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

toolchest.humann3(
    inputs,
    output_path=None,
    tool_args="",
    taxonomic_profile=None,
    mode=toolchest.tools.humann3.HUMAnN3Mode.HUMANN,
    input_pathways=None,
    output_primary_name=None,
    is_async=False,
)
toolchest$humann3(
    inputs,
    output_path = NULL,
    tool_args = "",
    is_async = FALSE
)

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 Inputs and Outputs.

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 Inputs and Outputs.

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) 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.

output_primary_name

(optional) If you're using a mode that produces an individual output file, set the name here.

tool_args

all other arguments

(optional) A string containing additional arguments to be passed to HUMAnN, formatted as if using 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 toolchest_client.tools.humann.HUMAnN3Mode – e.g. toolchest_client.tools.humann.HUMAnN3Mode.RENORM_TABLE.

Tool Versions

Toolchest supports version 3.1.1 of HUMAnN.

Databases

Toolchest currently supports the following databases for HUMAnN:

database_namedatabase_versionDescription
ChocoPhlAnN/AThe ChocoPhlAn database, provided by the Huttenhower lab. This database is required, and is not user configurable. Used via the --nucleotide-database argument.
UniRef901The 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.


Did this page help you?