HUMAnN2#
Add to module run order:
#BioModule biolockj.module.classifier.wgs.Humann2Classifier
Description#
Profile the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.
Properties#
Properties are the name=value pairs in the configuration file.
HUMAnN2 properties:#
| Property | Description |
|---|---|
| exe.humann2 | executable Path for the "humann2" executable; if not supplied, any script that needs the humann2 command will assume it is on the PATH. default: null |
| humann2.humann2JoinTableParams | list The parameters to be used with humann2_join_tables default: null |
| humann2.humann2Params | list The humann2 executable params default: null |
| humann2.humann2RenormTableParams | list The parameters to use with humann2_renorm_table default: null |
| humann2.nuclDB | file path Directory containing the nucleotide database default: null |
| humann2.protDB | file path Directory containing the protein nucleotide database default: null |
General properties applicable to this module:#
| Property | Description |
|---|---|
| cluster.batchCommand | string Terminal command used to submit jobs on the cluster default: null |
| cluster.jobHeader | string Header written at top of worker scripts default: null |
| cluster.modules | list List of cluster modules to load at start of worker scripts default: null |
| cluster.prologue | string To run at the start of every script after loading cluster modules (if any) default: null |
| cluster.statusCommand | string Terminal command used to check the status of jobs on the cluster default: null |
| docker.saveContainerOnExit | boolean If Y, docker run command will NOT include the --rm flag default: null |
| docker.verifyImage | boolean In check dependencies, run a test to verify the docker image. default: null |
| script.defaultHeader | string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash |
| script.numThreads | integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8 |
| script.numWorkers | integer Set number of samples to process per script (if parallel processing) default: 1 |
| script.permissions | string Used as chmod permission parameter (ex: 774) default: 770 |
| script.timeout | integer Sets # of minutes before worker scripts times out. default: null |
Details#
version: 0.0.0 none
Adds modules#
pre-requisite modules
none found
post-requisite modules
biolockj.module.implicit.parser.wgs.Humann2Parser
Docker#
If running in docker, this module will run in a docker container from this image:
biolockjdevteam/humann2_classifier:v1.3.18
This can be modified using the following properties:
Humann2Classifier.imageOwner
Humann2Classifier.imageName
Humann2Classifier.imageTag
Citation#
Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Schwarzberg Lipson K, Knight R, Caporaso JG, Segata N, Huttenhower C.
Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods 15: 962-968 (2018).
http://huttenhower.sph.harvard.edu/humann2
BioLockJ module developed by Mike Siota