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DSL2

Merged Celine Noirot requested to merge dev into master

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
  • upadate documentation
  • chunk assambly to reduce process time of filtering step

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