PearMergeReads#
Add to module run order:
#BioModule biolockj.module.seq.PearMergeReads
Description#
Run pear, the Paired-End reAd mergeR
Properties#
Properties are the name=value
pairs in the configuration file.
PearMergeReads properties:#
Property | Description |
---|---|
exe.pear | executable Path for the "pear" executable; if not supplied, any script that needs the pear command will assume it is on the PATH. default: null |
pearMergeReads.pearParams | string optionally pass additional parameters to pear. 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 |
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 none
Adds modules#
pre-requisite modules
none found
post-requisite modules
none found
Docker#
If running in docker, this module will run in a docker container from this image:
biolockjdevteam/pear:v1.2.9
This can be modified using the following properties:
PearMergeReads.imageOwner
PearMergeReads.imageName
PearMergeReads.imageTag
Citation#
Jiajie Zhang, Kassian Kobert, Tomáš Flouri, Alexandros Stamatakis, PEAR: a fast and accurate Illumina Paired-End reAd mergeR, Bioinformatics, Volume 30, Issue 5, 1 March 2014, Pages 614–620, https://doi.org/10.1093/bioinformatics/btt593
https://cme.h-its.org/exelixis/web/software/pear/doc.html
Module developed by Mike Sioda