ForEachSample#
Add to module run order:
#BioModule biolockj.module.diy.ForEachSample
Description#
Like GenMod, but done for each sample listed in the metadata.
Properties#
Properties are the name=value pairs in the configuration file.
ForEachSample properties:#
| Property | Description |
|---|---|
| genMod.codeLine | string A line of code to create a one-line script. This is mutually exclusive with genMod.scriptPath. This is the preferred option for particularly simple scripts. This code will be executed using whatever system is specified by genMod.launcher. default: null |
| genMod.launcher | string Define executable language command if it is not included in your $PATH default: null |
| genMod.param | string parameters to pass to the user's script default: null |
| genMod.resources | list of file paths path to one or more files to be copied to the module resource folder. default: null |
| genMod.scriptPath | file path path to user script default: null |
| metadata.filePath | file path If absolute file path, use file as metadata. If directory path, must find exactly 1 file within, to use as metadata. -> The row names of the metadata are used as the looping mechanism for this module. 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 |
| metadata.filePath | file path If absolute file path, use file as metadata. If directory path, must find exactly 1 file within, to use as metadata. -> The row names of the metadata are used as the looping mechanism for this module. 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: 1.0.0
This is an extention of the GenMod module.
For the purpose of this module, a sample is defined as a row of the metadata file.The user script is run using a command:
[launcher] <script> <sample> [params]
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/blj_basic:v1.3.18
This can be modified using the following properties:
ForEachSample.imageOwner
ForEachSample.imageName
ForEachSample.imageTag
Citation#
Module developed by Ivory Blakley