Examples with CobaltMigrationCommand com.hartwig.pipeline.tertiary.cobalt.CobaltMigrationCommand used on opensource projects

Example 1 with CobaltMigrationCommand

use of com.hartwig.pipeline.tertiary.cobalt.CobaltMigrationCommand in project pipeline5 by hartwigmedical.

the class CobaltMigration method execute.

@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket runtimeBucket, final BashStartupScript commands, final RuntimeFiles executionFlags) {
    // Inputs
    final String set = inputs.get("set").inputValue();
    final String tumorSampleName = inputs.get("tumor_sample").inputValue();
    final String referenceSampleName = inputs.get("ref_sample").inputValue();
    final GoogleStorageLocation remoteInputDirectory = cobaltArchiveDirectoryInput(set);
    // Download old files
    commands.addCommand(() -> copyInputCommand(remoteInputDirectory));
    final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V37);
    commands.addCommand(() -> new CobaltMigrationCommand(resourceFiles, referenceSampleName, tumorSampleName).asBash());
    // Store output
    final GoogleStorageLocation archiveStorageLocation = cobaltArchiveDirectoryOutput(set);
    commands.addCommand(new CopyLogToOutput(executionFlags.log(), "run.log"));
    commands.addCommand(new OutputUpload(archiveStorageLocation));
    return VirtualMachineJobDefinition.cobalt(commands, ResultsDirectory.defaultDirectory());
}