Changelog

v1.0.6

Features

• GUNC will now report the number of failed genomes if some fail when running in batch mode.

Bugfixes

• Fixed cases where number of mapped genes might be different when running smaller genomes individually vs grouped.

• Fixed cases where gunc would fail if _-_ was in a sequence identifier.

• Fixed cases where contig colour in visualisation was incorrect.

• Fixed incorrect ordering of taxonomic levels in plot if user supplies them in an incorrect order.

• Allow GUNC to continue if some genomes fail diamond mapping.

• Fixed crash if diamond fails to map anything to GUNC reference.

• Fixed bug where GUNC goes into infinite loop if an input filename is merged.fa

Other

• class and order are now included in contig assignment output file (@aaronmussig)

• Fix pandas deprecation waring (@tmaklin)

• Added fixes for pandas FutureWarning (changing behaviour of Series.idxmax)

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