Changelog

v1.0.5

Features

  • Added option to plot specific contigs

  • Added option to plot ALL contigs

Bugfixes

  • Handle cases in which no genes are called with a more useful error message.

  • Added check if temp_dir exists before starting analysis.

Other

  • Removed dependency on zgrep (for compatability with nf-core tests)

v1.0.4

Features

  • Added contig_taxonomy_output option to output detailed taxonomy assignment count per contig.

Bugfixes

  • Fix version of dependancy in conda recipe: requests>=2.22.0

v1.0.3

Bugfixes

  • Running with genecalls as iput failed

  • GUNC plot contig_display_num displayed a defined number of genes instead of contigs

v1.0.2

Features

  • GUNC can now be run with GTDB database

  • Added option to download GTDB_GUNC database

  • Input file options can be gene_calls (faa) instead of fna if –gene_calls flag is set

  • Input genecalls can be gzipped

  • Output maxCSS file is now sorted

Bugfixes

  • Fix version of dependancy: requests>=2.22.0 (older versions not compatable)

  • Better error message if gunc_db does not exist

  • checkm_merge didnt work with unless checkm qa was run with -o 2

Other

  • Documentation updates

    • Links to synthetic datasets added

    • Citations for diamond and prodigal added

    • Clarified how checkM should be run for checkm_merge

    • Corrected command for download_db

  • Check if fasta is given with -f option instead of list of filepaths

v1.0.1

Bugfixes

  • Running from genecounts failed

  • Fixed case where pass.GUNC output was converted to ints

  • Fixed silently ignoring input samples that did not map to reference

Other

  • Better error message if ouput_dir doesnt exist

  • Documentation updates

v1.0.0

Features

  • Added option to download the GUNC_DB file

  • Added option to merge GUNC output with checkM output

  • Added option to create interactive HTML based visualisation

  • Added option to run all fastas in a directory

  • Added option to provide input filepaths in a file

  • Added min_mapped_genes option so scores are not calculated when there are not enough genes

  • Added use_species_level option for determining tax_level with maxCSS score

  • Can now accept gzipped fna files (with .gz ending)

  • Allow GUNC_DB to be supplied using an env var

  • Updated arguments to a subcommand structure

  • Complete rewrite of how scores are calculated

  • Gene calling is now done in parallel

Bugfixes

  • genome2taxonomy was not included in pip package

  • GUNC failed if nothing left after minor clade filtering

  • If duplicate filenames were in input, output files were overwritten

  • Inputs that dont map any genes to GUNC_DB were silently missing in output

Other

  • Documentation updates

  • sklearn dependency removed

  • Added the bioconda recipe to repo

  • Added check for zgrep, prodigal and diamond

  • Changed output names to match those in paper

  • Fixed diamond version to 2.0.4 (needs to be compatable with GUNC_DB)

  • Better quality LOGOs

  • Diamond logs are silenced

  • Timestamps added to log output

Initial Release v0.1.2 (2020-10-14)

  • First release