Panacota

Changes:

**General**
- Use of number of CPUs available to the process instead of the total number of CPUs on the machine (issue 37). (NB: Mac OS users will still be using the total number of CPUs)
- Update conda recipe to be compatible with python > 3.6 (issue 38)

**prepare**:
- new option to download a single strain (issue 17)

**tree**:
- new option: write distance matrix when using fastME (issue 36)

Fix issue 16 : bootstrapping from "PanACoTA all" module via configfile is now working

Changes:

**all:**
fixes issue 11 (cutN not taken into account when launched from configfile)

**pangenome:**
- Fixes issue 14
- changes in output directory structure (all mmseqs files in a separate directory, and simpler default pangenome filename)

**corepers:**
possibility to give a subset of genomes for the coregenome (instead of all genomes found in pan)

**align:**
- Add possibility to ask for proteic alignments concatenated by genomes (in addition to nucleic ones)
- fix logger detail issue
- genome names can now contain a '.'

**tree:**
- add TEST parameter when using IQtree
- fix problem if user has iqtree2 version called by iqtree command.

Changes:

**Module 'all'**
- configuration file for 'all' module: when running 'all' subcommand, it is now possible to choose all parameters for all modules, using a configuration file.

**Module prepare**
- 0 included when we ask for a mash min_dist = 0
- add choice for NCBI section: genbank or refseq
- add possibility to give a ncbi taxid (*-t*, for a subspecies or a specific strain) in addition to ncbi species taxid (*-T*)

**Module annotate**
- prodigal now uses training mode on the first genome (the one with best quality) before annotating all genomes
- fix bug *logger has no attribute detail*

**Changes:**

- **Major change**: new module to run everything in a row: 'all' module. See `PanACoTA all -h`
- Fix bug when there is a binary file in the genomes repository
- IQtree2 is the default software when running `PanACoTA tree`. To use IQtree versions 1.x, use `-s iqtree` option

CHANGES:

- fix problems while formatting genomes annotated by prokka
- add new option, to select the assembly level of genomes to download from NCBI