Release 2.8.1

[farchaab]

Summary

Small release to work with latest snakemake and apptainer versions

Changes

• d9aa7b7 Renamed singularity rule directive to container
• 23df594 96195e2 Updated python-r docker
• eacc7a3 Removed commented rule (prepare_low_coverage_contigs_report)
• 7c30357 Replaced dynamic with checkpoint
• 336a537 eb575f1 Added shell triple quotes for awk command visibility
• 6ccf75b Updated checkM container
• 97aa260 Imrpoved plot_gene_presence_heatmap.R formatting

Fixes

• 92e29dd f64f981 e920fc8 Fixed tabs and indentations
• 5573ebb Fixed singularity attribute error
• 3ebf8de Fixed conda attribute error
• 8ce1d29 Fixed centrifuge conda env
• 227f214 Fixed path to bakta db
• 3640729 5362038 Fixed pandas colwidth to 1
• 1c1a78c 621b420 Replaced biopython's GC to gc_fraction
• bdf70ce Fixed conda env in report_resistance

[tpillone]

Thank you for the PR!
Could you make sure that you can generate the output "phylogeny/checkm/tree.nwk"?