DSL2

[FriederikeHanssen]

Move this pipeline to use DSL2. Simultaneously, its functionality can be converted into a sub workflow, so it can be easily included in other pipelines. This would make it also easy to keep the subworkflow and the stand-alone pipeline in sync. Changes in the subworkflow would be propagated to both.

[FriederikeHanssen]

This is currently in the works. Left to do:

• [x] Fix naming for extracting reads of specific chromosomes
• [x] Post conversion QC (FastQC)
• [x] MultiQC report:
  • [x] FastQC naming pre/post
• [x] Detect paired-end or single-end (use branch on output to populate input for ALIGNMENT_TO_FASTQ or SAMTOOLS_COLLATEFASTQ)
• [x] Add single-end extraction
• [x] Add flags
• [x] Update documentation
• [x] Update modules
• [x] Merge template
• [x] Add md5sums ymls

Optional features:

• [x] Compute index, if not provided
• [x] Igenomes support for automatic reference retrieval