Project structure

[messersc]

Draft for v0.6.0

• new structure that includes Project in paths
• adopt bclconvert (only in tandem with above)
• enforce black formatting

[messersc]

TODO

• [x] test with flowcells other than miseq
• [ ] incorporate needed extra options for bclconvert. Need argparse switches, config fields, plus need to be written to samplesheet by the wrapper (with either bash or python)
  • which ones do we need?
• [x] remove global conda env seq-qc currently used for faster debugging
• [x] put singularity images somewhere sensible
• [x] more than one bases mask is currently not handled by bclconvert, do we need that?