GenomeAssembly#
Add to module run order:
#BioModule biolockj.module.assembly.GenomeAssembly
Description#
Assemble WGS sequences with MetaSPAdes, bin contigs with Metabat2 and check quality with checkM.
Properties#
Properties are the name=value pairs in the configuration file.
GenomeAssembly properties:#
none
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/genome_assembly:v1.2.0
This can be modified using the following properties:
GenomeAssembly.imageOwner
GenomeAssembly.imageName
GenomeAssembly.imageTag
Citation#
checkM database
https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
HMMER
http://eddylab.org/software/hmmer/hmmer.tar.gz
MASH
https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
Metabat2
https://bitbucket.org/berkeleylab/metabat/downloads/metabat-static-binary-linux-x64_v2.12.1.tar.gz
MetaSPAdes
https://github.com/ablab/spades/releases/download/v3.13.0/SPAdes-3.13.0-Linux.tar.gz
PPLACER
https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip
PRODIGAL
https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux
Module developed by Shan Sun
BioLockJ v1.4.2