From fa50992cf38f333faf77b78ce7309a7707db90cd Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 27 Jan 2025 11:25:32 -0800 Subject: [PATCH] Allow nimble plot to run and not produce an HTML file --- .../org/labkey/singlecell/run/NimbleHelper.java | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java index d6cf466a1..b48c5cb14 100644 --- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java +++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java @@ -292,17 +292,9 @@ public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, Strin output.addSequenceOutput(results, basename + ": nimble align", "Nimble Results", rs.getRowId(), null, genome.getGenomeId(), description); + // NOTE: situations like zero alignments would result in no report being created. Rely on the code in doAlign to verify proper execution of nimble File reportHtml = getReportHtmlFileFromResults(results); - if (!reportHtml.exists()) - { - if (SequencePipelineService.get().hasMinLineCount(results, 2)) - { - long lineCount = SequencePipelineService.get().getLineCount(results); - _ctx.getLogger().debug("Found {} lines in file {}", lineCount, results.getPath()); - throw new PipelineJobException("Unable to find file: " + reportHtml.getPath()); - } - } - else + if (reportHtml.exists()) { output.addSequenceOutput(reportHtml, basename + ": nimble report", NIMBLE_REPORT_CATEGORY, rs.getRowId(), null, genome.getGenomeId(), description); } @@ -554,7 +546,7 @@ public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineSt if (!plotResultsHtml.exists()) { - throw new PipelineJobException("Missing file: " + plotResultsHtml.getPath()); + ctx.getLogger().info("No report HTML generated, but nimble plot had exit code 0"); } } else