use of com.hartwig.pipeline.execution.vm.unix.ExportPathCommand in project pipeline5 by hartwigmedical.
the class GridssRerun method execute.
@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket runtimeBucket, final BashStartupScript commands, final RuntimeFiles executionFlags) {
// Inputs
final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V37);
final String set = inputs.get("set").inputValue();
final String tumorSampleName = inputs.get("tumor_sample").inputValue();
final String referenceSampleName = inputs.get("reference_sample").inputValue();
final InputFileDescriptor remoteTumorFile = inputs.get("tumor_cram");
final InputFileDescriptor remoteReferenceFile = inputs.get("ref_cram");
final InputFileDescriptor runData = inputs.get();
final RemoteLocationsApi locationsApi = new RemoteLocationsApi(runData.billedProject(), tumorSampleName);
InputDownload tumorBamDownload = new InputDownload(locationsApi.getTumorAlignment());
InputDownload tumorBamIndexDownload = new InputDownload(locationsApi.getTumorAlignmentIndex());
InputDownload referenceBamDownload = new InputDownload(locationsApi.getReferenceAlignment());
InputDownload referenceBamIndexDownload = new InputDownload(locationsApi.getReferenceAlignmentIndex());
final InputFileDescriptor remoteTumorIndex = remoteTumorFile.index();
final InputFileDescriptor remoteReferenceIndex = remoteReferenceFile.index();
final String localTumorFile = localFilename(remoteTumorFile);
final String localReferenceFile = localFilename(remoteReferenceFile);
final String tumorBamPath = localTumorFile.replace("cram", "bam");
final String refBamPath = localReferenceFile.replace("cram", "bam");
Driver driver = new Driver(resourceFiles, VmDirectories.outputFile(tumorSampleName + ".assembly.bam")).tumorSample(tumorSampleName, tumorBamPath).referenceSample(referenceSampleName, refBamPath);
GridssAnnotation viralAnnotation = new GridssAnnotation(resourceFiles, false);
SubStageInputOutput unfilteredVcfOutput = driver.andThen(viralAnnotation).apply(SubStageInputOutput.empty(tumorSampleName));
final OutputFile unfilteredVcf = unfilteredVcfOutput.outputFile();
final OutputFile unfilteredVcfIndex = unfilteredVcf.index(".tbi");
final GoogleStorageLocation unfilteredVcfRemoteLocation = remoteUnfilteredVcfArchivePath(set, tumorSampleName);
final GoogleStorageLocation unfilteredVcfIndexRemoteLocation = index(unfilteredVcfRemoteLocation, ".tbi");
// COMMANDS
commands.addCommand(new ExportPathCommand(new BwaCommand()));
commands.addCommand(new ExportPathCommand(new SamtoolsCommand()));
commands.addCommand(() -> remoteTumorFile.toCommandForm(localTumorFile));
commands.addCommand(() -> remoteTumorIndex.toCommandForm(localFilename(remoteTumorIndex)));
commands.addCommand(() -> remoteReferenceFile.toCommandForm(localReferenceFile));
commands.addCommand(() -> remoteReferenceIndex.toCommandForm(localFilename(remoteReferenceIndex)));
if (!localTumorFile.equals(tumorBamPath)) {
commands.addCommands(cramToBam(localTumorFile));
}
if (!localReferenceFile.equals(refBamPath)) {
commands.addCommands(cramToBam(localReferenceFile));
}
commands.addCommands(unfilteredVcfOutput.bash());
commands.addCommand(() -> unfilteredVcf.copyToRemoteLocation(unfilteredVcfRemoteLocation));
commands.addCommand(() -> unfilteredVcfIndex.copyToRemoteLocation(unfilteredVcfIndexRemoteLocation));
commands.addCommand(new OutputUpload(GoogleStorageLocation.of(runtimeBucket.name(), "gridss"), executionFlags));
return VirtualMachineJobDefinition.structuralCalling(commands, ResultsDirectory.defaultDirectory());
}
use of com.hartwig.pipeline.execution.vm.unix.ExportPathCommand in project pipeline5 by hartwigmedical.
the class Gridss method gridssCommands.
private List<BashCommand> gridssCommands(final Driver driver, final String sampleName) {
SubStageInputOutput unfilteredVcfOutput = driver.andThen(new RepeatMasker()).andThen(new GridssAnnotation(resourceFiles, false)).apply(SubStageInputOutput.empty(sampleName));
unfilteredVcf = unfilteredVcfOutput.outputFile().path();
List<BashCommand> commands = new ArrayList<>();
commands.add(new ExportPathCommand(new BwaCommand()));
commands.add(new ExportPathCommand(new SamtoolsCommand()));
commands.addAll(unfilteredVcfOutput.bash());
return commands;
}
use of com.hartwig.pipeline.execution.vm.unix.ExportPathCommand in project pipeline5 by hartwigmedical.
the class GridssBackport method execute.
@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket runtimeBucket, final BashStartupScript startupScript, final RuntimeFiles executionFlags) {
final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V37);
final InputFileDescriptor template = inputs.get("set");
final String set = inputs.get("set").inputValue();
final String sample = inputs.get("tumor_sample").inputValue();
final String bamFile = String.format("gs://hmf-gridss/assembly/%s/%s.assembly.bam.sv.bam", set, sample);
final String vcfFile = String.format("gs://hmf-gridss/original/%s/%s.gridss.unfiltered.vcf.gz", set, sample);
final InputFileDescriptor inputBam = ImmutableInputFileDescriptor.builder().from(template).inputValue(bamFile).build();
final InputFileDescriptor inputBamIndex = inputBam.index();
final InputFileDescriptor inputVcf = ImmutableInputFileDescriptor.builder().from(template).inputValue(vcfFile).build();
final InputFileDescriptor inputVcfIndex = inputVcf.index();
// 1. Set up paths
startupScript.addCommand(new ExportPathCommand(new BwaCommand()));
startupScript.addCommand(new ExportPathCommand(new SamtoolsCommand()));
// 2. Download input files
startupScript.addCommand(inputBam::copyToLocalDestinationCommand);
startupScript.addCommand(inputBamIndex::copyToLocalDestinationCommand);
startupScript.addCommand(inputVcf::copyToLocalDestinationCommand);
startupScript.addCommand(inputVcfIndex::copyToLocalDestinationCommand);
// 3. Get sample names
startupScript.addCommand(() -> format("sampleNames=$(zgrep -m1 CHROM %s)", inputVcf.localDestination()));
startupScript.addCommand(() -> "sample0=$(echo $sampleNames | cut -d \" \" -f 10)");
startupScript.addCommand(() -> "sample1=$(echo $sampleNames | cut -d \" \" -f 11)");
// 4. Create empty bams (and their working directories)
final String emptyBam1 = String.format("%s/${%s}", VmDirectories.INPUT, "sample0");
final String emptyBam1Working = workingDir(emptyBam1) + ".sv.bam";
final String emptyBam2 = String.format("%s/${%s}", VmDirectories.INPUT, "sample1");
final String emptyBam2Working = workingDir(emptyBam2) + ".sv.bam";
startupScript.addCommand(() -> format("samtools view -H %s | samtools view -o %s", inputBam.localDestination(), emptyBam1));
startupScript.addCommand(() -> format("samtools view -H %s | samtools view -o %s", inputBam.localDestination(), emptyBam2));
startupScript.addCommand(() -> format("mkdir -p %s", dirname(emptyBam1Working)));
startupScript.addCommand(() -> format("mkdir -p %s", dirname(emptyBam2Working)));
startupScript.addCommand(() -> format("cp %s %s", emptyBam1, emptyBam1Working));
startupScript.addCommand(() -> format("cp %s %s", emptyBam2, emptyBam2Working));
// 5. SoftClipsToSplitReads
final String newAssemblyBam = workingDir(inputBam.localDestination());
startupScript.addCommand(() -> format("mkdir -p %s", dirname(newAssemblyBam)));
startupScript.addCommand(new SoftClipsToSplitReads(inputBam.localDestination(), resourceFiles.refGenomeFile(), newAssemblyBam));
// 6. Allocate Evidence
final OutputFile newRawVcf = OutputFile.of(sample, "gridss_" + Versions.GRIDSS.replace(".", "_") + ".raw", FileTypes.GZIPPED_VCF);
startupScript.addCommand(new AllocateEvidence(emptyBam1, emptyBam2, newAssemblyBam, inputVcf.localDestination(), newRawVcf.path(), resourceFiles.refGenomeFile(), resourceFiles.gridssPropertiesFile()));
// 7. Gridss Annotation
final SubStageInputOutput annotation = new GridssAnnotation(resourceFiles, true).apply(SubStageInputOutput.of(sample, newRawVcf, Collections.emptyList()));
startupScript.addCommands(annotation.bash());
// 8. Archive targeted output
final OutputFile unfilteredVcf = annotation.outputFile();
final OutputFile unfilteredVcfIndex = unfilteredVcf.index(".tbi");
final GoogleStorageLocation unfilteredVcfRemoteLocation = remoteUnfilteredVcfArchivePath(set, sample);
final GoogleStorageLocation unfilteredVcfIndexRemoteLocation = index(unfilteredVcfRemoteLocation, ".tbi");
startupScript.addCommand(() -> unfilteredVcf.copyToRemoteLocation(unfilteredVcfRemoteLocation));
startupScript.addCommand(() -> unfilteredVcfIndex.copyToRemoteLocation(unfilteredVcfIndexRemoteLocation));
// 9. Upload all output
startupScript.addCommand(new OutputUpload(GoogleStorageLocation.of(runtimeBucket.name(), "gridss"), executionFlags));
return VirtualMachineJobDefinition.structuralCalling(startupScript, ResultsDirectory.defaultDirectory());
}
use of com.hartwig.pipeline.execution.vm.unix.ExportPathCommand in project pipeline5 by hartwigmedical.
the class GridssPanelTumor method execute.
@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket runtimeBucket, final BashStartupScript commands, final RuntimeFiles executionFlags) {
InputFileDescriptor descriptor = inputs.get();
final String sampleId = descriptor.inputValue();
// download tumor BAM
final String tumorBam = String.format("%s.non_umi_dedup.bam", sampleId);
final String tumorBamIndex = String.format("%s.non_umi_dedup.bam.bai", sampleId);
commands.addCommand(() -> format("gsutil -u hmf-crunch cp %s/%s* %s", PANEL_BAM_BUCKET, tumorBam, VmDirectories.INPUT));
// Inputs
final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V38);
commands.addCommand(new ExportPathCommand(new BwaCommand()));
commands.addCommand(new ExportPathCommand(new SamtoolsCommand()));
// run Gridss variant calling
final String gridssToolDir = String.format("%s/%s/%s", VmDirectories.TOOLS, GRIDSS_TOOL_DIR, Versions.GRIDSS);
final String gridssJar = String.format("%s/gridss.jar", gridssToolDir);
commands.addCommand(() -> format("chmod a+x %s", gridssJar));
final String gridssOutputVcf = String.format("%s/%s.gridss.driver.vcf.gz", VmDirectories.OUTPUT, sampleId);
final StringJoiner gridssArgs = new StringJoiner(" ");
gridssArgs.add(String.format("--output %s", gridssOutputVcf));
gridssArgs.add(String.format("--assembly %s/%s.gridss.assembly.vcf.gz", VmDirectories.OUTPUT, sampleId));
gridssArgs.add(String.format("--workingdir %s/gridss_working", VmDirectories.OUTPUT));
gridssArgs.add(String.format("--reference %s", resourceFiles.refGenomeFile()));
gridssArgs.add(String.format("--jar %s", gridssJar));
gridssArgs.add(String.format("--blacklist %s", resourceFiles.gridssBlacklistBed()));
gridssArgs.add(String.format("--configuration %s", resourceFiles.gridssPropertiesFile()));
gridssArgs.add(String.format("--labels %s", sampleId));
gridssArgs.add(String.format("--threads %s", Bash.allCpus()));
gridssArgs.add("--jvmheap 31G");
gridssArgs.add("--externalaligner");
gridssArgs.add(String.format("%s/%s", VmDirectories.INPUT, tumorBam));
// nohup /data/tools/gridss/2.13.2/gridss
// --output ./FR16648841.gridss.driver.vcf.gz
// --assembly ./FR16648841.assembly.bam
// --workingdir ./gridss_working
// --reference /data/resources/bucket/reference_genome/38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
// --jar /data/tools/gridss/2.13.2/gridss.jar
// --blacklist /data/resources/public/gridss_repeatmasker_db/38/ENCFF001TDO.38.bed
// --configuration /data/resources/public/gridss_config/gridss.properties
// --labels FR16648841
// --jvmheap 31G
// --threads 4
// --externalaligner
// FR16648841.chr21_slice1.bam &
commands.addCommand(() -> format("%s/gridss %s", gridssToolDir, gridssArgs.toString()));
// VersionedToolCommand with bash:
// /opt/tools/gridss/2.13.2/gridss_annotate_vcf_repeatmasker
// --output /data/output/CPCT12345678T.gridss.repeatmasker.vcf.gz
// --jar /opt/tools/gridss/2.13.2/gridss.jar
// -w /data/output
// --rm /opt/tools/repeatmasker/4.1.1/RepeatMasker
// /data/output/CPCT12345678T.gridss.driver.vcf.gz
// final String gridssToolDir = String.format("%s/%s/%s/", VmDirectories.TOOLS, GRIDSS_TOOL_DIR, Versions.GRIDSS);
final String rmOutputVcf = String.format("%s/%s.gridss.repeatmasker.vcf.gz", VmDirectories.OUTPUT, sampleId);
final StringJoiner rmArgs = new StringJoiner(" ");
rmArgs.add(String.format("--output %s", rmOutputVcf));
rmArgs.add(String.format("--jar %s", gridssJar));
rmArgs.add(String.format("-w %s", VmDirectories.OUTPUT));
rmArgs.add(String.format("--rm %s", REPEAT_MASKER_TOOL));
rmArgs.add(gridssOutputVcf);
commands.addCommand(() -> format("%s/gridss_annotate_vcf_repeatmasker %s", gridssToolDir, rmArgs.toString()));
// AnnotateInsertedSequence with bash:
// java -Xmx8G -Dsamjdk.create_index=true
// -Dsamjdk.use_async_io_read_samtools=true -Dsamjdk.use_async_io_write_samtools=true
// -Dsamjdk.use_async_io_write_tribble=true -Dsamjdk.buffer_size=4194304
// -cp /opt/tools/gridss/2.13.2/gridss.jar gridss.AnnotateInsertedSequence
// REFERENCE_SEQUENCE=/opt/resources/virus_reference_genome/human_virus.fa
// INPUT=/data/output/CPCT12345678T.gridss.repeatmasker.vcf.gz
// OUTPUT=/data/output/CPCT12345678T.gridss.unfiltered.vcf.gz
// ALIGNMENT=APPEND WORKER_THREADS=12
final String finalOutputVcf = String.format("%s/%s.gridss.unfiltered.vcf.gz", VmDirectories.OUTPUT, sampleId);
final StringJoiner vmArgs = new StringJoiner(" ");
GridssCommand.JVM_ARGUMENTS.forEach(x -> vmArgs.add(x));
final StringJoiner annInsSeqArgs = new StringJoiner(" ");
annInsSeqArgs.add(String.format("REFERENCE_SEQUENCE=%s", resourceFiles.gridssVirusRefGenomeFile()));
annInsSeqArgs.add(String.format("INPUT=%s", rmOutputVcf));
annInsSeqArgs.add(String.format("OUTPUT=%s", finalOutputVcf));
annInsSeqArgs.add(String.format("ALIGNMENT=APPEND WORKER_THREADS=%s", Bash.allCpus()));
commands.addCommand(() -> format("java -Xmx8G -Dsamjdk.create_index=true %s -cp %s gridss.AnnotateInsertedSequence %s", vmArgs.toString(), gridssJar, annInsSeqArgs.toString()));
commands.addCommand(new OutputUpload(GoogleStorageLocation.of(runtimeBucket.name(), "gridss"), executionFlags));
return VirtualMachineJobDefinition.structuralCalling(commands, ResultsDirectory.defaultDirectory());
}
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