priorities #75
Description
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