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.