CD hit is run on proteins to improve performance eggnog database is loaded in ram to save time too.

some bugs fixed, update config to deal with checkM2 parameter for example, update doc and singularity recipe

• Fix some issues
• Update docs
• Add coassembly
• Replace bin refinement with binette (more efficient and faster): https://github.com/genotoul-bioinfo/Binette
• Several optimisation with pyfastx
• prokka replacement by prodigual, tRNAScanSE and barrnap (faster)

• Fix remaining conflicts from last realease
• Update documentation
• Fix sample name in taxonomic affiliation plots
• Update multiqc config #210
• Add header to metaWRAP scripts

DSL2 version

• pass to DSL2 to get 2 workflow (Short-read and HiFi)
• gene are named with feature (prot/rrna)
• aln2taxaffi.py refactored to use new_taxdump and prot.accession2taxid.FULL
• add header in diamond output and use it while parsing
• replace mosdepth by samtools coverage
• replace bedtools bamtofastq by samtools fastq
• check gff valididy after prokka
• simplify config files
• update documentation
• chunk assembly to reduce process time of filtering step