chore(main): release 1.4.0

[ids-bioinformatics]

🤖 I have created a release beep boop

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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[ids-bioinformatics]

🤖 Release is at https://github.com/RIVM-bioinformatics/ViroConstrictor/releases/tag/v1.4.0 🌻