From e712037de95e01b3012443c95b8ef3b9a06cf3fb Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 5 Feb 2025 10:37:05 -0800 Subject: [PATCH 1/5] Improve logging --- .../labkey/sequenceanalysis/run/alignment/SVTyperStep.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/SVTyperStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/SVTyperStep.java index 2c5b7a629..7f41b3111 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/SVTyperStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/SVTyperStep.java @@ -113,6 +113,8 @@ else if (!svVcf.exists()) jsonArgs.add("-l"); jsonArgs.add(coverageJson.getPath()); + jsonArgs.add("--verbose"); + File doneFile = new File(ctx.getWorkingDirectory(), "json.done"); ctx.getFileManager().addIntermediateFile(doneFile); if (doneFile.exists()) @@ -151,6 +153,8 @@ else if (!svVcf.exists()) svtyperArgs.add("-l"); svtyperArgs.add(coverageJson.getPath()); + svtyperArgs.add("--verbose"); + if (threads != null) { svtyperArgs.add("--core"); From 19aec1312584de599d03318573946aba276c9b80 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 7 Feb 2025 09:54:07 -0800 Subject: [PATCH 2/5] Ensure SnpEff marks genome modified --- .../org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java index 02330ab17..70f91bcf7 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java @@ -8,6 +8,7 @@ import org.labkey.api.pipeline.PipelineJobService; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; +import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenomeManager; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper; import org.labkey.api.util.FileUtil; @@ -159,6 +160,8 @@ else if ("gbk".equalsIgnoreCase(ext)) //params.add(basename); execute(params); + + ReferenceGenomeManager.get().markGenomeModified(genome, getLogger()); } From de48ea37ab028427c7bf9d589952932964f6dc8d Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 9 Feb 2025 14:53:13 -0800 Subject: [PATCH 3/5] Update param defaults --- .../api-src/org/labkey/api/singlecell/CellHashingService.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java b/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java index 9939f706c..95a1fcf2d 100644 --- a/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java +++ b/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java @@ -132,7 +132,7 @@ public static CellHashingService.CellHashingParameters createFromStep(SequenceOu ret.callerDisagreementThreshold = step.getProvider().getParameterByName("callerDisagreementThreshold").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null); ret.doTSNE = step.getProvider().getParameterByName("doTSNE").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false); ret.doNotAllowResume = step.getProvider().getParameterByName("doNotAllowResume").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false); - ret.retainRawCountFile = step.getProvider().getParameterByName("retainRawCountFile").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true); + ret.retainRawCountFile = step.getProvider().getParameterByName("retainRawCountFile").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false); ret.failIfUnexpectedHtosFound = step.getProvider().getParameterByName("failIfUnexpectedHtosFound").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true); ret.htoReadset = htoReadset; ret.parentReadset = parentReadset; @@ -177,7 +177,7 @@ public static CellHashingParameters createFromJson(BARCODE_TYPE type, File webse ret.callerDisagreementThreshold = params.get("callerDisagreementThreshold") == null ? null : params.getDouble("callerDisagreementThreshold"); ret.doTSNE = params.optBoolean("doTSNE", false); ret.doNotAllowResume = params.optBoolean("doNotAllowResume", false); - ret.retainRawCountFile = params.optBoolean("retainRawCountFile", true); + ret.retainRawCountFile = params.optBoolean("retainRawCountFile", false); ret.failIfUnexpectedHtosFound = params.optBoolean("failIfUnexpectedHtosFound", true); ret.htoReadset = htoReadset; ret.parentReadset = parentReadset; From 413825dbc52072159a8a58b36b568a2a659b7248 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 11 Feb 2025 10:09:47 -0800 Subject: [PATCH 4/5] Add detail to Plink/KING output --- .../sequenceanalysis/run/variant/PlinkPcaStep.java | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java index 01ce28d43..bf231cdaa 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java @@ -228,8 +228,17 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep throw new PipelineJobException("Unable to find expected file: " + outputFile); } + String description = null; + if (kingCutoff != null) + { + long includedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.in.id")) - 1; + long excludedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.out.id")) - 1; + + description = String.format("KING cutoff: %f, included IDs: %d, excluded IDs: %d", kingCutoff, includedIds, excludedIds); + } + output.addOutput(outputFile, "PLink PCA"); - output.addSequenceOutput(outputFile, "PLink PCA for: " + inputVCF.getName() + (setName == null ? "" : ", for: " + setName), "PLink PCA", null, null, genome.getGenomeId(), null); + output.addSequenceOutput(outputFile, "PLink PCA for: " + inputVCF.getName() + (setName == null ? "" : ", for: " + setName), "PLink PCA", null, null, genome.getGenomeId(), description); } @Override From 7be1c3acbb2aa148b8cd07add395d63e0abb8d09 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 11 Feb 2025 10:10:55 -0800 Subject: [PATCH 5/5] Add detail to Plink/KING output --- .../org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java index bf231cdaa..4c5c204e8 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java @@ -231,8 +231,8 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep String description = null; if (kingCutoff != null) { - long includedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.in.id")) - 1; - long excludedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.out.id")) - 1; + long includedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.in.id")); + long excludedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.out.id")); description = String.format("KING cutoff: %f, included IDs: %d, excluded IDs: %d", kingCutoff, includedIds, excludedIds); }