QiimeClosedRefClassifier#
Add to module run order:
#BioModule biolockj.module.classifier.r16s.QiimeClosedRefClassifier
Description#
Pick OTUs using a closed reference database and construct an OTU table via the QIIME script pick_closed_reference_otus.py
Properties#
Properties are the name=value
pairs in the configuration file.
QiimeClosedRefClassifier 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 |
exe.awk | executable Path for the "awk" executable; if not supplied, any script that needs the awk command will assume it is on the PATH. 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 picks OTUs using a closed reference database and constructs an OTU table via the QIIME script pick_closed_reference_otus.py. Taxonomy is assigned using a pre-defined taxonomy map of reference sequence OTU to taxonomy. This is the fastest OTU picking method since samples can be processed in parallel batches. Before the QIIME script is run, batches are prepared in the temp directory, with each batch directory containing a fasta directory with script.batchSize fasta files and a QIIME mapping file, created with awk, called batchMapping.tsv for the batch of samples. 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:
QiimeClosedRefClassifier.imageOwner
QiimeClosedRefClassifier.imageName
QiimeClosedRefClassifier.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