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

Example 6 with JavaJarCommand

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

the class Gripss method formCommand.

protected List<BashCommand> formCommand(final List<String> arguments) {
    List<BashCommand> commands = Lists.newArrayList();
    commands.add(new JavaJarCommand("gripss", Versions.GRIPSS, "gripss.jar", "16G", arguments));
    return commands;
}

Example 7 with JavaJarCommand

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

the class LinxSomatic method buildCommands.

private List<BashCommand> buildCommands(final SomaticRunMetadata metadata) {
    List<String> arguments = Lists.newArrayList();
    arguments.add(String.format("-sample %s", metadata.tumor().sampleName()));
    arguments.add(String.format("-sv_vcf %s", purpleStructuralVariantsDownload.getLocalTargetPath()));
    arguments.add(String.format("-purple_dir %s", purpleOutputDirDownload.getLocalTargetPath()));
    arguments.add(String.format("-ref_genome_version %s", resourceFiles.version()));
    arguments.add(String.format("-output_dir %s", VmDirectories.OUTPUT));
    arguments.add(String.format("-fragile_site_file %s", resourceFiles.fragileSites()));
    arguments.add(String.format("-line_element_file %s", resourceFiles.lineElements()));
    arguments.add(String.format("-ensembl_data_dir %s", resourceFiles.ensemblDataCache()));
    arguments.add("-check_fusions");
    arguments.add(String.format("-known_fusion_file %s", resourceFiles.knownFusionData()));
    arguments.add("-check_drivers");
    arguments.add(String.format("-driver_gene_panel %s", resourceFiles.driverGenePanel()));
    arguments.add("-write_vis_data");
    return List.of(new JavaJarCommand("linx", Versions.LINX, "linx.jar", "8G", arguments), new LinxVisualisationsCommand(metadata.tumor().sampleName(), VmDirectories.OUTPUT, resourceFiles.version()));
}

Example 8 with JavaJarCommand

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

the class Orange method buildCommands.

private List<BashCommand> buildCommands(final SomaticRunMetadata metadata) {
    final String pipelineVersionFilePath = VmDirectories.INPUT + "/orange_pipeline.version.txt";
    final String pipelineVersion = Versions.pipelineMajorMinorVersion();
    final List<String> primaryTumorDoids = metadata.tumor().primaryTumorDoids();
    String linxPlotDir = linxOutputDir.getLocalTargetPath() + "/plot";
    return List.of(new MkDirCommand(linxPlotDir), () -> "echo '" + pipelineVersion + "' | tee " + pipelineVersionFilePath, new JavaJarCommand("orange", Versions.ORANGE, "orange.jar", "16G", List.of("-output_dir", VmDirectories.OUTPUT, "-doid_json", resourceFiles.doidJson(), "-primary_tumor_doids", primaryTumorDoids.isEmpty() ? "\"\"" : "\"" + String.join(";", primaryTumorDoids) + "\"", "-max_evidence_level", MAX_EVIDENCE_LEVEL, "-tumor_sample_id", metadata.tumor().sampleName(), "-reference_sample_id", metadata.reference().sampleName(), "-ref_sample_wgs_metrics_file", refMetrics.getLocalTargetPath(), "-tumor_sample_wgs_metrics_file", tumMetrics.getLocalTargetPath(), "-ref_sample_flagstat_file", refFlagstat.getLocalTargetPath(), "-tumor_sample_flagstat_file", tumFlagstat.getLocalTargetPath(), "-sage_germline_gene_coverage_tsv", sageGermlineGeneCoverageTsv.getLocalTargetPath(), "-sage_somatic_ref_sample_bqr_plot", sageSomaticRefSampleBqrPlot.getLocalTargetPath(), "-sage_somatic_tumor_sample_bqr_plot", sageSomaticTumorSampleBqrPlot.getLocalTargetPath(), "-purple_gene_copy_number_tsv", purpleGeneCopyNumberTsv.getLocalTargetPath(), "-purple_germline_driver_catalog_tsv", purpleGermlineDriverCatalog.getLocalTargetPath(), "-purple_germline_variant_vcf", purpleGermlineVcf.getLocalTargetPath(), "-purple_plot_directory", purpleOutputDir.getLocalTargetPath() + "/plot", "-purple_purity_tsv", purplePurityTsv.getLocalTargetPath(), "-purple_qc_file", purpleQCFile.getLocalTargetPath(), "-purple_somatic_driver_catalog_tsv", purpleSomaticDriverCatalog.getLocalTargetPath(), "-purple_somatic_variant_vcf", purpleSomaticVcf.getLocalTargetPath(), "-linx_fusion_tsv", linxFusionTsv.getLocalTargetPath(), "-linx_breakend_tsv", linxBreakEndTsv.getLocalTargetPath(), "-linx_driver_catalog_tsv", linxDriverCatalogTsv.getLocalTargetPath(), "-linx_driver_tsv", linxDriverTsv.getLocalTargetPath(), "-linx_plot_directory", linxPlotDir, "-cuppa_result_csv", cuppaResultCsv.getLocalTargetPath(), "-cuppa_summary_plot", cuppaSummaryPlot.getLocalTargetPath(), "-cuppa_feature_plot", cuppaFeaturePlot.getLocalTargetPath(), "-chord_prediction_txt", chordPredictionTxt.getLocalTargetPath(), "-peach_genotype_tsv", peachGenotypeTsv.getLocalTargetPath(), "-protect_evidence_tsv", protectEvidenceTsv.getLocalTargetPath(), "-annotated_virus_tsv", annotatedVirusTsv.getLocalTargetPath(), "-pipeline_version_file", pipelineVersionFilePath, "-cohort_mapping_tsv", resourceFiles.orangeCohortMapping(), "-cohort_percentiles_tsv", resourceFiles.orangeCohortPercentiles())));
}

Example 9 with JavaJarCommand

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

the class LinxGermline method buildCommand.

private List<BashCommand> buildCommand(final SomaticRunMetadata metadata, final InputMode inputMode) {
    List<String> arguments = Lists.newArrayList();
    arguments.add(String.format("-sample %s", metadata.sampleName()));
    arguments.add("-germline");
    arguments.add(String.format("-sv_vcf %s", gripssGermlineVariantsDownload.getLocalTargetPath()));
    arguments.add(String.format("-ref_genome_version %s", resourceFiles.version()));
    arguments.add(String.format("-output_dir %s", VmDirectories.OUTPUT));
    arguments.add(String.format("-line_element_file %s", resourceFiles.lineElements()));
    arguments.add(String.format("-ensembl_data_dir %s", resourceFiles.ensemblDataCache()));
    arguments.add(String.format("-driver_gene_panel %s", resourceFiles.driverGenePanel()));
    arguments.add(String.format("-germine_pon_sv_file %s", resourceFiles.svBreakpointPon()));
    arguments.add(String.format("-germine_pon_sgl_file %s", resourceFiles.svBreakendPon()));
    return Collections.singletonList(new JavaJarCommand("linx", Versions.LINX, "linx.jar", "8G", arguments));
}