From 806a1fb2698c21afe65f6c194d5618194a38d1c9 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 16 Jan 2025 10:46:49 -0800 Subject: [PATCH] Drop --include-technical --- .../sequenceanalysis/pipeline/SequenceAlignmentTask.java | 2 +- .../sequenceanalysis/run/RestoreSraDataHandler.java | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java index 0ec9d6ac6..19ea891a7 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java @@ -2022,7 +2022,7 @@ else if (sraIDs.contains(rd.getSra_accession())) outDir.mkdirs(); } - Pair downloaded = sra.downloadSra(rd.getSra_accession(), unzippedOutDir, rd.isPairedEnd()); + Pair downloaded = sra.downloadSra(rd.getSra_accession(), unzippedOutDir, rd.isPairedEnd(), false); File moved1 = new File(outDir, downloaded.first.getName()); if (moved1.exists()) { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java index 1970b4fb7..8779afda1 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java @@ -384,7 +384,7 @@ public void processFilesRemote(List readsets, JobContext ctx) throws Un File expectedFile2 = rd.getFileId2() == null ? null : ctx.getSequenceSupport().getCachedData(rd.getFileId2()); FastqDumpWrapper wrapper = new FastqDumpWrapper(ctx.getLogger()); - Pair files = wrapper.downloadSra(accession, ctx.getOutputDir(), rd.isPairedEnd()); + Pair files = wrapper.downloadSra(accession, ctx.getOutputDir(), rd.isPairedEnd(), false); long lines1 = SequenceUtil.getLineCount(files.first) / 4; ctx.getJob().getLogger().debug("Reads in " + files.first.getName() + ": " + lines1); @@ -459,13 +459,16 @@ public FastqDumpWrapper(@Nullable Logger logger) super(logger); } - public Pair downloadSra(String dataset, File outDir, boolean expectPaired) throws PipelineJobException + public Pair downloadSra(String dataset, File outDir, boolean expectPaired, boolean includeTechnical) throws PipelineJobException { List args = new ArrayList<>(); args.add(getExe().getPath()); // NOTE: we probably want the --split-3 behavior, which is the default for fasterq-dump - args.add("--include-technical"); + if (includeTechnical) + { + args.add("--include-technical"); + } Integer threads = SequencePipelineService.get().getMaxThreads(getLogger()); if (threads != null)