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

[aryarm]

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
  • [x] also here
• [x] execute the aligners with only one fastq file
  • [x] STAR1
  • [x] STAR2
  • [x] BWA1
  • [x] BWA2
• [x] remove the --is_paired_end parameter 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 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 (see #77)
  • [ ] make it default to 10, if not provided