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@ids-bioinformatics ids-bioinformatics released this 18 Sep 15:11
v1.4.0
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1.4.0 (2023-09-18)

Features

  • add "NONE" input for primers and gff's support to the match_ref process (1581c78)
  • add all the match_ref analysis scripts (1581c78)
  • add the match_ref snakemake workflow (1581c78)
  • add the match_reference process (1581c78)
  • only initiate the match_ref wrapping process whenever it is set on the commandline or through the samplesheet (1581c78)

Bug Fixes

  • add fix for unformatted printed message (98386c1)
  • enforce a "None" string instead of a Nonetype used for reference prep (f4f7490)
  • ensure "match-ref" and "segmented" columns are always added to samplesheet (98386c1)
  • ensure a string value like "NA" will not be interpreted as NaN in pandas.read_csv() (ecaca5e)
  • pad the number in primer names in the amplicon_coverages script so the amplicons are sorted correctly (cab3a8c)
  • solve index out of range bug in amplicon_coverages script (ca95a8a)
  • suppress the strict-channel-priorities logmessage from snakemake (1654891)
  • workaround to make sure the found segments can properly be 'exploded' in the resulting dataframe (9db4a42)

Dependencies

  • remove anaconda channel from selfupdating method (3db1cfb)
  • remove the anaconda and defaults channels as providers in conda environment recipes, set nodefaults (08ed236)
  • replace gffpandas in script to AminoExtract functions (599da1f)
  • update AminoExtract to version 0.3.1 (08e4a22)
  • use a forked/patched version of gffpandas instead of the pypi version (circumvent a bug in the original repo) (08e4a22)

Documentation

  • update the documentation site to represent the new match-ref and segmented arguments both on commandline and and in samplesheet (94c5ca0)
  • updated docstring for function check_samplesheet_rows() (98386c1)
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