mg7: mg7 v1.0.0-M2

This milestone release is huge. It contains a lot of improvements and some important fixes. Here are some higlights:

• Features and improvements:

  • #4, #15: The BLAST reference database and IDs mapping is now configurable
  • #17: Added RNACentral reference DB (as the default one now)
  • #18: BLAST options are now configurable
  • #16: A dataflow API was improved and a pipeline without the Flash step was added
  • #20 #24: For pipelines without Flash you can choose between FASTA and FASTQ input format
  • Output tables improvements:
    • #10: Added CSV-headers
    • #19, #23, #27: Added taxonomic rank and name columns
    • #6: Split each counts table on two: direct/accumulated
    • #30: Zero direct counts are filtered out

• Important fixes:

  • #28: Bio4j-NCBITaxonomy database was updated with an important fix for the taxonomic names
  • #26: Ongoing effort to solve the "Too many open files" exception has been moved to ohnosequences/loquat#56

See the full list of pull requests merged in this release in the v1.0-M2 milestone.