phylociraptor v0.9.6

Changes since last release:
4f22187 bump version to 0.9.6
b0502e0 phylociraptor: add -F and change the behavior of -f so that -F and -f correspond to the snakemake equivalents.
b54a62b change behavior of aggregate_best_models to take checkpoints as input
fd2e9e7 modeltest: Only create statistics and mean bootstrap for genes with filtered alignments. This should fix #18
2808272 speed up filtering alignments based on nparsimony and nseqs
0a54dca model: Remove maxmem parameter
9ae1507 setup/orthology: Change file extension to fasta instead of fna to avoid confusion if protein files are provided.
4d62154 report: Handle custom config.yaml files for --figure
b6d8604 orthology: Cosmetics for busco mode output
14b57f3 phylociraptor: Modifications to the script to accompany the last commit
1986f46 all modes: Fix problem with custom config.yaml file when data/config.yaml does not exist
19cf799 phylociraptor: Print error message when cluster config file does not exist.
0451e20 orthology: it is now possible to run orthology starting from a set of protein sequences. mode=protein in the samples csv file. This only works when using BUSCO5
95b047b setup: Additional small changes to genome_download.py. Better error messages and removed debug output
f26d8f5 setup: The genome download script should now download older assembly accessions correctly
a800a14 Fix typo in README
927acdb speciestree: Extend use of random seed also to astral
38451d8 phylociraptor: Quickfix for phylociraptor check. Now only the done files will be evaluated for speciestree, njtree and mltree. May have to be revisited. Temporarily fixes #15
29047af Add badges to readme
a5994ba orthology: Double check names in CSV file with names already in resulst/assemblies to identify better if samples have been removed and prevent orthology runs for samples not in CSV file.
cd1d65a Add license
2513ced tree: remove dedicated maxmem option from config file for iqtree. This can still be passed on to iqtree with additional_params
988c234 orthology: When BUSCO5 is specified the default behaviour is now to use metaeuk. This is also the deafult of BUSCO5. By specifying an augustus species this is overwritten and augustus is used instead. This does not alter the BUSCO3 behaviour where an augustus species is still mandatory
ecb5115 config: Add new seed option for reproducibility of iqtree and raxml. Remove -redo from iqtree as default option. Change iqtree threading to -nt threads instead of -nt AUTO and maxthreads
d06b88c create one central place to change all containers: data/containers.yaml
4dbe6b5 minimal-example: Fix typos in commands