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