RarefySeqs#

Add to module run order:
#BioModule biolockj.module.seq.RarefySeqs

Description#

Randomly sub-sample sequences to reduce all samples to the configured maximum.

Properties#

Properties are the name=value pairs in the configuration file.

RarefySeqs properties:#

Property Description
rarefySeqs.max numeric
Randomly select this number of sequences to keep in each sample
default: null
rarefySeqs.min numeric
Discard samples with less than minimum number of sequences
default: 1

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.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 Randomly sub-sample sequences to reduce all samples to the configured maximum rarefySeqs.max. Samples with less than the minimum number of reads rarefySeqs.min are discarded.
This module will add biolockj.module.implicit.RegisterNumReads if there is not already a module to count starting reads per sample.
If the input data are paired reads, this module will add a sequence merger, based on property pipeline.defaultSeqMerger (currently: biolockj.module.seq.PearMergeReads).

Adds modules#

pre-requisite modules
pipeline-dependent
post-requisite modules
none found

Docker#

If running in docker, this module will run in a docker container from this image:

biolockjdevteam/biolockj_controller:v1.4.2

This can be modified using the following properties:
RarefySeqs.imageOwner
RarefySeqs.imageName
RarefySeqs.imageTag

Citation#

Module developed by Mike Sioda
BioLockJ v1.4.2