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

v1.0.2

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

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