QiimeOpenRefClassifier#
Add to module run order:
#BioModule biolockj.module.classifier.r16s.QiimeOpenRefClassifier
Description#
Run the QIIME pick_open_reference_otus.py script on all fasta sequence files
Properties#
Properties are the name=value
pairs in the configuration file.
QiimeOpenRefClassifier properties:#
Property | Description |
---|---|
exe.vsearch | executable Path for the "vsearch" executable; if not supplied, any script that needs the vsearch command will assume it is on the PATH. default: null |
qiime.params | list Parameters for qiime default: null |
qiime.pynastAlignDB | file path path to define ~/.qiime_config pynast_template_alignment_fp default: null |
qiime.refSeqDB | file path path to define ~/.qiime_config pick_otus_reference_seqs_fp and assign_taxonomy_reference_seqs_fp default: null |
qiime.removeChimeras | boolean if vsearch is needed for chimera removal default: Y |
qiime.taxaDB | file path path to define ~/.qiime_config assign_taxonomy_id_to_taxonomy_fp default: null |
qiime.vsearchParams | list Parameters for vsearch 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 |
pipeline.defaultFastaConverter | string Java class name for default module used to convert files into fasta format default: biolockj.module.seq.AwkFastaConverter |
pipeline.defaultSeqMerger | string Java class name for default module used combined paired read files default: biolockj.module.seq.PearMergeReads |
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 This module runs the QIIME pick_open_reference_otus.py script on all fasta sequence files in a single script since clusters not identified in the reference database are assigned by a clustering algorithm. Additional parameters for this script are set using exe.classifierParams. If qiime.removeChimeras = "Y", vsearch is used to find chimeric sequences in the output and the QIIME script filter_otus_from_otu_table.py is run to remove them from ./output/otu_table.biom. Inherits from QiimeClassifier.
Adds modules#
pre-requisite modules
pipeline-dependent
post-requisite modules
biolockj.module.implicit.qiime.QiimeClassifier
biolockj.module.implicit.parser.r16s.QiimeParser
Docker#
If running in docker, this module will run in a docker container from this image:
biolockjdevteam/qimme_classifier:v1.1
This can be modified using the following properties:
QiimeOpenRefClassifier.imageOwner
QiimeOpenRefClassifier.imageName
QiimeOpenRefClassifier.imageTag
Citation#
QIIME allows analysis of high-throughput community sequencing data
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303
(needs further citation)
http://www.wernerlab.org/software/macqiime/citations