From 42b41fa5fb4caa8e6f398df875e934e839693c80 Mon Sep 17 00:00:00 2001 From: Sebastian Benjamin Date: Fri, 22 May 2026 14:53:30 -0700 Subject: [PATCH 01/16] Add starcat tool --- singlecell/resources/chunks/RunStarCAT.R | 12 +++++ .../labkey/singlecell/SingleCellModule.java | 2 + .../pipeline/singlecell/RunStarCAT.java | 53 +++++++++++++++++++ 3 files changed, 67 insertions(+) create mode 100644 singlecell/resources/chunks/RunStarCAT.R create mode 100644 singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunStarCAT.java diff --git a/singlecell/resources/chunks/RunStarCAT.R b/singlecell/resources/chunks/RunStarCAT.R new file mode 100644 index 000000000..924c0e437 --- /dev/null +++ b/singlecell/resources/chunks/RunStarCAT.R @@ -0,0 +1,12 @@ +for (datasetId in names(seuratObjects)) { + printName(datasetId) + seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) + + seuratObj <- CellMembrane::RunStarCAT(seuratObj, reference = reference, assayName = assayName, outputDirectory = tempfile(pattern = 'starcat_')) + + saveData(seuratObj, datasetId) + + # Cleanup + rm(seuratObj) + gc() +} diff --git a/singlecell/src/org/labkey/singlecell/SingleCellModule.java b/singlecell/src/org/labkey/singlecell/SingleCellModule.java index f1ce9357e..36cbb0282 100644 --- a/singlecell/src/org/labkey/singlecell/SingleCellModule.java +++ b/singlecell/src/org/labkey/singlecell/SingleCellModule.java @@ -97,6 +97,7 @@ import org.labkey.singlecell.pipeline.singlecell.RunScGate; import org.labkey.singlecell.pipeline.singlecell.RunScGateBuiltin; import org.labkey.singlecell.pipeline.singlecell.RunSingleR; +import org.labkey.singlecell.pipeline.singlecell.RunStarCAT; import org.labkey.singlecell.pipeline.singlecell.RunVision; import org.labkey.singlecell.pipeline.singlecell.ScoreCellCycle; import org.labkey.singlecell.pipeline.singlecell.SeuratPrototype; @@ -248,6 +249,7 @@ public static void registerPipelineSteps() SequencePipelineService.get().registerPipelineStep(new RunPCA.Provider()); SequencePipelineService.get().registerPipelineStep(new RunPHATE.Provider()); SequencePipelineService.get().registerPipelineStep(new RunSingleR.Provider()); + SequencePipelineService.get().registerPipelineStep(new RunStarCAT.Provider()); SequencePipelineService.get().registerPipelineStep(new ClassifyTNKByExpression.Provider()); SequencePipelineService.get().registerPipelineStep(new RunConga.Provider()); SequencePipelineService.get().registerPipelineStep(new FindClustersAndDimRedux.Provider()); diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunStarCAT.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunStarCAT.java new file mode 100644 index 000000000..6bce09f39 --- /dev/null +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunStarCAT.java @@ -0,0 +1,53 @@ +package org.labkey.singlecell.pipeline.singlecell; + +import org.json.JSONObject; +import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; +import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; +import org.labkey.api.singlecell.pipeline.SeuratToolParameter; +import org.labkey.api.singlecell.pipeline.SingleCellStep; + +import java.util.Arrays; + +public class RunStarCAT extends AbstractCellMembraneStep +{ + public RunStarCAT(PipelineContext ctx, RunStarCAT.Provider provider) + { + super(provider, ctx); + } + + public static class Provider extends AbstractPipelineStepProvider + { + public Provider() + { + super("RunStarCAT", "Run StarCAT", "CellMembrane/StarCAT", "This will run StarCAT to project cells onto a reference (e.g. TCAT.V1) and append per-cell scores and program usage to metadata.", Arrays.asList( + SeuratToolParameter.create("reference", "Reference", "Either a built-in StarCAT reference name (e.g. TCAT.V1, MYELOID.GLIOMA.V1, BONEMARROW.CD34POS.HSPC.V1) or a path to a custom reference .tsv/.txt file.", "ldk-simplecombo", new JSONObject() + {{ + put("multiSelect", false); + put("allowBlank", false); + put("editable", true); + put("forceSelection", false); + put("storeValues", "TCAT.V1;MYELOID.GLIOMA.V1;BONEMARROW.CD34POS.HSPC.V1"); + put("initialValues", "TCAT.V1"); + put("delimiter", ";"); + put("joinReturnValue", true); + }}, "TCAT.V1"), + SeuratToolParameter.create("assayName", "Assay Name", "The name of the assay containing the counts matrix passed to StarCAT.", "textfield", new JSONObject() + {{ + put("allowBlank", false); + }}, "RNA") + ), null, null); + } + + @Override + public RunStarCAT create(PipelineContext ctx) + { + return new RunStarCAT(ctx, this); + } + } + + @Override + public String getFileSuffix() + { + return "starcat"; + } +} From 75b9ebe98d67dc53ee137870dd26422ddba7c4ca Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 23 May 2026 12:21:43 +0000 Subject: [PATCH 02/16] Bump qs in /jbrowse in the npm_and_yarn group across 1 directory Bumps the npm_and_yarn group with 1 update in the /jbrowse directory: [qs](https://github.com/ljharb/qs). Updates `qs` from 6.14.2 to 6.15.2 - [Changelog](https://github.com/ljharb/qs/blob/main/CHANGELOG.md) - [Commits](https://github.com/ljharb/qs/compare/v6.14.2...v6.15.2) --- updated-dependencies: - dependency-name: qs dependency-version: 6.15.2 dependency-type: indirect dependency-group: npm_and_yarn ... Signed-off-by: dependabot[bot] --- jbrowse/package-lock.json | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 88baf553b..78316c067 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -5749,9 +5749,9 @@ "license": "MIT" }, "node_modules/body-parser": { - "version": "1.20.4", - "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.4.tgz", - "integrity": "sha512-ZTgYYLMOXY9qKU/57FAo8F+HA2dGX7bqGc71txDRC1rS4frdFI5R7NhluHxH6M0YItAP0sHB4uqAOcYKxO6uGA==", + "version": "1.20.5", + "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.5.tgz", + "integrity": "sha512-3grm+/2tUOvu2cjJkvsIxrv/wVpfXQW4PsQHYm7yk4vfpu7Ekl6nEsYBoJUL6qDwZUx8wUhQ8tR2qz+ad9c9OA==", "dev": true, "license": "MIT", "dependencies": { @@ -5763,7 +5763,7 @@ "http-errors": "~2.0.1", "iconv-lite": "~0.4.24", "on-finished": "~2.4.1", - "qs": "~6.14.0", + "qs": "~6.15.1", "raw-body": "~2.5.3", "type-is": "~1.6.18", "unpipe": "~1.0.0" @@ -7480,15 +7480,15 @@ } }, "node_modules/express": { - "version": "4.22.1", - "resolved": "https://registry.npmjs.org/express/-/express-4.22.1.tgz", - "integrity": "sha512-F2X8g9P1X7uCPZMA3MVf9wcTqlyNp7IhH5qPCI0izhaOIYXaW9L535tGA3qmjRzpH+bZczqq7hVKxTR4NWnu+g==", + "version": "4.22.2", + "resolved": "https://registry.npmjs.org/express/-/express-4.22.2.tgz", + "integrity": "sha512-IuL+Elrou2ZvCFHs18/CIzy2Nzvo25nZ1/D2eIZlz7c+QUayAcYoiM2BthCjs+EBHVpjYjcuLDAiCWgeIX3X1Q==", "dev": true, "license": "MIT", "dependencies": { "accepts": "~1.3.8", "array-flatten": "1.1.1", - "body-parser": "~1.20.3", + "body-parser": "~1.20.5", "content-disposition": "~0.5.4", "content-type": "~1.0.4", "cookie": "~0.7.1", @@ -7507,7 +7507,7 @@ "parseurl": "~1.3.3", "path-to-regexp": "~0.1.12", "proxy-addr": "~2.0.7", - "qs": "~6.14.0", + "qs": "~6.15.1", "range-parser": "~1.2.1", "safe-buffer": "5.2.1", "send": "~0.19.0", @@ -10530,9 +10530,9 @@ } }, "node_modules/qs": { - "version": "6.14.2", - "resolved": "https://registry.npmjs.org/qs/-/qs-6.14.2.tgz", - "integrity": "sha512-V/yCWTTF7VJ9hIh18Ugr2zhJMP01MY7c5kh4J870L7imm6/DIzBsNLTXzMwUA3yZ5b/KBqLx8Kp3uRvd7xSe3Q==", + "version": "6.15.2", + "resolved": "https://registry.npmjs.org/qs/-/qs-6.15.2.tgz", + "integrity": "sha512-Rzq0KEyX/w/tEybncDgdkZrJgVUsUMk3xjh3t5bv3S1HTAtg+uOYt72+ZfwiQwKdysThkTBdL/rTi6HDmX9Ddw==", "license": "BSD-3-Clause", "dependencies": { "side-channel": "^1.1.0" From ec64b2b78fd444c7da2ce7d9c0c7cca6dd62cffe Mon Sep 17 00:00:00 2001 From: bbimber Date: Sat, 23 May 2026 06:58:52 -0700 Subject: [PATCH 03/16] Update octokit/request-action --- .github/workflows/build.yml | 2 +- .github/workflows/build_latest.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index eb3c0794e..7a01ac2f6 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest steps: - name: "Find default branch" - uses: octokit/request-action@v2.x + uses: octokit/request-action@v3.0.0 id: get_default_branch with: route: GET /repos/${{ github.repository }} diff --git a/.github/workflows/build_latest.yml b/.github/workflows/build_latest.yml index f194da930..43b8146c0 100644 --- a/.github/workflows/build_latest.yml +++ b/.github/workflows/build_latest.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: "Find default branch" - uses: octokit/request-action@v2.x + uses: octokit/request-action@v3.0.0 id: get_default_branch with: route: GET /repos/${{ github.repository }} From d02d0485f16ede47af1139ee3193f84e875493f6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 28 May 2026 03:02:26 +0000 Subject: [PATCH 04/16] Bump tmp in /jbrowse in the npm_and_yarn group across 1 directory Bumps the npm_and_yarn group with 1 update in the /jbrowse directory: [tmp](https://github.com/raszi/node-tmp). Updates `tmp` from 0.2.5 to 0.2.7 - [Changelog](https://github.com/raszi/node-tmp/blob/master/CHANGELOG.md) - [Commits](https://github.com/raszi/node-tmp/compare/v0.2.5...v0.2.7) --- updated-dependencies: - dependency-name: tmp dependency-version: 0.2.7 dependency-type: indirect dependency-group: npm_and_yarn ... Signed-off-by: dependabot[bot] --- jbrowse/package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 78316c067..339043262 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -12240,9 +12240,9 @@ } }, "node_modules/tmp": { - "version": "0.2.5", - "resolved": "https://registry.npmjs.org/tmp/-/tmp-0.2.5.tgz", - "integrity": "sha512-voyz6MApa1rQGUxT3E+BK7/ROe8itEx7vD8/HEvt4xwXucvQ5G5oeEiHkmHZJuBO21RpOf+YYm9MOivj709jow==", + "version": "0.2.7", + "resolved": "https://registry.npmjs.org/tmp/-/tmp-0.2.7.tgz", + "integrity": "sha512-e0votIpp4Uo2AJYSzVHV6xCcawuiez3DzqDAbrTc3YxBkplN6e+dM13ZeIcZnDg/QpSuU2zfZ3rzwY8ukEnaXw==", "dev": true, "license": "MIT", "engines": { From e41af6e0b32ac2618fb0f9e02e2adf1cbaf40dd7 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 28 May 2026 06:37:02 -0700 Subject: [PATCH 05/16] Add WhatsHap phasing step --- .../SequenceAnalysisModule.java | 2 + .../run/variant/WhatsHapStep.java | 173 ++++++++++++++++++ 2 files changed, 175 insertions(+) create mode 100644 SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java index 3251e7f21..93688d270 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java @@ -183,6 +183,7 @@ import org.labkey.sequenceanalysis.run.variant.VariantFiltrationStep; import org.labkey.sequenceanalysis.run.variant.VariantQCStep; import org.labkey.sequenceanalysis.run.variant.VariantsToTableStep; +import org.labkey.sequenceanalysis.run.variant.WhatsHapStep; import org.labkey.sequenceanalysis.util.Barcoder; import org.labkey.sequenceanalysis.util.ChainFileValidator; import org.labkey.sequenceanalysis.util.ScatterGatherUtils; @@ -374,6 +375,7 @@ public static void registerPipelineSteps() SequencePipelineService.get().registerPipelineStep(new BcftoolsFixploidyStep.Provider()); SequencePipelineService.get().registerPipelineStep(new BcftoolsFillFromFastaStep.Provider()); SequencePipelineService.get().registerPipelineStep(new SVAnnotateStep.Provider()); + SequencePipelineService.get().registerPipelineStep(new WhatsHapStep.Provider()); //handlers SequenceAnalysisService.get().registerFileHandler(new LiftoverHandler()); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java new file mode 100644 index 000000000..47f5fb547 --- /dev/null +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java @@ -0,0 +1,173 @@ +package org.labkey.sequenceanalysis.run.variant; + +import htsjdk.samtools.util.Interval; +import htsjdk.variant.vcf.VCFFileReader; +import htsjdk.variant.vcf.VCFHeader; +import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.Nullable; +import org.labkey.api.data.Container; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.TableInfo; +import org.labkey.api.data.TableSelector; +import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.pipeline.PipelineJobException; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryService; +import org.labkey.api.sequenceanalysis.SequenceAnalysisService; +import org.labkey.api.sequenceanalysis.SequenceOutputFile; +import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider; +import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; +import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider; +import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; +import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport; +import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; +import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep; +import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl; +import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep; +import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper; +import org.labkey.api.util.FileUtil; +import org.labkey.api.util.PageFlowUtil; +import org.labkey.sequenceanalysis.SequenceAnalysisSchema; + +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; + +public class WhatsHapStep extends AbstractCommandPipelineStep implements VariantProcessingStep +{ + public WhatsHapStep(PipelineStepProvider provider, PipelineContext ctx) + { + super(provider, ctx, new WhatsHapStep.WhatsHapWrapper(ctx.getLogger())); + } + + public static class Provider extends AbstractVariantProcessingStepProvider implements SupportsPedigree + { + public Provider() + { + super("WhatsHap", "WhatsHap", "", "This will run WhatsHap to phase the VCF using BAM/CRAM data", List.of( + + ), null, "https://whatshap.readthedocs.io/en/latest/"); + } + + @Override + public WhatsHapStep create(PipelineContext ctx) + { + return new WhatsHapStep(this, ctx); + } + } + + @Override + public void init(PipelineJob job, SequenceAnalysisJobSupport support, List inputFiles) throws PipelineJobException + { + if (inputFiles.size() != 1) + { + throw new PipelineJobException("This step expects a single VCF as input"); + } + + // look up BAM/CRAMs: + for (SequenceOutputFile so : inputFiles) + { + List samples; + try (VCFFileReader reader = new VCFFileReader(so.getFile())) + { + VCFHeader header = reader.getFileHeader(); + samples = header.getSampleNamesInOrder(); + } + + if (samples.isEmpty()) + { + throw new IllegalStateException("No samples found in VCF file"); + } + + ArrayList toCache = new ArrayList<>(); + Container targetContainer = getPipelineCtx().getJob().getContainer().isWorkbookOrTab() ? getPipelineCtx().getJob().getContainer().getParent() : getPipelineCtx().getJob().getContainer(); + TableInfo outputFiles = QueryService.get().getUserSchema(getPipelineCtx().getJob().getUser(), targetContainer, SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_OUTPUTFILES); + for (String sample : samples) + { + // Find readsets for this genome: + SimpleFilter filter1 = new SimpleFilter(FieldKey.fromString("readset/name"), sample). + addCondition(FieldKey.fromString("library_id"), so.getLibrary_id()). + addCondition(FieldKey.fromString("category"), "Alignment"); + + List alignments = new TableSelector(outputFiles, PageFlowUtil.set("rowid"), filter1, null).getArrayList(Integer.class); + if (alignments.isEmpty()) + { + throw new PipelineJobException("Unable to find alignment for: " + sample); + } + + SequenceOutputFile alignmentFile = SequenceOutputFile.getForId(Collections.max(alignments)); + toCache.add(alignmentFile.getDataId()); + support.cacheExpData(alignmentFile.getExpData()); + } + + support.cacheObject(CACHE_KEY, toCache); + } + } + + private final String CACHE_KEY = "~cached_readsets~"; + + private List getCachedBams() throws PipelineJobException + { + List cachedFiles = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(List.class, Long.class)); + + return cachedFiles.stream().map(x -> getPipelineCtx().getSequenceSupport().getCachedData(x)).toList(); + } + + @Override + public Output processVariants(File inputVCF, File outputDirectory, ReferenceGenome genome, @Nullable List intervals) throws PipelineJobException + { + VariantProcessingStepOutputImpl output = new VariantProcessingStepOutputImpl(); + + output.addInput(inputVCF, "Input VCF"); + output.addInput(genome.getWorkingFastaFile(), "Reference Genome"); + + File vcfOut = FileUtil.appendName(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(inputVCF.getName()) + ".phased.vcf.gz"); + + List args = new ArrayList<>(); + args.add(getWrapper().getExe().getPath()); + args.add("-o"); + args.add(vcfOut.getPath()); + args.add("--reference"); + args.add(genome.getWorkingFastaFile().getPath()); + args.add(inputVCF.getPath()); + for (File f : getCachedBams()) + { + args.add(f.getPath()); + } + + getWrapper().execute(args); + + if (!vcfOut.exists()) + { + throw new PipelineJobException("Missing file: " + vcfOut.getPath()); + } + + try + { + SequenceAnalysisService.get().ensureVcfIndex(vcfOut, getPipelineCtx().getLogger()); + } + catch (IOException e) + { + throw new PipelineJobException(e); + } + + output.addSequenceOutput(vcfOut, "Phased VCF: " + inputVCF.getName(), "Phased VCF", null, null, genome.getGenomeId(), null); + + return output; + } + + public static class WhatsHapWrapper extends AbstractCommandWrapper + { + public WhatsHapWrapper(@Nullable Logger logger) + { + super(logger); + } + + public File getExe() + { + return SequencePipelineService.get().getExeForPackage("WHATSHAPPATH", "whatshap"); + } + } +} From 5106e7ebf913770e72faac5300c4f928d27459bd Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 28 May 2026 09:21:29 -0700 Subject: [PATCH 06/16] Drop SupportsPedigree in whatshap --- .../org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java index 47f5fb547..c5034e251 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java @@ -42,7 +42,7 @@ public WhatsHapStep(PipelineStepProvider provider, PipelineContext ctx) super(provider, ctx, new WhatsHapStep.WhatsHapWrapper(ctx.getLogger())); } - public static class Provider extends AbstractVariantProcessingStepProvider implements SupportsPedigree + public static class Provider extends AbstractVariantProcessingStepProvider { public Provider() { From 7396d6f1a9f4a1804051b7eac5b716262e3abc92 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 28 May 2026 10:09:24 -0700 Subject: [PATCH 07/16] Use correct method for list deserialization --- .../org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java index c5034e251..7b3d81f6a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java @@ -110,7 +110,7 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List getCachedBams() throws PipelineJobException { - List cachedFiles = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(List.class, Long.class)); + List cachedFiles = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructCollectionType(List.class, Long.class)); return cachedFiles.stream().map(x -> getPipelineCtx().getSequenceSupport().getCachedData(x)).toList(); } From 8957ad392cbe0121fb1fbfe37aeb23b46317594e Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 28 May 2026 17:52:28 -0700 Subject: [PATCH 08/16] Use correct method for list deserialization --- .../pipeline/SequenceJobSupportImpl.java | 10 +++++++++- .../sequenceanalysis/run/variant/WhatsHapStep.java | 5 +++-- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java index ed7e7a126..7d66ab47f 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java @@ -6,6 +6,7 @@ import org.junit.Assert; import org.junit.Test; import org.labkey.api.collections.IntHashMap; +import org.labkey.api.collections.LongArrayList; import org.labkey.api.collections.LongHashMap; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExperimentService; @@ -28,6 +29,7 @@ import java.io.StringReader; import java.io.StringWriter; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashMap; @@ -319,6 +321,7 @@ public void testSerializeWithMap() throws Exception js1._cachedObjects.put("cachedInt", 1); js1._cachedObjects.put("cachedString", "foo"); js1._cachedObjects.put("cachedLong", 2L); + js1._cachedObjects.put("cachedListLong", new LongArrayList(Arrays.asList(1L, 2L))); LongHashMap longMap = new LongHashMap<>(); longMap.put(1L, 2L); @@ -349,10 +352,15 @@ public void testSerializeWithMap() throws Exception assertEquals("Object not serialized with correct key type", Integer.class, serializedMap.keySet().iterator().next().getClass()); assertNotNull("Map keys not serialized properly", serializedMap.get(1)); - LongHashMap serializedLongMap = (LongHashMap)deserialized.getCachedObject("cachedLongMap", LongHashMap.class); + LongHashMap serializedLongMap = deserialized.getCachedObject("cachedLongMap", LongHashMap.class); assertEquals("LongMap not serialized properly", 1, serializedLongMap.size()); assertEquals("Object not serialized with correct key type", Long.class, serializedLongMap.keySet().iterator().next().getClass()); assertNotNull("LongMap keys not serialized properly", serializedLongMap.get(1L)); + + List serializedListLong = deserialized.getCachedObject("cachedListLong", mapper.getTypeFactory().constructType(LongArrayList.class)); + assertEquals("List not serialized properly", 2, serializedListLong.size()); + assertNotNull("List values not serialized properly", serializedListLong.get(1)); + assertNotNull("List values not serialized properly", serializedListLong.get(2)); } @Test diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java index 7b3d81f6a..1b6753018 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java @@ -5,6 +5,7 @@ import htsjdk.variant.vcf.VCFHeader; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; +import org.labkey.api.collections.LongArrayList; import org.labkey.api.data.Container; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.TableInfo; @@ -81,7 +82,7 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List toCache = new ArrayList<>(); + ArrayList toCache = new LongArrayList(); Container targetContainer = getPipelineCtx().getJob().getContainer().isWorkbookOrTab() ? getPipelineCtx().getJob().getContainer().getParent() : getPipelineCtx().getJob().getContainer(); TableInfo outputFiles = QueryService.get().getUserSchema(getPipelineCtx().getJob().getUser(), targetContainer, SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_OUTPUTFILES); for (String sample : samples) @@ -110,7 +111,7 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List getCachedBams() throws PipelineJobException { - List cachedFiles = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructCollectionType(List.class, Long.class)); + List cachedFiles = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructType(LongArrayList.class)); return cachedFiles.stream().map(x -> getPipelineCtx().getSequenceSupport().getCachedData(x)).toList(); } From 3a8ab2a6dd5f155fd3d1a8333acbf024e4110157 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 28 May 2026 21:01:53 -0700 Subject: [PATCH 09/16] Test fix --- .../sequenceanalysis/pipeline/SequenceJobSupportImpl.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java index 7d66ab47f..ad5d41b8e 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java @@ -359,8 +359,8 @@ public void testSerializeWithMap() throws Exception List serializedListLong = deserialized.getCachedObject("cachedListLong", mapper.getTypeFactory().constructType(LongArrayList.class)); assertEquals("List not serialized properly", 2, serializedListLong.size()); - assertNotNull("List values not serialized properly", serializedListLong.get(1)); - assertNotNull("List values not serialized properly", serializedListLong.get(2)); + assertEquals("List values not serialized properly", 1L, (long)serializedListLong.get(0)); + assertEquals("List values not serialized properly", 2L, (long)serializedListLong.get(1)); } @Test From 63a737a7e1e3d04b559000c8d680da5386cd0a5d Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 29 May 2026 08:00:42 -0700 Subject: [PATCH 10/16] Add missing argument --- .../org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java | 1 + 1 file changed, 1 insertion(+) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java index 1b6753018..5285b8026 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/WhatsHapStep.java @@ -128,6 +128,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno List args = new ArrayList<>(); args.add(getWrapper().getExe().getPath()); + args.add("phase"); args.add("-o"); args.add(vcfOut.getPath()); args.add("--reference"); From ee84ccb197386968468aa1b088a4ed3f91b5ac8f Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 3 Jun 2026 07:48:39 -0700 Subject: [PATCH 11/16] Update dependencies --- jbrowse/package-lock.json | 1198 +++++++++++++++++-------------------- 1 file changed, 564 insertions(+), 634 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 339043262..fe65e9a6c 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -62,12 +62,11 @@ "integrity": "sha512-Elp+iwUx5rN5+Y8xLt5/GRoG20WGoDCQ/1Fb+1LiGtvwbDavuSk0jhD/eZdckHAuzcDzccnkv+rEjyWfRx18gg==" }, "node_modules/@babel/code-frame": { - "version": "7.29.0", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.29.0.tgz", - "integrity": "sha512-9NhCeYjq9+3uxgdtp20LSiJXJvN0FeCtNGpJxuMFZ1Kv3cWUNb6DOhJwUvcVCzKGR66cw4njwM6hrJLqgOwbcw==", - "license": "MIT", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.29.7.tgz", + "integrity": "sha512-Aup7aUOfpbAUg2ROOJN6Iw5f9DMBlzu0mIkm/malLQFN/YQgO48wCj0Kxa3sEHJvPVFg7siR+qRInwXd2qhQKw==", "dependencies": { - "@babel/helper-validator-identifier": "^7.28.5", + "@babel/helper-validator-identifier": "^7.29.7", "js-tokens": "^4.0.0", "picocolors": "^1.1.1" }, @@ -76,11 +75,10 @@ } }, "node_modules/@babel/compat-data": { - "version": "7.29.0", - "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.29.0.tgz", - "integrity": "sha512-T1NCJqT/j9+cn8fvkt7jtwbLBfLC/1y1c7NtCeXFRgzGTsafi68MRv8yzkYSapBnFA6L3U2VSc02ciDzoAJhJg==", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.29.7.tgz", + "integrity": "sha512-locTkQyKvwIEgBzVrn8693ebc97F2U8ZHjbXwDXJ5Fn2TCpNwTlKcaKLkdHop5c/icOFE7qt7Q9JC5hnKNa6Gg==", "dev": true, - "license": "MIT", "engines": { "node": ">=6.9.0" } @@ -123,13 +121,12 @@ "dev": true }, "node_modules/@babel/generator": { - "version": "7.29.1", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.29.1.tgz", - "integrity": "sha512-qsaF+9Qcm2Qv8SRIMMscAvG4O3lJ0F1GuMo5HR/Bp02LopNgnZBC/EkbevHFeGs4ls/oPz9v+Bsmzbkbe+0dUw==", - "license": "MIT", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.29.7.tgz", + "integrity": "sha512-DkXD5OJQaAQIdZ1bt3UZdEnHAn9Imd3IVBdX03UFe+ony9Ojw5pzr9YVKGDY1jt+Gcn/FnGkNf8r+Vj5NOJWtQ==", "dependencies": { - "@babel/parser": "^7.29.0", - "@babel/types": "^7.29.0", + "@babel/parser": "^7.29.7", + "@babel/types": "^7.29.7", "@jridgewell/gen-mapping": "^0.3.12", "@jridgewell/trace-mapping": "^0.3.28", "jsesc": "^3.0.2" @@ -139,26 +136,25 @@ } }, "node_modules/@babel/helper-annotate-as-pure": { - "version": "7.27.3", - "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.27.3.tgz", - "integrity": "sha512-fXSwMQqitTGeHLBC08Eq5yXz2m37E4pJX1qAU1+2cNedz/ifv/bVXft90VeSav5nFO61EcNgwr0aJxbyPaWBPg==", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.29.7.tgz", + "integrity": "sha512-OoK6239jHPuSQOoS0kfTVKn0b/rVTk0seKq4Gd2UMLtmOVLjDC0ki3e+c90Trqv2gMfvJFqkiljrr568+qddiw==", "dev": true, "dependencies": { - "@babel/types": "^7.27.3" + "@babel/types": "^7.29.7" }, "engines": { "node": ">=6.9.0" } }, "node_modules/@babel/helper-compilation-targets": { - "version": "7.28.6", - "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.28.6.tgz", - "integrity": "sha512-JYtls3hqi15fcx5GaSNL7SCTJ2MNmjrkHXg4FSpOA/grxK8KwyZ5bubHsCq8FXCkua6xhuaaBit+3b7+VZRfcA==", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.29.7.tgz", + "integrity": "sha512-wem6WaBj4NaVYVdNhLPPVacES6ZJ+KBBfSkTMD3YZxbP3rm3Di85tJU5ljaUNhaOynt+Aj0xruhYuzQBt8n71g==", "dev": true, - "license": "MIT", "dependencies": { - "@babel/compat-data": "^7.28.6", - "@babel/helper-validator-option": "^7.27.1", + "@babel/compat-data": "^7.29.7", + "@babel/helper-validator-option": "^7.29.7", "browserslist": "^4.24.0", "lru-cache": "^5.1.1", "semver": "^6.3.1" @@ -168,18 +164,17 @@ } }, "node_modules/@babel/helper-create-class-features-plugin": { - "version": "7.28.6", - 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"https://registry.npmjs.org/sass-loader/-/sass-loader-16.0.7.tgz", - "integrity": "sha512-w6q+fRHourZ+e+xA1kcsF27iGM6jdB8teexYCfdUw0sYgcDNeZESnDNT9sUmmPm3ooziwUJXGwZJSTF3kOdBfA==", + "version": "16.0.8", + "resolved": "https://registry.npmjs.org/sass-loader/-/sass-loader-16.0.8.tgz", + "integrity": "sha512-hcov4ZwZJIGbEuyNr9EmiTmZueyrxSToE6GOzoZnq5JM7ecRO7ttyvilPn+VmRsqiP16+VYZzVnGZj/hzZgKBA==", "dev": true, - "license": "MIT", "dependencies": { "neo-async": "^2.6.2" }, @@ -11950,8 +11881,9 @@ }, "node_modules/strip-ansi": { "version": "6.0.1", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", + "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", "dev": true, - "license": "MIT", "dependencies": { "ansi-regex": "^5.0.1" }, @@ -12413,7 +12345,6 @@ "resolved": "https://registry.npmjs.org/unicode-canonical-property-names-ecmascript/-/unicode-canonical-property-names-ecmascript-2.0.1.tgz", "integrity": "sha512-dA8WbNeb2a6oQzAQ55YlT5vQAWGV9WXOsi3SskE3bcCdM0P4SDd+24zS/OCacdRq5BkdsRj9q3Pg6YyQoxIGqg==", "dev": true, - "license": "MIT", "engines": { "node": ">=4" } @@ -12423,7 +12354,6 @@ "resolved": "https://registry.npmjs.org/unicode-match-property-ecmascript/-/unicode-match-property-ecmascript-2.0.0.tgz", "integrity": "sha512-5kaZCrbp5mmbz5ulBkDkbY0SsPOjKqVS35VpL9ulMPfSl0J0Xsm+9Evphv9CoIZFwre7aJoa94AY6seMKGVN5Q==", "dev": true, - "license": "MIT", "dependencies": { "unicode-canonical-property-names-ecmascript": "^2.0.0", "unicode-property-aliases-ecmascript": "^2.0.0" @@ -12437,7 +12367,6 @@ "resolved": "https://registry.npmjs.org/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-2.2.1.tgz", "integrity": "sha512-JQ84qTuMg4nVkx8ga4A16a1epI9H6uTXAknqxkGF/aFfRLw1xC/Bp24HNLaZhHSkWd3+84t8iXnp1J0kYcZHhg==", "dev": true, - "license": "MIT", "engines": { "node": ">=4" } @@ -12447,7 +12376,6 @@ "resolved": "https://registry.npmjs.org/unicode-property-aliases-ecmascript/-/unicode-property-aliases-ecmascript-2.2.0.tgz", "integrity": "sha512-hpbDzxUY9BFwX+UeBnxv3Sh1q7HFxj48DTmXchNgRa46lO8uj3/1iEn3MiNUYTg1g9ctIqXCCERn8gYZhHC5lQ==", "dev": true, - "license": "MIT", "engines": { "node": ">=4" } @@ -12703,10 +12631,9 @@ } }, "node_modules/webpack": { - "version": "5.105.4", - "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.105.4.tgz", - "integrity": "sha512-jTywjboN9aHxFlToqb0K0Zs9SbBoW4zRUlGzI2tYNxVYcEi/IPpn+Xi4ye5jTLvX2YeLuic/IvxNot+Q1jMoOw==", - "license": "MIT", + "version": "5.106.2", + "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.106.2.tgz", + "integrity": "sha512-wGN3qcrBQIFmQ/c0AiOAQBvrZ5lmY8vbbMv4Mxfgzqd/B6+9pXtLo73WuS1dSGXM5QYY3hZnIbvx+K1xxe6FyA==", "dependencies": { "@types/eslint-scope": "^3.7.7", "@types/estree": "^1.0.8", @@ -12724,9 +12651,8 @@ "events": "^3.2.0", "glob-to-regexp": "^0.4.1", "graceful-fs": "^4.2.11", - "json-parse-even-better-errors": "^2.3.1", "loader-runner": "^4.3.1", - "mime-types": "^2.1.27", + "mime-db": "^1.54.0", "neo-async": "^2.6.2", "schema-utils": "^4.3.3", "tapable": "^2.3.0", @@ -12799,17 +12725,15 @@ } }, "node_modules/webpack-cli": { - "version": "7.0.2", - "resolved": "https://registry.npmjs.org/webpack-cli/-/webpack-cli-7.0.2.tgz", - "integrity": "sha512-dB0R4T+C/8YuvM+fabdvil6QE44/ChDXikV5lOOkrUeCkW5hTJv2pGLE3keh+D5hjYw8icBaJkZzpFoaHV4T+g==", + "version": "7.0.3", + "resolved": "https://registry.npmjs.org/webpack-cli/-/webpack-cli-7.0.3.tgz", + "integrity": "sha512-2E2C6A1e2El7791zQgTH7LPIuwLjRliow9OHS/qlJc9pwhZlCoL/uiwqd/1WSlXT83wJfmfDbkcqHXuXoPJZ3g==", "dev": true, - "license": "MIT", "dependencies": { - "@discoveryjs/json-ext": "^1.0.0", + "@discoveryjs/json-ext": "^1.1.0", "commander": "^14.0.3", "cross-spawn": "^7.0.6", "envinfo": "^7.14.0", - "fastest-levenshtein": "^1.0.12", "import-local": "^3.0.2", "interpret": "^3.1.1", "rechoir": "^0.8.0", @@ -12840,11 +12764,10 @@ } }, "node_modules/webpack-cli/node_modules/@discoveryjs/json-ext": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/@discoveryjs/json-ext/-/json-ext-1.0.0.tgz", - "integrity": "sha512-dDlz3W405VMFO4w5kIP9DOmELBcvFQGmLoKSdIRstBDubKFYwaNHV1NnlzMCQpXQFGWVALmeMORAuiLx18AvZQ==", + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/@discoveryjs/json-ext/-/json-ext-1.1.0.tgz", + "integrity": "sha512-Xc3VhU02wqZ1HvHRJUwL09HkZSTvidqY5Ya0NXBSYOxAp+Ln9dcJr9fySI+CkONzP3PekQo9WdzCv0PGER/mOA==", "dev": true, - "license": "MIT", "engines": { "node": ">=14.17.0" } @@ -13079,6 +13002,14 @@ "node": ">=10.13.0" } }, + "node_modules/webpack/node_modules/mime-db": { + "version": "1.54.0", + "resolved": "https://registry.npmjs.org/mime-db/-/mime-db-1.54.0.tgz", + "integrity": "sha512-aU5EJuIN2WDemCcAp2vFBfp/m4EAhWJnUNSSw0ixs7/kXbd6Pg64EmwJkNdFhB8aWt1sH2CTXrLxo/iAGV3oPQ==", + "engines": { + "node": ">= 0.6" + } + }, "node_modules/websocket-driver": { "version": "0.7.4", "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.7.4.tgz", @@ -13146,11 +13077,10 @@ "license": "MIT" }, "node_modules/ws": { - "version": "8.19.0", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.19.0.tgz", - "integrity": "sha512-blAT2mjOEIi0ZzruJfIhb3nps74PRWTCz1IjglWEEpQl5XS/UNama6u2/rjFkDDouqr4L67ry+1aGIALViWjDg==", + "version": "8.21.0", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.21.0.tgz", + "integrity": "sha512-Vsp28b7DRcimFQvrqu2Wek3z1iYxDCWqHYB8Qsnk/S4RfaCQzPGPyBNuVjJV3cd6UiKtUtp6sNM77gWvzcCH+g==", "dev": true, - "license": "MIT", "engines": { "node": ">=10.0.0" }, From 6116ed2953bfea308b2fa48476ec7b54ba86f40d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 4 Jun 2026 14:05:24 +0000 Subject: [PATCH 12/16] Bump react-router Bumps the npm_and_yarn group with 1 update in the /jbrowse directory: [react-router](https://github.com/remix-run/react-router/tree/HEAD/packages/react-router). Updates `react-router` from 6.30.3 to 6.30.4 - [Release notes](https://github.com/remix-run/react-router/releases) - [Changelog](https://github.com/remix-run/react-router/blob/react-router@6.30.4/packages/react-router/CHANGELOG.md) - [Commits](https://github.com/remix-run/react-router/commits/react-router@6.30.4/packages/react-router) --- updated-dependencies: - dependency-name: react-router dependency-version: 6.30.4 dependency-type: indirect dependency-group: npm_and_yarn ... Signed-off-by: dependabot[bot] --- jbrowse/package-lock.json | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index fe65e9a6c..e0be57a60 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -4588,9 +4588,9 @@ } }, "node_modules/@remix-run/router": { - "version": "1.23.2", - "resolved": "https://registry.npmjs.org/@remix-run/router/-/router-1.23.2.tgz", - "integrity": "sha512-Ic6m2U/rMjTkhERIa/0ZtXJP17QUi2CbWE7cqx4J58M8aA3QTfW+2UlQ4psvTX9IO1RfNVhK3pcpdjej7L+t2w==", + "version": "1.23.3", + "resolved": "https://registry.npmjs.org/@remix-run/router/-/router-1.23.3.tgz", + "integrity": "sha512-4An71tdz9X8+3sI4Qqqd2LWd9vS39J7sqd9EU4Scw7TJE/qB10Flv/UuqbPVgfQV9XoK8Np6jNquZitnZq5i+Q==", "license": "MIT", "engines": { "node": ">=14.0.0" @@ -10676,12 +10676,12 @@ } }, "node_modules/react-router": { - "version": "6.30.3", - "resolved": "https://registry.npmjs.org/react-router/-/react-router-6.30.3.tgz", - "integrity": "sha512-XRnlbKMTmktBkjCLE8/XcZFlnHvr2Ltdr1eJX4idL55/9BbORzyZEaIkBFDhFGCEWBBItsVrDxwx3gnisMitdw==", + "version": "6.30.4", + "resolved": "https://registry.npmjs.org/react-router/-/react-router-6.30.4.tgz", + "integrity": "sha512-SVUsDe+DybHM/WmYKIVYhZh1o5Dcuf16yM6WjG02Q9XVFMZIJyHYhwrr6bFBXZkVP6z69kNkMyBCujt8FaFLJA==", "license": "MIT", "dependencies": { - "@remix-run/router": "1.23.2" + "@remix-run/router": "1.23.3" }, "engines": { "node": ">=14.0.0" @@ -10691,13 +10691,13 @@ } }, "node_modules/react-router-dom": { - "version": "6.30.3", - "resolved": "https://registry.npmjs.org/react-router-dom/-/react-router-dom-6.30.3.tgz", - "integrity": "sha512-pxPcv1AczD4vso7G4Z3TKcvlxK7g7TNt3/FNGMhfqyntocvYKj+GCatfigGDjbLozC4baguJ0ReCigoDJXb0ag==", + "version": "6.30.4", + "resolved": "https://registry.npmjs.org/react-router-dom/-/react-router-dom-6.30.4.tgz", + "integrity": "sha512-q4HvNl+mmDdkS0g+MqiBZNteQJCuimWoOyHMy4T/RQLAn9Z29+E91QXRaxOujeMl2HTzRSS0KFPd7lxX3PjV0Q==", "license": "MIT", "dependencies": { - "@remix-run/router": "1.23.2", - "react-router": "6.30.3" + "@remix-run/router": "1.23.3", + "react-router": "6.30.4" }, "engines": { "node": ">=14.0.0" From 86605c95ed726f8bb6c63b7df7484b5946cff97d Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 5 Jun 2026 13:36:50 -0700 Subject: [PATCH 13/16] Ensure bismark ends with sorted BAM --- .../org/labkey/api/sequenceanalysis/pipeline/SamSorter.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamSorter.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamSorter.java index b47205089..b48c1e168 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamSorter.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamSorter.java @@ -40,7 +40,7 @@ public File execute(File input, @Nullable File output, SAMFileHeader.SortOrder s boolean replaceOriginal = output == null; if (output == null) { - output = new File(getOutputDir(input), FileUtil.getBaseName(input) + ".sorted" + "." + FileUtil.getExtension(input)); + output = FileUtil.appendName(getOutputDir(input), FileUtil.getBaseName(input) + ".sorted" + "." + FileUtil.getExtension(input)); } List params = new ArrayList<>(); From 8b225fb93b6a15ac790cc8a2b14ab31b0bd32ae6 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 7 Jun 2026 10:03:06 -0700 Subject: [PATCH 14/16] Include RIRA/Unknown in seurat description --- .../resources/chunks/RunRiraClassification.R | 2 +- .../analysis/AbstractSingleCellHandler.java | 14 +++++++++++--- .../pipeline/singlecell/RunRiraClassification.java | 6 ++++++ 3 files changed, 18 insertions(+), 4 deletions(-) diff --git a/singlecell/resources/chunks/RunRiraClassification.R b/singlecell/resources/chunks/RunRiraClassification.R index 1e7d5932a..89740793e 100644 --- a/singlecell/resources/chunks/RunRiraClassification.R +++ b/singlecell/resources/chunks/RunRiraClassification.R @@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) { printName(datasetId) seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) - seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) + seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, maxAllowedUnknown = maxAllowedUnknown) seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java index a7d112298..635ed6f77 100644 --- a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java +++ b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java @@ -948,6 +948,7 @@ public static String getOutputDescription(JSONObject jsonParams, Logger log, Fil int totalDiscordant = 0; int lowOrNegative = 0; int totalDoublet = 0; + int totalUnknown = 0; double totalSaturation = 0.0; Set subjectIds = new HashSet<>(); @@ -1073,6 +1074,10 @@ else if ("NotUsed".equals(val)) cellsLackingCDR3++; } } + else if ("Unknown".equals(line[riraIdx])) + { + totalUnknown++; + } } if (subjectIdIdx > 0) @@ -1122,12 +1127,15 @@ else if ("NotUsed".equals(val)) } else if (riraIdx == -1 || traIdx == -1) { - descriptions.add("TCR information not present"); + if (riraIdx != -1) + { + descriptions.add("TCR information not present"); + } } - if (!subjectIds.isEmpty()) + if (riraIdx != -1) { - descriptions.add("Distinct SubjectIds: " + subjectIds.size()); + descriptions.add("% RIRA/Unknown: " + pf.format((double)totalUnknown / (double)totalCells)); } } catch (IOException e) diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java index c66640268..ceb614a1e 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java @@ -27,6 +27,12 @@ public Provider() SeuratToolParameter.create("retainProbabilityMatrix", "Retain Probability Matrix", "If true, the celltypist probability_matrix with per-class probabilities will be stored in meta.data", "checkbox", new JSONObject() {{ put("checked", true); + }}, true), + SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown", "If provided, ", "ldk-numberfield", new JSONObject() + {{ + put("minValue", 0); + put("maxValue", 1); + put("decimalPrecision", 2); }}, true) ), null, null); } From 6bf3fff77ff3a3faf9175a67e3d6f277a1eb8523 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 8 Jun 2026 13:16:38 -0700 Subject: [PATCH 15/16] Improve handling of RIRA filters --- singlecell/resources/chunks/UpdateSeuratPrototype.R | 2 +- .../pipeline/singlecell/RunRiraClassification.java | 4 ++-- .../pipeline/singlecell/UpdateSeuratPrototype.java | 8 +++++++- 3 files changed, 10 insertions(+), 4 deletions(-) diff --git a/singlecell/resources/chunks/UpdateSeuratPrototype.R b/singlecell/resources/chunks/UpdateSeuratPrototype.R index ad6a7725a..2c6681daf 100644 --- a/singlecell/resources/chunks/UpdateSeuratPrototype.R +++ b/singlecell/resources/chunks/UpdateSeuratPrototype.R @@ -26,7 +26,7 @@ for (datasetId in names(seuratObjects)) { } if (runRira) { - seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) + seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, maxAllowedUnknown = maxAllowedUnknown) seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) } diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java index ceb614a1e..9ee51c7b0 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java @@ -28,12 +28,12 @@ public Provider() {{ put("checked", true); }}, true), - SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown", "If provided, ", "ldk-numberfield", new JSONObject() + SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown", "If provided, this step will throw an error is more than this fraction of cells fail the check for disallowed UCell combinations", "ldk-numberfield", new JSONObject() {{ put("minValue", 0); put("maxValue", 1); put("decimalPrecision", 2); - }}, true) + }}, 0.1) ), null, null); } diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java index fad042f96..2518b0d1a 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java @@ -63,7 +63,13 @@ public Provider() SeuratToolParameter.create("keepOriginal", "Keep Copy of Original File", "If checked, the original file will be copied with the file extension '.bk'", "checkbox", new JSONObject() {{ put("checked", false); - }}, false) + }}, false), + SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown (RIRA)", "If provided, this step will throw an error is more than this fraction of cells fail the check for disallowed UCell combinations", "ldk-numberfield", new JSONObject() + {{ + put("minValue", 0); + put("maxValue", 1); + put("decimalPrecision", 2); + }}, 0.1) ), null, null); } From dde9a8c3422249ddc52cf2db83860d7d65db8791 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 8 Jun 2026 14:28:02 -0700 Subject: [PATCH 16/16] Bugfix to re-running RIRA --- singlecell/resources/chunks/UpdateSeuratPrototype.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/singlecell/resources/chunks/UpdateSeuratPrototype.R b/singlecell/resources/chunks/UpdateSeuratPrototype.R index 2c6681daf..56e48e7d5 100644 --- a/singlecell/resources/chunks/UpdateSeuratPrototype.R +++ b/singlecell/resources/chunks/UpdateSeuratPrototype.R @@ -26,9 +26,9 @@ for (datasetId in names(seuratObjects)) { } if (runRira) { - seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, maxAllowedUnknown = maxAllowedUnknown) - seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) - seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) + seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE, maxAllowedUnknown = maxAllowedUnknown) + seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE) + seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE) } if (runTNKClassification) {