v1.2.5

1.2.5 (2023-03-14)

Dependencies

• update AmpliGone to version 1.2.1 (7abaedd)
• update minimal mamba version to 1.0.0 (7ad5fe8)

Documentation

• add information badges to readme (53e818f)
• update installation instructions in docs (da57e82)

v1.2.4

1.2.4 (2023-03-02)

Dependencies

• use conda for installing aminoextract instead of pip (1855470)

v1.2.3

1.2.3 (2023-03-01)

Bug Fixes

• allow input fastq files that contain multiple dots (07994a2)
• ensure compability between the Influenza preset and illumina short read data (9a9f1d9)
• ensure match_preset_name() actually returns all required values (d49f238)
• update permissions for GH-actions workflows (1f760ba)

Documentation

• add citations file (1f760ba)
• update installation instructions for new environment file and environment creation with Mamba (84183a7)

Dependencies

• add python-magic version 0.4.27 to environment (84183a7)
• pin version of AminoExtract to 0.2.1 (84183a7)

v1.2.2

1.2.2 (2023-01-24)

Bug Fixes

• correctly parse presets when using a samplesheet (2ca2149)
• make the ViroConstrictor main entrypoint less case sensitive (43b27aa)

v1.2.1

1.2.1 (2023-01-19)

Bug Fixes

• correction in argument parser to avoid a NoneType AttributeError when all required information is passed through commandline options (f2acedf)

Dependencies

• correct the rich version in all base environment files (f2acedf)

v1.2.0

1.2.0 (2023-01-18)

Features

• add option to filted for minimum aligned length in clipper.py (d06caf5)
• add option to filter spliced reads in clipper.py (d06caf5)
• add support for working with presets for specific viral targets (29bfa3c)

Bug Fixes

• add .gff3 file extension as allowed to features flag (b4fdf5d)
• change Clipper settings to a per-platform config per preset (3d952bb)
• change the minimal alignment length in clipper.py to be a percentage of the reference length (68597e8)
• correct minimum aligned read length default value (60b9230)
• Fix extension checking for input files (6c4f91e)
• set snakemake keepgoing to True as a default (0076d52)
• use the correct columns of input BED file when there are more columns given than necessary (56b5259)
• workaround for Argument list too long error when parsing complex workflows (2835c44)

Performance Improvements

• change make_pickle rule to localrule (f41cc01)
• change threads in local execution mode to improve parallel performance (869c81a)

Dependencies

• add Rich as a dependency with version 13.. (e63cac7)
• update AmpliGone to version 1.2.0 (dfb22f1)

Documentation

• update documentation to include presets functionalities (adc5265)

v1.1.0

1.1.0 (2022-12-06)

Features

• add base of functionality to translate and write amino acid sequences (25884b7)
• translate and extract aminoacids sequences for multiple targets (657aaff)

Bug Fixes

• add the missing "FORWARD" and "REVERSE" primer keywords (74b92c6)
• change found features to np.nan if input reference and features file don't match (3e812e4)
• circumvent issue where null values cause problems in data translation steps (6007fca)
• correctly parse amino acids that have a name with a dot in it (3e14dd5)
• make sure all required info is present when no gff files are given (d589989)

Documentation

• clarify some sections in the docs (9bc4171)
• fix broken links (9bc4171)
• update documentation to match new functionality (9bc4171)

Dependencies

• add AminoExtract to dependency list (acb378e)
• change minimal python version to 3.10 (acb378e)
• pin AminoExtract version to v0.2.0 (cce1cf9)
• pin AminoExtract version to v0.2.1 (c0e869f)
• update TrueConsense to v0.5.0 and change rules accordingly (af15b9c)
• update TrueConsense version to 0.5.1 (b1a61e4)

v1.0.4

1.0.4 (2022-11-01)

Bug Fixes

• cleanly exit vcf_to_tsv.py script when vcf is empty after filtering (037467b)
• replace bcftools with python script to avoid bcftools shared libraries error (eefaead)

Dependencies

• remove bcftools as a dependency (eefaead)
• remove the entire Mutations environment as it is no longer necessary (eefaead)

v1.0.3

1.0.3 (2022-10-12)

Dependencies

• pin snakemake to version 7.15.2 for dependency compatibility (0914b56)
• set snakemake 7.15.2 as a minimal version in setup.py (0914b56)

v1.0.2

1.0.2 (2022-08-15)

Dependencies

• update AmpliGone to version 1.1.0 (153719d)
• update included snakemake version to 7.12.x (e59edf9)
• use the bioconda channel to install AmpliGone instead of pip (0f1fd65)