Examples with SampleLocationData com.hartwig.batch.utils.SampleLocationData used on opensource projects

Example 1 with SampleLocationData

use of com.hartwig.batch.utils.SampleLocationData in project pipeline5 by hartwigmedical.

the class GripssPurpleLinx method runSample.

private void runSample(final BashStartupScript startupScript, final ResourceFiles resourceFiles, final String sampleId, final Map<String, SampleLocationData> sampleLocationsMap) {
    final SampleLocationData sampleLocations = sampleLocationsMap.containsKey(sampleId) ? sampleLocationsMap.get(sampleId) : SampleLocationData.fromRemoteLocationsApi(sampleId, new RemoteLocationsApi("hmf-crunch", sampleId));
    // download required input files
    String gridssVcf = sampleLocations.localFileRef(sampleLocations.GridssVcf);
    startupScript.addCommand(() -> sampleLocations.formDownloadRequest(sampleLocations.GridssVcf, false));
    // run Gripss
    final StringJoiner gripssArgs = new StringJoiner(" ");
    gripssArgs.add(String.format("-sample %s", sampleId));
    gripssArgs.add(String.format("-reference %s", sampleLocations.ReferenceId));
    gripssArgs.add(String.format("-ref_genome %s", resourceFiles.refGenomeFile()));
    gripssArgs.add(String.format("-known_hotspot_file %s", resourceFiles.knownFusionPairBedpe()));
    // VmDirectories.INPUT, PON_BE
    gripssArgs.add(String.format("-pon_sgl_file %s", resourceFiles.gridssBreakendPon()));
    gripssArgs.add(String.format("-pon_sv_file %s", resourceFiles.gridssBreakpointPon()));
    gripssArgs.add(String.format("-vcf %s", gridssVcf));
    gripssArgs.add(String.format("-output_dir %s", VmDirectories.OUTPUT));
    gripssArgs.add(String.format("-log_debug"));
    String gripssJar = String.format("%s/%s", VmDirectories.TOOLS, GRIPSS_JAR);
    // String gripssJar = String.format("%s/gripss/%s/gripss.jar", VmDirectories.TOOLS, Versions.GRIPSS);
    startupScript.addCommand(() -> format("java -Xmx30G -jar %s %s", gripssJar, gripssArgs.toString()));
    final String gripssUnfilteredVcf = String.format("%s/%s.gripss.vcf.gz", VmDirectories.OUTPUT, sampleId);
    final String gripssFilteredVcf = String.format("%s/%s.gripss.filtered.vcf.gz", VmDirectories.OUTPUT, sampleId);
    // Pave somatic
    final String paveSomaticVcf = String.format("%s/%s.sage.somatic.filtered.pave.vcf.gz", VmDirectories.OUTPUT, sampleId);
    String sageSomaticVcf = sampleLocations.localFileRef(sampleLocations.SageSomaticVcf);
    startupScript.addCommand(() -> sampleLocations.formDownloadRequest(sampleLocations.SageSomaticVcf, false));
    StringJoiner paveSomaticArgs = new StringJoiner(" ");
    paveSomaticArgs.add(String.format("-sample %s", sampleId));
    paveSomaticArgs.add(String.format("-vcf_file %s", sageSomaticVcf));
    paveSomaticArgs.add(String.format("-ref_genome %s", resourceFiles.refGenomeFile()));
    paveSomaticArgs.add(String.format("-driver_gene_panel %s", resourceFiles.driverGenePanel()));
    paveSomaticArgs.add(String.format("-ensembl_data_dir %s", resourceFiles.ensemblDataCache()));
    paveSomaticArgs.add(String.format("-output_dir %s", VmDirectories.OUTPUT));
    paveSomaticArgs.add(String.format("-output_vcf_file %s", paveSomaticVcf));
    // String paveJar = String.format("%s/%s", VmDirectories.TOOLS, PAVE_JAR);
    String paveJar = String.format("%s/pave/%s/pave.jar", VmDirectories.TOOLS, Versions.PAVE);
    startupScript.addCommand(() -> format("java -jar %s %s", paveJar, paveSomaticArgs.toString()));
    // Pave germline
    final String paveGermlineVcf = String.format("%s/%s.sage.germline.filtered.pave.vcf.gz", VmDirectories.OUTPUT, sampleId);
    String sageGermlineVcf = sampleLocations.localFileRef(sampleLocations.SageGermlineVcf);
    startupScript.addCommand(() -> sampleLocations.formDownloadRequest(sampleLocations.SageGermlineVcf, false));
    StringJoiner paveGermlineArgs = new StringJoiner(" ");
    paveGermlineArgs.add(String.format("-sample %s", sampleId));
    paveGermlineArgs.add(String.format("-vcf_file %s", sageGermlineVcf));
    paveGermlineArgs.add(String.format("-ref_genome %s", resourceFiles.refGenomeFile()));
    paveGermlineArgs.add(String.format("-driver_gene_panel %s", resourceFiles.driverGenePanel()));
    paveGermlineArgs.add(String.format("-ensembl_data_dir %s", resourceFiles.ensemblDataCache()));
    paveGermlineArgs.add(String.format("-output_dir %s", VmDirectories.OUTPUT));
    paveGermlineArgs.add(String.format("-output_vcf_file %s", paveGermlineVcf));
    startupScript.addCommand(() -> format("java -jar %s %s", paveJar, paveGermlineArgs.toString()));
    // Purple
    // String amberDir = sampleLocations.localFileRef(sampleLocations.Amber);
    // startupScript.addCommand(() -> sampleLocations.formDownloadRequest(sampleLocations.Amber, true));
    String amberDir = VmDirectories.INPUT;
    String amberFiles = String.format("%s/*amber*", sampleLocations.Amber);
    startupScript.addCommand(() -> sampleLocations.formDownloadRequest(amberFiles, false));
    // String cobaltDir = sampleLocations.localFileRef(sampleLocations.Cobalt);
    // startupScript.addCommand(() -> sampleLocations.formDownloadRequest(sampleLocations.Cobalt, true));
    String cobaltDir = VmDirectories.INPUT;
    String cobaltFiles = String.format("%s/*cobalt*", sampleLocations.Cobalt);
    startupScript.addCommand(() -> sampleLocations.formDownloadRequest(cobaltFiles, false));
    final StringJoiner purpleArgs = new StringJoiner(" ");
    purpleArgs.add(String.format("-tumor %s", sampleId));
    purpleArgs.add(String.format("-reference %s", sampleLocations.ReferenceId));
    purpleArgs.add(String.format("-structural_vcf %s", gripssFilteredVcf));
    purpleArgs.add(String.format("-sv_recovery_vcf %s", gripssUnfilteredVcf));
    purpleArgs.add(String.format("-somatic_vcf %s", paveSomaticVcf));
    purpleArgs.add(String.format("-germline_vcf %s", paveGermlineVcf));
    purpleArgs.add(String.format("-amber %s", amberDir));
    purpleArgs.add(String.format("-cobalt %s", cobaltDir));
    purpleArgs.add(String.format("-ref_genome %s", resourceFiles.refGenomeFile()));
    purpleArgs.add(String.format("-gc_profile %s", resourceFiles.gcProfileFile()));
    purpleArgs.add(String.format("-somatic_hotspots %s", resourceFiles.sageSomaticHotspots()));
    purpleArgs.add(String.format("-germline_hotspots %s", resourceFiles.sageGermlineHotspots()));
    purpleArgs.add(String.format("-driver_gene_panel %s", resourceFiles.driverGenePanel()));
    purpleArgs.add(String.format("-ensembl_data_dir %s", resourceFiles.ensemblDataCache()));
    purpleArgs.add(String.format("-run_drivers"));
    purpleArgs.add(String.format("-no_charts"));
    purpleArgs.add(String.format("-threads %s", Bash.allCpus()));
    purpleArgs.add(String.format("-output_dir %s", VmDirectories.OUTPUT));
    // String purpleJar = String.format("%s/%s", VmDirectories.TOOLS, PURPLE_JAR);
    String purpleJar = String.format("%s/purple/%s/purple.jar", VmDirectories.TOOLS, Versions.PURPLE);
    startupScript.addCommand(() -> format("java -jar %s %s", purpleJar, purpleArgs.toString()));
    final String purpleSvVcf = String.format("%s/%s.purple.sv.vcf.gz", VmDirectories.OUTPUT, sampleId);
    // Linx
    final StringJoiner linxArgs = new StringJoiner(" ");
    linxArgs.add(String.format("-sample %s", sampleId));
    linxArgs.add(String.format("-sv_vcf %s", purpleSvVcf));
    linxArgs.add(String.format("-purple_dir %s", VmDirectories.OUTPUT));
    linxArgs.add(String.format("-fragile_site_file %s", resourceFiles.fragileSites()));
    linxArgs.add(String.format("-line_element_file %s", resourceFiles.lineElements()));
    linxArgs.add(String.format("-ensembl_data_dir %s", resourceFiles.ensemblDataCache()));
    linxArgs.add(String.format("-check_drivers"));
    linxArgs.add(String.format("-driver_gene_panel %s", resourceFiles.driverGenePanel()));
    linxArgs.add(String.format("-check_fusions"));
    linxArgs.add(String.format("-known_fusion_file %s", resourceFiles.knownFusionData()));
    linxArgs.add(String.format("-output_dir %s", VmDirectories.OUTPUT));
    String linxJar = String.format("%s/%s", VmDirectories.TOOLS, LINX_JAR);
    // String linxJar = String.format("%s/linx/%s/linx.jar", VmDirectories.TOOLS, Versions.LINX);
    startupScript.addCommand(() -> format("java -jar %s %s", linxJar, linxArgs.toString()));
}

Example 2 with SampleLocationData

use of com.hartwig.batch.utils.SampleLocationData in project pipeline5 by hartwigmedical.

the class GripssPurpleLinx method execute.

// private static String PON_BP = "gridss_pon_breakpoint.37.sorted.bedpe";
// private static String PON_BE = "gridss_pon_single_breakend.37.sorted.bed";
@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket runtimeBucket, final BashStartupScript startupScript, final RuntimeFiles executionFlags) {
    InputFileDescriptor descriptor = inputs.get();
    final String[] inputArguments = descriptor.inputValue().split(",");
    final List<String> sampleIds = Arrays.stream(inputArguments[0].split(";")).collect(Collectors.toList());
    Map<String, SampleLocationData> sampleLocations = null;
    if (inputArguments.length > 1) {
        sampleLocations = SampleLocationData.loadSampleLocations(inputArguments[1], sampleIds);
    } else {
        sampleLocations = Maps.newHashMap();
    }
    final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V37);
    // download required JARs and resources
    startupScript.addCommand(() -> format("gsutil -u hmf-crunch cp %s/%s/%s %s", BATCH_TOOLS_BUCKET, GRIPSS_DIR, GRIPSS_JAR, VmDirectories.TOOLS));
    startupScript.addCommand(() -> format("gsutil -u hmf-crunch cp %s/%s/%s %s", BATCH_TOOLS_BUCKET, PURPLE_DIR, PURPLE_JAR, VmDirectories.TOOLS));
    startupScript.addCommand(() -> format("gsutil -u hmf-crunch cp %s/%s/%s %s", BATCH_TOOLS_BUCKET, LINX_DIR, LINX_JAR, VmDirectories.TOOLS));
    for (String sampleId : sampleIds) {
        runSample(startupScript, resourceFiles, sampleId, sampleLocations);
    }
    // upload output
    startupScript.addCommand(new OutputUpload(GoogleStorageLocation.of(runtimeBucket.name(), "gpl"), executionFlags));
    // and copy the key output files to a single directory for convenience
    String gripssCombined = String.format("%s/gripss/", COMBINED_OUTPUT_DIR);
    String linxCombined = String.format("%s/linx/", COMBINED_OUTPUT_DIR);
    String purpleCombined = String.format("%s/purple/", COMBINED_OUTPUT_DIR);
    String paveCombined = String.format("%s/pave/", COMBINED_OUTPUT_DIR);
    startupScript.addCommand(() -> format("gsutil -m cp %s/*gripss*vcf* %s", VmDirectories.OUTPUT, gripssCombined));
    startupScript.addCommand(() -> format("gsutil -m cp %s/*sage.somatic.filtered.pave.vcf.gz* %s", VmDirectories.OUTPUT, paveCombined));
    startupScript.addCommand(() -> format("gsutil -m cp %s/*sage.germline.filtered.pave.vcf.gz* %s", VmDirectories.OUTPUT, paveCombined));
    // select files for subsequent Linx runs and/or comparison using Compar
    startupScript.addCommand(() -> format("gsutil -m cp %s/*linx*.tsv %s", VmDirectories.OUTPUT, linxCombined));
    startupScript.addCommand(() -> format("gsutil -m cp %s/*purple* %s", VmDirectories.OUTPUT, purpleCombined));
    startupScript.addCommand(() -> format("gsutil -m cp %s/*driver.catalog* %s", VmDirectories.OUTPUT, purpleCombined));
    return ImmutableVirtualMachineJobDefinition.builder().name("gpl").startupCommand(startupScript).performanceProfile(custom(12, 32)).namespacedResults(ResultsDirectory.defaultDirectory()).build();
}