Bugfix to nimble awk command to output gzip

bbimber · bbimber · commit fdfd1ae12745 · 2022-12-06T10:50:14.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -365,7 +365,7 @@ else if (!resultsGz.exists())
         {
             SimpleScriptWrapper runner = new SimpleScriptWrapper(getPipelineCtx().getLogger());
             File alignmentOutputFile2 = new File(alignmentOutputFile.getParentFile(), alignmentOutputFile.getName().replace(".txt.gz", ".subset.txt.gz"));
-            runner.execute(Arrays.asList("/bin/bash", "-c", "zcat '" + alignmentOutputFile.getPath() + "' | awk -F '\t' ' $1!=\"\" ' > " + alignmentOutputFile2.getPath()));
+            runner.execute(Arrays.asList("/bin/bash", "-c", "zcat '" + alignmentOutputFile.getPath() + "' | awk -F '\t' ' $1!=\"\" ' | gzip -c > " + alignmentOutputFile2.getPath()));
         }
         else
         {

Original file line number	Diff line number	Diff line change
`@@ -365,7 +365,7 @@ else if (!resultsGz.exists())`
`365`	`365`	`{`
`366`	`366`	`SimpleScriptWrapper runner = new SimpleScriptWrapper(getPipelineCtx().getLogger());`
`367`	`367`	`File alignmentOutputFile2 = new File(alignmentOutputFile.getParentFile(), alignmentOutputFile.getName().replace(".txt.gz", ".subset.txt.gz"));`
`368`		`- runner.execute(Arrays.asList("/bin/bash", "-c", "zcat '" + alignmentOutputFile.getPath() + "' \| awk -F '\t' ' $1!=\"\" ' > " + alignmentOutputFile2.getPath()));`
	`368`	`+ runner.execute(Arrays.asList("/bin/bash", "-c", "zcat '" + alignmentOutputFile.getPath() + "' \| awk -F '\t' ' $1!=\"\" ' \| gzip -c > " + alignmentOutputFile2.getPath()));`
`369`	`369`	`}`
`370`	`370`	`else`
`371`	`371`	`{`