Humann

Other Changes

* Help messages were added to the humann2_benchmark tool.

New Features

* A new script, humann2_benchmark, was added which captures MaxRSS and elapsed time for any command and all subprocesses spawned.

Other Changes

* The gap fill option default was set to on.

New Features

* Viral pangenomes were added to the full chocophlan database download.

Other Changes

* The biom output format now uses the biom API to allow for empty matrices.
* All sequences that do not pass filtering are considered unaligned (even if they have alignments to the reference).

New Features

* The script humann2_infer_taxonomy has been updated to enable assignment of approximate taxonomic annotations to a greater proportion of unclassified UniRef90 and UniRef50 stratifications. To use the updated script, please also update your HUMAnN utility mapping files (humann2_databases --download utility_mapping full $DIR).
* The script split stratified table has been updated to be compatible with gzip, bzip2, and biom formats.

New Features

* Added option "--remove-column-description-output" which will remove the description from the output file columns.
* Added build simple method for diamond install for users without cmake installed.

New Features

* Added biom input and output compatibility to the following scripts: humann2_infer_taxonomy, humann2_regroup_table, humann2_rename_table, humann2_renorm_table, humann2_rna_dna_norm, and humann2_strain_profiler.
* Added gzip and bz2 input file compatibility to the following scripts: humann2_join_tables, humann2_merge_abundance, and humann2_reduce_table.

Other Changes

* Added functional end to end and also tools tests for biom compatibility features.
* Sorted the reactions and pathways provided to MinPath. This removes stochasticity seen when running with Python3.
* Changed diamond version check option to "--version" as this is backwards compatible with the diamond v0.7 series.