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HUMAnN 3 is a workflow tool for profiling microbial pathways in metagenomic and metatranscriptomic data. To learn more about the tool, check out its homepage and GitHub repo.

Function Call


Function Arguments

See the Notes section below for more details.

Argument Use in place of: Description
inputs --input Path to a single file that will be passed in as input. FASTA and FASTQ formats (gzip compressed or uncompressed) are supported. Uncompressed SAM/BAM and M8 inputs are also supported. The files can be a local or remote, see Using Files.
output_path --output (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see Using Files.
output_primary_name (optional) (optional) If you're using a mode that produces an individual output file, set the name here.
taxonomic_profile --taxonomic-profile (optional) Path to a MetaPhlAn output tsv (taxonomic profile). Significantly accelerates execution if provided. See the HUMAnN 3 docs on the topic for more.
mode humann $MODE (optional) (optional) If you're running a humann3 utility scripts, put it here! Defaults to executing raw humann. This is an enum, see the note below this table for more.
input_pathways --input-pathways (optional) Path to input pathways from a humann run for use with humann_unpack_pathways mode.
tool_args all other arguments (optional) Additional arguments to be passed to MetaPhlAn. This should be a string of arguments like the command line.
is_async Whether to run a job asynchronously. See Async Runs for more.

Note on mode: mode is an enum, accessible at – e.g.

Tool Versions

Toolchest supports version 3.1.1 of HUMAnN.


Toolchest currently supports the following databases for HUMAnN:

database_name database_version Description
ChocoPhlAn N/A The ChocoPhlAn database, provided by the Huttenhower lab. This database is required, and is not user configurable. Used via the --nucleotide-database argument.
UniRef90 1 The UniRef 90 database. Used via the --protein-database argument.

Supported Additional Arguments

  • --bypass-nucleotide-index
  • --bypass-nucleotide-search
  • --bypass-prescreen
  • --bypass-translated-search
  • --metaphlan-options
  • --prescreen-threshold
  • --bowtie2-options
  • --nucleotide-identity-threshold
  • --nucleotide-query-coverage-threshold
  • --nucleotide-subject-coverage-threshold"
  • --diamond-options
  • --evalue
  • --translated-identity-threshold
  • --translated-query-coverage-threshold
  • --translated-subject-coverage-threshold
  • --gap-fill
  • --minpath
  • --pathways
  • --xipe
  • --annotation-gene-index
  • --output-format
  • --output-max-decimals
  • --remove-column-description-output
  • --remove-stratified-output

Additional arguments can be specified under the tool_args argument.