DSL2

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

changed milestone to %V2.2 DSL2 transition

assigned to @celine.noirot

added 27 commits

• 2b23244c...54210901 - 26 commits from branch master
• 529e7714 - Merge branch 'master' into 'dev'

Compare with previous version

merged

mentioned in commit d90c0efa