support for single-end RNA-seq and ATAC-seq in the WASP subworkflow

It should be possible to support single-ended data, since WASP itself supports it.
- [x] create a config parameter to allow switching to single-ended support within the WASP subworkflow
- [x] parse the samples file differently depending on the config parameter
- [x] [read the FASTQs into the same dictionary as usual](https://github.com/aryarm/as_analysis/blob/faac4573c25e61b156c5fa7640b62cd7b16db3e5/Snakefile#L16)
- [x] also [here](https://github.com/aryarm/as_analysis/blob/faac4573c25e61b156c5fa7640b62cd7b16db3e5/Snakefile#L84)
- [x] execute the aligners with only one fastq file
- [x] [STAR1](https://github.com/aryarm/as_analysis/blob/994d3f21201ddea5313c429ea44d46c968f1d905/Snakefiles/Snakefile-WASP#L48)
- [x] [STAR2](https://github.com/aryarm/as_analysis/blob/994d3f21201ddea5313c429ea44d46c968f1d905/Snakefiles/Snakefile-WASP#L135)
- [x] [BWA1](https://github.com/aryarm/as_analysis/blob/994d3f21201ddea5313c429ea44d46c968f1d905/Snakefiles/Snakefile-WASP#L67)
- [x] [BWA2](https://github.com/aryarm/as_analysis/blob/994d3f21201ddea5313c429ea44d46c968f1d905/Snakefiles/Snakefile-WASP#L154)
- [x] remove [the `--is_paired_end` parameter](https://github.com/aryarm/as_analysis/blob/faac4573c25e61b156c5fa7640b62cd7b16db3e5/Snakefiles/Snakefile-WASP#L108) from `find_intersecting_snps.py` and have it output only one fastq file
- [x] use the `rmdup.py` script instead of the [`rmdup_pe.py` script](https://github.com/aryarm/as_analysis/blob/994d3f21201ddea5313c429ea44d46c968f1d905/Snakefiles/snp2h5_rules.smk#L15) within the `rmdup` rule of the WASP subworkflow
- [ ] add a config option for [the SNP filtering criteria in `prepare_counts-rna.r` and `prepare-counts.r`](https://github.com/aryarm/as_analysis/blob/faac4573c25e61b156c5fa7640b62cd7b16db3e5/scripts/prepare_counts-rna.r#L57) (see #77)
- [ ] make it default to 10, if not provided

Start by reading the SNP filtering logic at the referenced line in scripts/prepare_counts-rna.r and scripts/prepare-counts.r, then review issue #77 for the intended configuration option. Done means both scripts accept the configurable SNP filtering criterion and default it to 10 when no value is provided.

Written by the indexing model from the issue text.