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#BioModule com.github.fodorlab.fastqc.Simple_FastQC
Run FastQC on sequence files.
Properties are the name=value pairs in the configuration file.
| Property | Description |
|---|---|
| fastqc.param | string Parameters used with FastQC; not validated in any way. Avoid using '-o/--outdir', this is automatically set to the module's output folder. default: null |
| 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 |
version: 0.0.0 none
pre-requisite modules
none found
post-requisite modules
none found
If running in docker, this module will run in a docker container from this image:
biocontainers/fastqc:v0.11.9_cv8
This can be modified using the following properties:
Simple_FastQC.imageOwner
Simple_FastQC.imageName
Simple_FastQC.imageTag
Module developed by Ivory Blakley to facilitate using FastQC with BioLockJ.
FastQC is produced by Babraham Bioinformatics