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Quick Start on Cromwell

This section walks you through the steps of running pipeline using demo data on a managed Cromwell server.

Environment Setup​

  • A running instance of a Cromwell server.

  • Install Cromshell and configure it to connect with the Cromwell server you are using. You may refer to the documentation on Cromshell README.

Build Inputs​

We provide options for building example inputs that you may use as a reference to configure a Terra workspace or Cromwell submissions (advanced) with your own data. Please refer to this page for instructions on how to build these inputs.

MELT​

Important: The example input files contain MELT inputs that are NOT public (see Requirements). These include:

  • GATKSVPipelineSingleSample.melt_docker and GATKSVPipelineBatch.melt_docker - MELT docker URI (see Docker readme)
  • GATKSVPipelineSingleSample.ref_std_melt_vcfs - Standardized MELT VCFs (GatherBatchEvidence) The input values are provided only as an example and are not publicly accessible.
  • In order to include MELT, these values must be provided by the user. MELT can be disabled by deleting these inputs and setting GATKSVPipelineBatch.use_melt to false.

Execution​

> mkdir gatksv_run && cd gatksv_run
> mkdir wdl && cd wdl
> cp $GATK_SV_ROOT/wdl/*.wdl .
> zip dep.zip *.wdl
> cd ..
> bash scripts/inputs/build_default_inputs.sh -d $GATK_SV_ROOT
> cp $GATK_SV_ROOT/inputs/build/ref_panel_1kg/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json GATKSVPipelineBatch.my_run.json
> cromshell submit wdl/GATKSVPipelineBatch.wdl GATKSVPipelineBatch.my_run.json cromwell_config.json wdl/dep.zip

where cromwell_config.json is a Cromwell workflow options file. Note users will need to re-populate batch/sample-specific parameters (e.g. BAMs and sample IDs).