v3.0.0

• base python version 3.11 or newer is now required
• With toml transition, all '-' in workflows have been removed (mRNA-seq -> mRNAseq).
• makePairs workflow has been initiated
• pytest / lint have been moved to a [actions] optional dependency
• docs requirements have been moved to a [docs] optional dependency
• version is no longer set in init, but in toml file
• mamba requirement is dropped, tests ported to conda
• cluster.yaml is deprecated in favor of profiles, condaEnvDir is now specified to be set in the profile rather then in another yaml file.
• dependency pins dropped, snakemake >= 8 required.
• createEnvs has changed, autoDetectCondaDir has been removed (as it needs to be set in snakemake profile).
• all rule-specific log redirectives have been removed, let profile capture and save to specific files.
• DAG plotting has been made dependent on graphviz, if graphviz is not available as a library (happens if installed via conda) or if dot is not available in path, the DAG is printed out in ASCII format to a txt file
• regex changes in createIndices changed to match lines starting with >, spikeinExt is appended at the end.
• regex change in threeprimeseq mode that simplifies the wildcard constraint (though should have the same functionality).
• default adapter trimming for Illumina stranded library prep (CTGTCTCTTATACACATCT) instead of TruSeq adapter (AGATCGGAAGAGC)
• commented out temped sortedByName bam files under SNPsplit rules, as they don't seem to be generated (perhaps this was some older version's default)
• createEnvs has some basic profile checks (wether conda-frontend is set, if a prefix is set, etc.)