Examples with CopyLogToOutput com.hartwig.pipeline.execution.vm.CopyLogToOutput used on opensource projects

Example 1 with CopyLogToOutput

use of com.hartwig.pipeline.execution.vm.CopyLogToOutput in project pipeline5 by hartwigmedical.

the class AmberRerunTumorOnly 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 InputFileDescriptor remoteTumorFile = inputs.get("tumor_cram");
    final InputFileDescriptor remoteTumorIndex = remoteTumorFile.index();
    final String localTumorFile = localFilename(remoteTumorFile);
    // Download tumor
    commands.addCommand(() -> remoteTumorFile.toCommandForm(localTumorFile));
    commands.addCommand(() -> remoteTumorIndex.toCommandForm(localFilename(remoteTumorIndex)));
    final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V37);
    commands.addCommand(() -> AmberCommandBuilder.newBuilder(resourceFiles).tumor(tumorSampleName, localTumorFile).build().asBash());
    // Store output
    final GoogleStorageLocation archiveStorageLocation = amberArchiveDirectory(set);
    commands.addCommand(new CopyLogToOutput(executionFlags.log(), "run.log"));
    commands.addCommand(new OutputUpload(archiveStorageLocation));
    return VirtualMachineJobDefinition.amber(commands, ResultsDirectory.defaultDirectory());
}

Example 2 with CopyLogToOutput

use of com.hartwig.pipeline.execution.vm.CopyLogToOutput 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());
}

Example 3 with CopyLogToOutput

use of com.hartwig.pipeline.execution.vm.CopyLogToOutput in project pipeline5 by hartwigmedical.

the class CobaltRerun 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 InputFileDescriptor remoteTumorFile = inputs.get("tumor_cram");
    final InputFileDescriptor remoteReferenceFile = inputs.get("ref_cram");
    final InputFileDescriptor remoteTumorIndex = remoteTumorFile.index();
    final InputFileDescriptor remoteReferenceIndex = remoteReferenceFile.index();
    final String localTumorFile = localFilename(remoteTumorFile);
    final String localReferenceFile = localFilename(remoteReferenceFile);
    // Download tumor
    commands.addCommand(() -> remoteTumorFile.toCommandForm(localTumorFile));
    commands.addCommand(() -> remoteTumorIndex.toCommandForm(localFilename(remoteTumorIndex)));
    // Download normal
    commands.addCommand(() -> remoteReferenceFile.toCommandForm(localReferenceFile));
    commands.addCommand(() -> remoteReferenceIndex.toCommandForm(localFilename(remoteReferenceIndex)));
    final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V37);
    commands.addCommand(() -> CobaltCommandBuilder.newBuilder(resourceFiles).reference(referenceSampleName, localReferenceFile).tumor(tumorSampleName, localTumorFile).build().asBash());
    // Store output
    final GoogleStorageLocation archiveStorageLocation = cobaltArchiveDirectory(set);
    commands.addCommand(new CopyLogToOutput(executionFlags.log(), "run.log"));
    commands.addCommand(new OutputUpload(archiveStorageLocation));
    return VirtualMachineJobDefinition.amber(commands, ResultsDirectory.defaultDirectory());
}

Example 4 with CopyLogToOutput

use of com.hartwig.pipeline.execution.vm.CopyLogToOutput in project pipeline5 by hartwigmedical.

the class CobaltTumorOnlyRerun 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 InputFileDescriptor remoteTumorFile = inputs.get("tumor_cram");
    final InputFileDescriptor remoteTumorIndex = remoteTumorFile.index();
    final String localTumorFile = localFilename(remoteTumorFile);
    // Download tumor
    commands.addCommand(() -> remoteTumorFile.toCommandForm(localTumorFile));
    commands.addCommand(() -> remoteTumorIndex.toCommandForm(localFilename(remoteTumorIndex)));
    final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V37);
    commands.addCommand(() -> CobaltCommandBuilder.newBuilder(resourceFiles).tumor(tumorSampleName, localTumorFile).build().asBash());
    // Store output
    final GoogleStorageLocation archiveStorageLocation = cobaltArchiveDirectory(set);
    commands.addCommand(new CopyLogToOutput(executionFlags.log(), "run.log"));
    commands.addCommand(new OutputUpload(archiveStorageLocation));
    return VirtualMachineJobDefinition.amber(commands, ResultsDirectory.defaultDirectory());
}

Example 5 with CopyLogToOutput

use of com.hartwig.pipeline.execution.vm.CopyLogToOutput in project pipeline5 by hartwigmedical.

the class PurpleGermline method execute.

@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket runtimeBucket, final BashStartupScript commands, final RuntimeFiles executionFlags) {
    commands.addCommands(bashCommands(inputs));
    commands.addCommand(new CopyLogToOutput(executionFlags.log(), "run.log"));
    commands.addCommand(new OutputUpload(GoogleStorageLocation.of(runtimeBucket.name(), "purple"), executionFlags));
    return VirtualMachineJobDefinition.purple(commands, ResultsDirectory.defaultDirectory());
}