From bd6708e134ecd76b9939d29832e1b56726310766 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Tue, 20 Feb 2024 12:54:09 -0800
Subject: [PATCH] Remove workaround with nimble and allow nimble to directly
 output gzipped output

---
 .../labkey/singlecell/run/NimbleHelper.java   | 24 ++++---------------
 1 file changed, 5 insertions(+), 19 deletions(-)

diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
index f8b1133ee..07056c31d 100644
--- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
+++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -440,7 +440,7 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
             alignArgs.add(strandedness);
         }
 
-        File alignmentTsvBase = new File(getPipelineCtx().getWorkingDirectory(), "alignResults." + (genomes.size() == 1 ? genomes.get(0).genomeId + "." : "") + "txt");
+        File alignmentTsvBase = new File(getPipelineCtx().getWorkingDirectory(), "alignResults." + (genomes.size() == 1 ? genomes.get(0).genomeId + "." : "") + "txt.gz");
 
         alignArgs.add("--reference");
         alignArgs.add(localRefJsons.stream().map(x -> "/work/" + x.getName()).collect(Collectors.joining(",")));
@@ -461,8 +461,8 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
         boolean dockerRan = runUsingDocker(alignArgs, output, "align.all");
         for (NimbleGenome genome : genomes)
         {
-            File alignResultsTsv = new File(getPipelineCtx().getWorkingDirectory(), "alignResults." + genome.genomeId + ".txt");
-            if (dockerRan && !alignResultsTsv.exists())
+            File alignResultsGz = new File(getPipelineCtx().getWorkingDirectory(), "alignResults." + genome.genomeId + ".txt.gz");
+            if (dockerRan && !alignResultsGz.exists())
             {
                 File doneFile = getNimbleDoneFile(getPipelineCtx().getWorkingDirectory(), "align.all");
                 if (doneFile.exists())
@@ -470,24 +470,10 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
                     doneFile.delete();
                 }
 
-                throw new PipelineJobException("Expected to find file: " + alignResultsTsv.getPath());
+                throw new PipelineJobException("Expected to find file: " + alignResultsGz.getPath());
             }
 
-            File alignResultsGz = new File(alignResultsTsv.getPath() + ".gz");
-            if (dockerRan)
-            {
-                if (alignResultsGz.exists())
-                {
-                    getPipelineCtx().getLogger().debug("Deleting pre-existing gz output: " + alignResultsGz.getName());
-                    alignResultsGz.delete();
-                }
-
-                // NOTE: perform compression outside of nimble until nimble bugs fixed
-                getPipelineCtx().getLogger().debug("Compressing results TSV file");
-                alignResultsGz = Compress.compressGzip(alignResultsTsv);
-                alignResultsTsv.delete();
-            }
-            else if (!alignResultsGz.exists())
+            if (!alignResultsGz.exists())
             {
                 throw new PipelineJobException("Expected to find gz file: " + alignResultsGz.getPath());
             }