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additionalInputParams.md

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Additional Input Parameter Specification

In addition to runParams.yml which contains the majority of configuration parameters, an additional .yml (qcAndArchR.yml) is used to store parameters used for Quality Control and Automated ArchR analysis.


Modifying QC and ArchR params

By default qcAndArchR.yml is specified as the yml to be parsed to access these QC and ArchR params in the nextflow.config. If you wish to modify these params the following steps are recommended:

  1. Take a look at qcAndArchR.yml for a description of each parameter
  2. Make a copy of qcAndArchR.yml to a directory of your choice:
    cp ScaleBio/ScaleTagToolkit/references/parameters/qcAndArchR.yml <pathToYmlCopy>
  3. **Modify the copy at pathToYmlCopy to suit your needs
  4. To use your newly defined .yml add:
    qcAndArchRParams: <pathToYmlCopy> in your runParams.yml (the yml being passed to -params-file argument)

**Warning all parameters specified in qcAndArchR.yml are required and must be defined in your new .yml.