From f65aef11c92360337bad6645a8fbc8828c75ab36 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 4 Nov 2020 11:30:34 -0800 Subject: [PATCH 01/15] Add support for cellranger vdj --inner-enrichment-primers --- .../CellRangerCellHashingHandler.java | 2 +- .../tcrdb/pipeline/CellRangerVDJUtils.java | 2 +- .../tcrdb/pipeline/CellRangerVDJWrapper.java | 27 +++++++++++++++++++ 3 files changed, 29 insertions(+), 2 deletions(-) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java index 00be83f8c..79c2bcc53 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java @@ -248,7 +248,7 @@ public static File processBarcodeFile(SequenceOutputHandler.JobContext ctx, File //prepare whitelist of cell indexes File cellBarcodeWhitelist = utils.getValidCellIndexFile(); Set uniqueBarcodes = new HashSet<>(); - ctx.getLogger().debug("writing cell barcodes"); + ctx.getLogger().debug("writing cell barcodes, using file: " + perCellTsv.getPath()); try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(cellBarcodeWhitelist), ',', CSVWriter.NO_QUOTE_CHARACTER);CSVReader reader = new CSVReader(IOUtil.openFileForBufferedUtf8Reading(perCellTsv), '\t')) { int rowIdx = 0; diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java index f9d8ce89d..41748d31a 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java @@ -376,7 +376,7 @@ public File runRemoteVdjCellHashingTasks(PipelineStepOutput output, String outpu File cellBarcodeWhitelist = getValidCellIndexFile(); Set uniqueBarcodes = new HashSet<>(); Set uniqueBarcodesIncludingNoCDR3 = new HashSet<>(); - _log.debug("writing cell barcodes"); + _log.debug("writing cell barcodes, using file: " + perCellTsv.getPath()); try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(cellBarcodeWhitelist), ',', CSVWriter.NO_QUOTE_CHARACTER); CSVReader reader = new CSVReader(Readers.getReader(perCellTsv), ',')) { int rowIdx = 0; diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java index 613f72914..64c53ba96 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java @@ -68,6 +68,7 @@ public CellRangerVDJWrapper(@Nullable Logger logger) public static final String TARGET_ASSAY = "targetAssay"; public static final String DELETE_EXISTING_ASSAY_DATA = "deleteExistingAssayData"; + public static final String INNER_ENRICHMENT_PRIMERS = "innerEnrichmentPrimers"; public static class VDJProvider extends AbstractAlignmentStepProvider { @@ -82,6 +83,9 @@ public VDJProvider() ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--force-cells"), "force-cells", "Force Cells", "Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot.", "ldk-integerfield", new JSONObject(){{ put("minValue", 0); }}, null), + ToolParameterDescriptor.create(INNER_ENRICHMENT_PRIMERS, "Inner Enrichment Primers", "An option comma-separated list of the inner primers used for TCR enrichment. These will be used for trimming.", "textfield", new JSONObject(){{ + + }}, true), ToolParameterDescriptor.create(TARGET_ASSAY, "Target Assay", "Results will be loaded into this assay. If no assay is selected, a table will be created with nothing in the DB.", "tcr-assayselectorfield", new JSONObject(){{ put("autoSelectAssay", false); }}, null), @@ -296,6 +300,29 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, File inputFast File indexDir = AlignerIndexUtil.getIndexDir(referenceGenome, getIndexCachedDirName(getPipelineCtx().getJob())); args.add("--reference=" + indexDir.getPath()); + String primers = StringUtils.trimToNull(getProvider().getParameterByName(INNER_ENRICHMENT_PRIMERS).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null)); + if (primers != null) + { + File primerFile = new File(outputDirectory, "primers.txt"); + try (PrintWriter writer = PrintWriters.getPrintWriter(primerFile)) + { + Arrays.stream(primers.split(",")).forEach(x -> { + x = StringUtils.trimToNull(x); + if (x != null) + { + writer.println(x); + } + }); + } + catch (IOException e) + { + throw new PipelineJobException(e); + } + + output.addIntermediateFile(primerFile); + args.add("--inner-enrichment-primers=" + primerFile.getPath()); + } + args.addAll(getClientCommandArgs("=")); Integer maxThreads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger()); From cbf62febf88f5107cd9fbfdf2018175b53d266b0 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 4 Nov 2020 11:38:41 -0800 Subject: [PATCH 02/15] Add support for cellranger vdj --disable-ui --- tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java index 64c53ba96..a50cc0f23 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java @@ -83,6 +83,9 @@ public VDJProvider() ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--force-cells"), "force-cells", "Force Cells", "Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot.", "ldk-integerfield", new JSONObject(){{ put("minValue", 0); }}, null), + ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--disable--ui"), "disable--ui", "Disable UI", "If checked, this will run cellranger with the optional web-based UI disabled.", "checkbox", new JSONObject(){{ + put("checked", true); + }}, true), ToolParameterDescriptor.create(INNER_ENRICHMENT_PRIMERS, "Inner Enrichment Primers", "An option comma-separated list of the inner primers used for TCR enrichment. These will be used for trimming.", "textfield", new JSONObject(){{ }}, true), From 633d7f4344d56503f6d849ad93e68a33e57b58da Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 4 Nov 2020 12:11:06 -0800 Subject: [PATCH 03/15] Larger input and validation for cellranger primer input --- .../labkey/tcrdb/pipeline/CellRangerVDJWrapper.java | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java index a50cc0f23..7b9c53fbf 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java @@ -86,9 +86,10 @@ public VDJProvider() ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--disable--ui"), "disable--ui", "Disable UI", "If checked, this will run cellranger with the optional web-based UI disabled.", "checkbox", new JSONObject(){{ put("checked", true); }}, true), - ToolParameterDescriptor.create(INNER_ENRICHMENT_PRIMERS, "Inner Enrichment Primers", "An option comma-separated list of the inner primers used for TCR enrichment. These will be used for trimming.", "textfield", new JSONObject(){{ - - }}, true), + ToolParameterDescriptor.create(INNER_ENRICHMENT_PRIMERS, "Inner Enrichment Primers", "An option comma-separated list of the inner primers used for TCR enrichment. These will be used for trimming.", "textarea", new JSONObject(){{ + put("height", 100); + put("width", 400); + }}, null), ToolParameterDescriptor.create(TARGET_ASSAY, "Target Assay", "Results will be loaded into this assay. If no assay is selected, a table will be created with nothing in the DB.", "tcr-assayselectorfield", new JSONObject(){{ put("autoSelectAssay", false); }}, null), @@ -306,6 +307,9 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, File inputFast String primers = StringUtils.trimToNull(getProvider().getParameterByName(INNER_ENRICHMENT_PRIMERS).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null)); if (primers != null) { + primers = primers.replaceAll("\\s+", ","); + primers = primers.replaceAll(",+", ","); + File primerFile = new File(outputDirectory, "primers.txt"); try (PrintWriter writer = PrintWriters.getPrintWriter(primerFile)) { From 039f82a8c61cb89cfa98115dd909096e7b8969e4 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 4 Nov 2020 12:12:51 -0800 Subject: [PATCH 04/15] cellranger param is a switch --- tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java index 7b9c53fbf..8ebd7ea51 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java @@ -83,7 +83,7 @@ public VDJProvider() ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--force-cells"), "force-cells", "Force Cells", "Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot.", "ldk-integerfield", new JSONObject(){{ put("minValue", 0); }}, null), - ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--disable--ui"), "disable--ui", "Disable UI", "If checked, this will run cellranger with the optional web-based UI disabled.", "checkbox", new JSONObject(){{ + ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--disable--ui"), "disable--ui", "Disable UI", "If checked, this will run cellranger with the optional web-based UI disabled.", "checkbox", new JSONObject(){{ put("checked", true); }}, true), ToolParameterDescriptor.create(INNER_ENRICHMENT_PRIMERS, "Inner Enrichment Primers", "An option comma-separated list of the inner primers used for TCR enrichment. These will be used for trimming.", "textarea", new JSONObject(){{ From e0cb5a706759c210038b5dca9555da68903ebdc2 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 4 Nov 2020 13:21:10 -0800 Subject: [PATCH 05/15] Fix param name --- tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java index 8ebd7ea51..3a7cdd341 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java @@ -83,7 +83,7 @@ public VDJProvider() ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--force-cells"), "force-cells", "Force Cells", "Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot.", "ldk-integerfield", new JSONObject(){{ put("minValue", 0); }}, null), - ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--disable--ui"), "disable--ui", "Disable UI", "If checked, this will run cellranger with the optional web-based UI disabled.", "checkbox", new JSONObject(){{ + ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--disable-ui"), "disable-ui", "Disable UI", "If checked, this will run cellranger with the optional web-based UI disabled.", "checkbox", new JSONObject(){{ put("checked", true); }}, true), ToolParameterDescriptor.create(INNER_ENRICHMENT_PRIMERS, "Inner Enrichment Primers", "An option comma-separated list of the inner primers used for TCR enrichment. These will be used for trimming.", "textarea", new JSONObject(){{ From 74e310e2ac5d5358bc2d81852c545919cc7eeefe Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 6 Nov 2020 15:11:32 -0800 Subject: [PATCH 06/15] set markdown output format --- .../src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java index 7d49bd571..06c8236e1 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java @@ -447,7 +447,7 @@ public void processFilesRemote(List inputFiles, JobContext c writer.println(); writer.println("setwd('/work')"); - writer.println("rmarkdown::render('" + rmdScript.getName() + "', clean=TRUE, output_file='" + outHtml.getName() + "')"); + writer.println("rmarkdown::render('" + rmdScript.getName() + "', clean=TRUE, output_format = 'html_document', output_file='" + outHtml.getName() + "')"); } catch (IOException e) { From 579191438a12956ffc9c3445d9c2cd27d24566df Mon Sep 17 00:00:00 2001 From: bbimber Date: Sat, 7 Nov 2020 15:35:57 -0800 Subject: [PATCH 07/15] If user supplies GTF file to seurat, use this instead of inferring --- .../pipeline/CellRangerSeuratHandler.java | 56 ++++++++++--------- 1 file changed, 29 insertions(+), 27 deletions(-) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java index 06c8236e1..8f988337a 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java @@ -60,6 +60,7 @@ public class CellRangerSeuratHandler extends AbstractParameterizedOutputHandler< { private FileType _fileType = new FileType("cloupe", false); public static final String SEURAT_MAX_THREADS = "seuratMaxThreads"; + private static final String GTF_FILE_ID = "gtfFileId"; public CellRangerSeuratHandler() { @@ -103,11 +104,11 @@ private static List getDefaultParams() put("storeValues", "simple;cca"); }}, "simple"), ToolParameterDescriptor.create(SEURAT_MAX_THREADS, "Seurat Max Threads", "Because seurat can behave badly with multiple threads, this allows a separate cap to be used from the main job. This will allow CITE-Seq-Count and other tools to run with more threads.", "ldk-integerfield", null, 1), - ToolParameterDescriptor.createExpDataParam("gtfFile", "Gene File", "This is the ID of a GTF file containing genes from this genome.", "sequenceanalysis-genomefileselectorfield", new JSONObject() + ToolParameterDescriptor.createExpDataParam(GTF_FILE_ID, "Gene File", "This is the ID of a GTF file containing genes from this genome.", "sequenceanalysis-genomefileselectorfield", new JSONObject() {{ put("extensions", Arrays.asList("gtf")); put("width", 400); - put("allowBlank", false); + put("allowBlank", true); }}, null) )); @@ -165,8 +166,6 @@ public boolean doSplitJobs() public class Processor implements SequenceOutputProcessor { - private static final String GTF_FILE_ID = "gtfFileIf"; - @Override public void init(PipelineJob job, SequenceAnalysisJobSupport support, List inputFiles, JSONObject params, File outputDir, List actions, List outputsToCreate) throws UnsupportedOperationException, PipelineJobException { @@ -184,19 +183,16 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List gtfIds = new HashSet<>(); - for (SequenceOutputFile so : inputFiles) + if (params.get(GTF_FILE_ID) == null) { - ExpData gtf = null; - ExpRun run = ExperimentService.get().getExpRun(so.getRunId()); - if (run != null) + job.getLogger().info("attempting to infer GTF:"); + + Set gtfIds = new HashSet<>(); + for (SequenceOutputFile so : inputFiles) { - List gtfDatas = run.getInputDatas("GTF File", null); - if (!gtfDatas.isEmpty()) - { - gtf = gtfDatas.get(0); - } - else + ExpData gtf = null; + ExpRun run = ExperimentService.get().getExpRun(so.getRunId()); + if (run != null) { //Because existing runs didnt explicitly track GTF as an input, try to infer: PipelineStatusFile sf = PipelineService.get().getStatusFile(run.getJobId()); @@ -226,23 +222,23 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List inputFiles, JobContext c RecordedAction action = new RecordedAction(getName()); ctx.addActions(action); - int gtfId = ctx.getSequenceSupport().getCachedObject(GTF_FILE_ID, Integer.class); + int gtfId = ctx.getParams().optInt(GTF_FILE_ID, -1); + if (gtfId == -1) + { + ctx.getLogger().debug("GTF file was not specified, defaulting to inferred file"); + gtfId = ctx.getSequenceSupport().getCachedObject(GTF_FILE_ID, Integer.class); + } + File gtfFile = ctx.getSequenceSupport().getCachedData(gtfId); if (!gtfFile.exists()) { From 035bc9d14bb116d15aad633a2bc4c205403f0cd9 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 10 Nov 2020 08:44:30 -0800 Subject: [PATCH 08/15] Add more options to LoFreq analysis --- tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java | 1 + 1 file changed, 1 insertion(+) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java index 8f988337a..e9b98234d 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java @@ -187,6 +187,7 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List gtfIds = new HashSet<>(); for (SequenceOutputFile so : inputFiles) { From b653dac595e315eafb38fd56e54aa08fe7045feb Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 11 Nov 2020 14:23:28 -0800 Subject: [PATCH 09/15] Cell hashing calling should not be performed when only one HTO is actually used --- .../org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java index e9b98234d..3330051a9 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerSeuratHandler.java @@ -692,11 +692,15 @@ else if (rs.getReadsetId() == null) throw new PipelineJobException(e); } - if (htosForReadset > 0) + if (htosForReadset > 1) { ctx.getLogger().info("Total HTOs for readset: " + htosForReadset); finalCalls.put(barcodePrefix, CellRangerCellHashingHandler.processBarcodeFile(ctx, barcodes, rs, htoReadset, so.getLibrary_id(), action, getClientCommandArgs(ctx.getParams()), false, SeuratCellHashingHandler.CATEGORY, true, perReadsetHtos, true)); } + else if (htosForReadset == 1) + { + ctx.getLogger().info("Only single HTO used for lane, skipping cell hashing calling"); + } else { ctx.getLogger().info("No HTOs found for readset"); From 18746c72b7966f289068d6e1348ab00a31ff540f Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 13 Nov 2020 10:39:38 -0800 Subject: [PATCH 10/15] Bugfix TagPcr metrics file parsing --- tcrdb/resources/external/scRNAseq/Seurat3.rmd | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/tcrdb/resources/external/scRNAseq/Seurat3.rmd b/tcrdb/resources/external/scRNAseq/Seurat3.rmd index a3911a6c7..e06fddaf7 100644 --- a/tcrdb/resources/external/scRNAseq/Seurat3.rmd +++ b/tcrdb/resources/external/scRNAseq/Seurat3.rmd @@ -1,13 +1,16 @@ --- title: 'Seurat scRNA-seq Analysis' +output: html_document + --- ```{r Setup} -knitr::opts_chunk$set(message=FALSE, warning=FALSE,echo=TRUE,error = FALSE) library(knitr) library(OOSAP) +knitr::opts_chunk$set(message=FALSE, warning=FALSE, echo=TRUE, error = FALSE) + cores <- Sys.getenv('SEQUENCEANALYSIS_MAX_THREADS') if (cores != ''){ print(paste0('Setting future::plan to ', cores, ' cores')) From 5ffa101e7ee3a1b49a66ddcc79a9b885638f00f6 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 16 Nov 2020 09:58:01 -0800 Subject: [PATCH 11/15] Show error in rmarkdown/html for better debugging --- tcrdb/resources/external/scRNAseq/Seurat3.rmd | 2 +- .../org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java | 2 +- tcrdb/src/org/labkey/tcrdb/pipeline/SeuratCiteSeqHandler.java | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tcrdb/resources/external/scRNAseq/Seurat3.rmd b/tcrdb/resources/external/scRNAseq/Seurat3.rmd index e06fddaf7..9fb58d5aa 100644 --- a/tcrdb/resources/external/scRNAseq/Seurat3.rmd +++ b/tcrdb/resources/external/scRNAseq/Seurat3.rmd @@ -9,7 +9,7 @@ output: html_document library(knitr) library(OOSAP) -knitr::opts_chunk$set(message=FALSE, warning=FALSE, echo=TRUE, error = FALSE) +knitr::opts_chunk$set(message=FALSE, warning=FALSE, echo=TRUE, error = TRUE) cores <- Sys.getenv('SEQUENCEANALYSIS_MAX_THREADS') if (cores != ''){ diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java index 79c2bcc53..3cd2ecf90 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java @@ -63,7 +63,7 @@ public static List getDefaultHashingParams(boolean incl ToolParameterDescriptor.create("scanEditDistances", "Scan Edit Distances", "If checked, CITE-seq-count will be run using edit distances from 0-3 and the iteration with the highest singlets will be used.", "checkbox", new JSONObject(){{ put("checked", false); }}, false), - ToolParameterDescriptor.create("editDistance", "Edit Distance", null, "ldk-integerfield", null, 3), + ToolParameterDescriptor.create("editDistance", "Edit Distance", null, "ldk-integerfield", null, 2), ToolParameterDescriptor.create("minCountPerCell", "Min Reads/Cell", null, "ldk-integerfield", null, 5), ToolParameterDescriptor.create("useSeurat", "Use Seurat Calling", "If checked, the seurat HTO calling algorithm will be used.", "checkbox", null, true), ToolParameterDescriptor.create("useMultiSeq", "Use MultiSeq Calling", "If checked, the MultiSeq HTO calling algorithm will be used.", "checkbox", null, true) diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/SeuratCiteSeqHandler.java b/tcrdb/src/org/labkey/tcrdb/pipeline/SeuratCiteSeqHandler.java index 853a68a0b..582b5dd92 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/SeuratCiteSeqHandler.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/SeuratCiteSeqHandler.java @@ -27,7 +27,7 @@ public class SeuratCiteSeqHandler extends AbstractParameterizedOutputHandler Date: Tue, 17 Nov 2020 14:23:28 -0800 Subject: [PATCH 12/15] Allow wildcards when specifying plate lists --- .../web/tcrdb/panel/LibraryExportPanel.js | 63 ++++++++++++++++++- 1 file changed, 61 insertions(+), 2 deletions(-) diff --git a/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js b/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js index 4988c82e5..b17e8cf4a 100644 --- a/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js +++ b/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js @@ -88,7 +88,7 @@ Ext4.define('TCRdb.panel.LibraryExportPanel', { border: false }, items: [{ - html: 'Add an ordered list of plates, using tab-delimited columns. The first column(s) are plate ID and library type (GEX, VDJ, CITE, or HTO). These can either be one column (i.e. G234-1, C234-1, H234-1, or T234-1), or as two columns (234-1 GEX or 234-1 HTO). An optional next column is the lane assignment (i.e. Novaseq1, HiSeq1, HiSeq2). Finally, an optional final column can be used to provide the alias for this pool. This is mostly used for CITE-Seq/HTOs, where multiple libraries are pre-pooled. See these examples:
' + + html: 'Add an ordered list of plates, using tab-delimited columns. The first column(s) are plate ID and library type (GEX, VDJ, CITE, or HTO). These can either be one column (i.e. G234-1, C234-1, H234-1, or T234-1), or as two columns (234-1 GEX or 234-1 HTO). An optional next column is the lane assignment (i.e. Novaseq1, HiSeq1, HiSeq2). Finally, an optional final column can be used to provide the alias for this pool. This is mostly used for CITE-Seq/HTOs, where multiple libraries are pre-pooled. Note, a wildcard can be used to specify all plates beginning with that prefix. See these examples:
' + '
' +
                                                 '234-2\tGEX
' +
                                                 '234-2\tVDJ
' +
@@ -101,6 +101,7 @@ Ext4.define('TCRdb.panel.LibraryExportPanel', {
                                                 '235-2\tHTO\tHiSeq2\tBNB-HTO-1
' +
                                                 'H235-2\tHiSeq1\tBNB-HTO-1
' +
                                                 'C235-2\tHiSeq1\tBNB-HTO-1' +
+                                                'C235-*\tHiSeq2\tBNB-HTO-2' +
                                             '
', border: false },{ @@ -171,6 +172,7 @@ Ext4.define('TCRdb.panel.LibraryExportPanel', { }, this); var hadError = false; + var wildcards = {}; Ext4.Array.forEach(text, function(r){ if (r.length < 2){ hadError = true; @@ -186,6 +188,12 @@ Ext4.define('TCRdb.panel.LibraryExportPanel', { Ext4.Array.forEach(r, function(val, idx){ r[idx] = Ext4.String.trim(val); }, this); + + if (r[0].match('\\*$')) { + var m = r[0].match('\\*$'); + var val = r[0].substr(0, m.index); + wildcards[val] = r; + } }, this); if (hadError) { @@ -193,7 +201,58 @@ Ext4.define('TCRdb.panel.LibraryExportPanel', { return; } - this.onSubmit(btn, text); + if (!Ext4.Object.isEmpty(wildcards)) { + LABKEY.Query.selectRows({ + method: 'POST', + containerPath: Laboratory.Utils.getQueryContainerPath(), + schemaName: 'tcrdb', + queryName: 'cdnas', + columns: 'rowid,plateId', + filterArray: [LABKEY.Filter.create('plateId', Ext4.Object.getKeys(wildcards).join(';'), LABKEY.Filter.Types.CONTAINS_ONE_OF)], + scope: this, + failure: LDK.Utils.getErrorCallback(), + success: function (results) { + if (results.rows.length) { + var prefixToPlate = {}; + Ext4.Array.forEach(results.rows, function (row) { + Ext4.Array.forEach(Ext4.Object.getKeys(wildcards), function (prefix) { + if (row.plateId && row.plateId.includes(prefix)) { + prefix = prefix + '*'; + prefixToPlate[prefix] = prefixToPlate[prefix] || []; + prefixToPlate[prefix].push(row.plateId); + } + }, this); + }, this); + + Ext4.Array.forEach(Ext4.Object.getKeys(prefixToPlate), function (prefix) { + prefixToPlate[prefix] = Ext4.unique(prefixToPlate[prefix]); + }, this); + + var updatedText = []; + var prefixes = Ext4.Object.getKeys(prefixToPlate); + Ext4.Array.forEach(text, function (r, idx) { + var plateId = r[0]; + if (prefixes.indexOf(plateId) == -1) { + updatedText.push(r); + } + else { + Ext4.Array.forEach(prefixToPlate[plateId], function(newPlate){ + var r2 = [].concat(r); + r2[0] = newPlate; + updatedText.push(r2); + }, this); + } + }, this); + + text = updatedText; + } + + this.onSubmit(btn, text); + } + }); + } else { + + } } }] }); From eb4fe290a344b06ba73e38ae99c5fc3066664b4c Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 17 Nov 2020 15:47:28 -0800 Subject: [PATCH 13/15] bugfix library export panel --- tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js b/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js index b17e8cf4a..2626e445d 100644 --- a/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js +++ b/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js @@ -251,7 +251,7 @@ Ext4.define('TCRdb.panel.LibraryExportPanel', { } }); } else { - + this.onSubmit(btn, text); } } }] From 6fdf04d0603ea99275b4e2a3f3e11389e3602854 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 18 Nov 2020 20:58:55 -0800 Subject: [PATCH 14/15] Reformat phiX --- tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js b/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js index 2626e445d..7e3354dc8 100644 --- a/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js +++ b/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js @@ -816,10 +816,10 @@ Ext4.define('TCRdb.panel.LibraryExportPanel', { var delim = instrument === 'Novogene' ? '\t' : ','; Ext4.Array.forEach(sortedRows, function (r) { - processType(readsetIds, rows, r, 'readsetId', 'GEX', 500, 1, 'G', null, false); - processType(readsetIds, rows, r, 'enrichedReadsetId', 'TCR', 700, 1, 'T', null, false); - processType(readsetIds, rows, r, 'hashingReadsetId', 'HTO', 182, 5, 'H', 'Cell hashing, 190bp amplicon. Please QC individually and pool in equal amounts per lane', true); - processType(readsetIds, rows, r, 'citeseqReadsetId', 'CITE', 182, 5, 'C', 'CITE-Seq, 190bp amplicon. Please QC individually and pool in equal amounts per lane', false); + processType(readsetIds, rows, r, 'readsetId', 'GEX', 500, 0.01, 'G', null, false); + processType(readsetIds, rows, r, 'enrichedReadsetId', 'TCR', 700, 0.01, 'T', null, false); + processType(readsetIds, rows, r, 'hashingReadsetId', 'HTO', 182, 0.05, 'H', 'Cell hashing, 190bp amplicon. Please QC individually and pool in equal amounts per lane', true); + processType(readsetIds, rows, r, 'citeseqReadsetId', 'CITE', 182, 0.05, 'C', 'CITE-Seq, 190bp amplicon. Please QC individually and pool in equal amounts per lane', false); }, this); //add missing barcodes: From 0f301adbdd3ca6c362142b3e28f8be250f336cf7 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 20 Nov 2020 13:17:11 -0800 Subject: [PATCH 15/15] Support custom cropping of F/R reads --- tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js b/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js index 7e3354dc8..e3d3b9934 100644 --- a/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js +++ b/tcrdb/resources/web/tcrdb/panel/LibraryExportPanel.js @@ -324,11 +324,11 @@ Ext4.define('TCRdb.panel.LibraryExportPanel', { var instrument = btn.up('tcrdb-libraryexportpanel').down('#instrument').getValue(); var plateId = btn.up('tcrdb-libraryexportpanel').down('#sourcePlates').getValue(); var delim = 'TAB'; - var extention = 'txt'; + var extension = 'txt'; var split = '\t'; if (instrument !== 'NextSeq (MPSSR)') { delim = 'COMMA'; - extention = 'csv'; + extension = 'csv'; split = ','; } @@ -336,7 +336,7 @@ Ext4.define('TCRdb.panel.LibraryExportPanel', { var rows = LDK.Utils.CSVToArray(Ext4.String.trim(val), split); LABKEY.Utils.convertToTable({ - fileName: plateId + '.' + extention, + fileName: plateId + '.' + extension, rows: rows, delim: delim });