KrakenClassifier#
Add to module run order:
#BioModule biolockj.module.classifier.wgs.KrakenClassifier
Description#
Classify WGS samples with KRAKEN.
Properties#
Properties are the name=value pairs in the configuration file.
KrakenClassifier properties:#
| Property | Description |
|---|---|
| exe.kraken | executable Path for the "kraken" executable; if not supplied, any script that needs the kraken command will assume it is on the PATH. default: null |
| kraken.db | file path file path to Kraken kmer database directory default: null |
| kraken.krakenParams | list additional parameters to use with kraken default: --only-classified-output, --preload |
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
Classify WGS samples with KRAKEN.
If running in docker, the default docker container contains a kmer database which will be used if no database is supplied through the kraken.db property.
Adds modules#
pre-requisite modules
none found
post-requisite modules
biolockj.module.implicit.parser.wgs.KrakenParser
Docker#
If running in docker, this module will run in a docker container from this image:
biolockjdevteam/kraken_classifier:v1.3.18
This can be modified using the following properties:
KrakenClassifier.imageOwner
KrakenClassifier.imageName
KrakenClassifier.imageTag
Citation#
Wood DE, Salzberg SL: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 2014, 15:R46.