use of com.hartwig.pipeline.execution.vm.unix.MvCommand in project pipeline5 by hartwigmedical.
the class GermlineCaller method commands.
@Override
public List<BashCommand> commands(final SingleSampleRunMetadata metadata) {
String referenceFasta = resourceFiles.refGenomeFile();
SubStageInputOutput callerOutput = new GatkGermlineCaller(bamDownload.getLocalTargetPath(), referenceFasta).andThen(new GenotypeGVCFs(referenceFasta)).apply(SubStageInputOutput.empty(metadata.sampleName()));
SubStageInputOutput snpFilterOutput = new SelectVariants("snp", Lists.newArrayList("SNP", "NO_VARIATION"), referenceFasta).andThen(new VariantFiltration("snp", SNP_FILTER_EXPRESSION, referenceFasta)).apply(callerOutput);
SubStageInputOutput indelFilterOutput = new SelectVariants("indels", Lists.newArrayList("INDEL", "MIXED"), referenceFasta).andThen(new VariantFiltration("indels", INDEL_FILTER_EXPRESSION, referenceFasta)).apply(SubStageInputOutput.of(metadata.sampleName(), callerOutput.outputFile(), Collections.emptyList()));
SubStageInputOutput combinedFilters = snpFilterOutput.combine(indelFilterOutput);
SubStageInputOutput finalOutput = new CombineFilteredVariants(indelFilterOutput.outputFile().path(), referenceFasta).andThen(new GermlineZipIndex()).apply(combinedFilters);
return ImmutableList.<BashCommand>builder().addAll(finalOutput.bash()).add(new MvCommand(finalOutput.outputFile().path(), outputFile.path())).add(new MvCommand(finalOutput.outputFile().path() + ".tbi", outputFile.path() + ".tbi")).build();
}
use of com.hartwig.pipeline.execution.vm.unix.MvCommand in project pipeline5 by hartwigmedical.
the class GermlineCaller method germlineCallerCommands.
public List<BashCommand> germlineCallerCommands(final SingleSampleRunMetadata metadata) {
String referenceFasta = resourceFiles.refGenomeFile();
SubStageInputOutput callerOutput = new GatkGermlineCaller(bamDownload.getLocalTargetPath(), referenceFasta).andThen(new GenotypeGVCFs(referenceFasta)).apply(SubStageInputOutput.empty(metadata.sampleName()));
SubStageInputOutput snpFilterOutput = new SelectVariants("snp", Lists.newArrayList("SNP", "NO_VARIATION"), referenceFasta).andThen(new VariantFiltration("snp", SNP_FILTER_EXPRESSION, referenceFasta)).apply(callerOutput);
SubStageInputOutput indelFilterOutput = new SelectVariants("indels", Lists.newArrayList("INDEL", "MIXED"), referenceFasta).andThen(new VariantFiltration("indels", INDEL_FILTER_EXPRESSION, referenceFasta)).apply(SubStageInputOutput.of(metadata.sampleName(), callerOutput.outputFile(), Collections.emptyList()));
SubStageInputOutput combinedFilters = snpFilterOutput.combine(indelFilterOutput);
SubStageInputOutput finalOutput = new CombineFilteredVariants(indelFilterOutput.outputFile().path(), referenceFasta).andThen(new GermlineZipIndex()).apply(combinedFilters);
return ImmutableList.<BashCommand>builder().addAll(finalOutput.bash()).add(new MvCommand(finalOutput.outputFile().path(), outputFile.path())).add(new MvCommand(finalOutput.outputFile().path() + ".tbi", outputFile.path() + ".tbi")).build();
}
use of com.hartwig.pipeline.execution.vm.unix.MvCommand in project pipeline5 by hartwigmedical.
the class SamtoolsBamToCram method execute.
@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket bucket, final BashStartupScript startupScript, final RuntimeFiles executionFlags) {
InputFileDescriptor input = inputs.get();
String outputFile = VmDirectories.outputFile(new File(input.inputValue()).getName().replaceAll("\\.bam$", ".cram"));
String localInput = format("%s/%s", VmDirectories.INPUT, new File(input.inputValue()).getName());
startupScript.addCommand(() -> input.toCommandForm(localInput));
startupScript.addCommands(new CramAndValidateCommands(localInput, outputFile, new RefGenome37ResourceFiles()).commands());
startupScript.addCommand(new MvCommand("/data/output/*.bam", "/data/tmp"));
startupScript.addCommand(new MvCommand("/data/output/*.bam.flagstat", "/data/tmp"));
startupScript.addCommand(new OutputUpload(GoogleStorageLocation.of(bucket.name(), "samtools"), executionFlags));
return VirtualMachineJobDefinition.builder().name("samtoolscram").startupCommand(startupScript).namespacedResults(ResultsDirectory.defaultDirectory()).workingDiskSpaceGb(650).performanceProfile(VirtualMachinePerformanceProfile.custom(6, 6)).build();
}
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