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rerunningScripts.md

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Dependency Installation

To rerun these scripts locally, their dependencies must be installed into a conda environment which will be used for execution. Using this command from the ScaleBio/ScaleTagToolkit/ an ArchR env named scalereport will be created:

conda env create --quiet -f envs/scalereport.conda.yml && conda clean -a --yes

Once created this environment can be activated:
conda activate scalereport

Rerunning scripts

The scripts run in workflow's cellFilter and report pipeline processes are bin/atacQcFilter.py and bin/generateReport.py respectively. The following steps can be used to rerun either script:

  1. Navigate to directory containing the pipeline output folder you wish to rerun the script for (the directory specified as outDir in your params)
  2. From this directory invoke the script as an executable by providing the absolute path to the script; specifying the help flag to learn more about the arguments to pass:
    /absolutePathToScaleBioRepo/ScaleTagToolkit/bin/<atacQcFilter.py|generateReport.py> --help
  3. Using the argument descriptions provided by passing the --help flag, invoke the script specifying -results as the pipeline output directory (outDir) you wish to rerun the script for.

Pipeline output for the QC and html reporting processes are found in <outDir>/QC and <ourDir>/reports respectively. To prevent overwriting the pipeline generated output an additional argument writeDir can be specified when running atacQcFilter.py:

  • Creating new QC output and saving it to <outDir>/QC/test:
    /absolutePathToScaleBioRepo/ScaleTagToolkit/bin/atacQcFilter.py --results <outDir> --sample <sampleName> --writeDir test

This newly created QC output can then be used to create an HTML report by specifying the same argument for qcDir. The new report will be written to a child directory of <outDir>/reports with the same name:

  • Creating a new HTML report based on the QC output in <outDir>/QC/test:
    /absolutePathToScaleBioRepo/ScaleTagToolkit/bin/generateReport.py --results <outDir> --sample <sampleName> --qcDir test --libStruct

Interpreting newly generated output:

For information on what the generated outputs represent and how they are used review our output documentation