ForEachFile#
Add to module run order:
#BioModule biolockj.module.diy.ForEachFile
Description#
Like GenMod, but done for each file in a previous module's output dir.
Properties#
Properties are the name=value pairs in the configuration file.
ForEachFile 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 |
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: 1.0.0
This is an extention of the GenMod module.
The given script is run for each file in the previous modules output dir. If there is no previous module, then the input files are used.The user script is run using a command:
[launcher] <script> <file path> [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:
ForEachFile.imageOwner
ForEachFile.imageName
ForEachFile.imageTag
Citation#
Module developed by Ivory Blakley