarm has mostly done this)
• ATAC-seq support ATAC-seq support #61, add support for peak regions for ASOC analysis #69 (@aryarm has mostly done this)
• Specifying samples simplify how samples are specified #72
• Small changes
  • gzipping fastas and GTFs allow gzipped FASTAs and GTFs when using STAR #64 (@aryarm is doing this)
  • remove quoting in CSVs remove quoting in CSVs output by R scripts #67 (@zrcjessica already has uncommited changes)
  • add error messages for empty dataframes add error messages for dataframes with 0 rows after filtering #68
  • changing name of ref allele proportion Change name of column for proportion of ref allele in rna.csv.gz #70
  • allow changing read depth cutoff add config option for supporting reads cutoff #77
• better documentation document meaning of columns in output of R scripts #78
• making this into a command-line tool and/or adding config option validation use snakemake validation #5, big picture: turning this into a command line tool #74