Aaftf

Added

- gzipped FastA files are supported by `AAFTF assess`
- Telomere info reported in assess

Added

- pypi packaging for install

Added

- Support --careful and --isolate mode for spades run; default is --careful which seems to be a little better in tests

Fixed

- Add dependencies to requirements.txt and environment.yml

Added
- support for fastp in trimming (`trim`) command which can now support merging (--merge) and de-duplication (--dedup) as well as 5' and 3' trimming options of fastp (--cutfront, --cuttail, --cutright).
- added tests and summary stats to compare performance of different trimming/merging strategies on final genome and gene content

Fixed
- fix bug in `mito` to correctly spell novoplasty program that is used
- revamped the resources.py to allow multiple files to represent mitochondria ref db for vector screening and alternative sourmash LCA databases - supporting gtdb-r207 and gtdb-rep-r207
- spades in `assemble` command support merged long singleton reads along with paired end input

Added

- Added NOVOplasty mediated mitochondrial assembly, `AAFTF mito`
- integrated `AAFTF mito` into `AAFTF pipeline`
- updated sourmash LCA database link and will download if not found

Added

- Issue 10 added GC% in the assessment report table
- Added --mem option to pilon to up the heapsize for java runs
- merged changes in namespace by gamcil and a tmpdir