From f3192f66df0fbe432ffdcc8341441576dc84a05a Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 23 Jun 2024 19:35:35 -0700 Subject: [PATCH] Paragraph: perform more cleanup --- .../labkey/sequenceanalysis/run/alignment/ParagraphStep.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java index 1a126204b..c1759fcd2 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java @@ -207,6 +207,11 @@ else if (header.getReadGroups().size() > 1) } ctx.getFileManager().addSequenceOutput(genotypes, "paraGRAPH Genotypes: " + so.getName(), "paraGRAPH Genoypes", so.getReadset(), null, so.getLibrary_id(), "Input VCF: " + svVcf.getName() + " (" + svVcfId + ")"); + + ctx.getFileManager().addIntermediateFile(new File(paragraphOutDir, "variants.json.gz")); + ctx.getFileManager().addIntermediateFile(new File(paragraphOutDir, "variants.vcf.gz")); + ctx.getFileManager().addIntermediateFile(new File(paragraphOutDir, "genotypes.json.gz")); + ctx.getFileManager().addIntermediateFile(new File(paragraphOutDir, "grmpy.log")); } } }