Bugfix to split VCF jobs (#130)

bbimber · web-flow · commit e803df78f8f3 · 2023-10-06T17:52:57.000-07:00
* Fix MCC jest tests

* Bugfix to split VCF jobs
diff --git a/mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java b/mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java
@@ -430,7 +430,7 @@ public void performAdditionalMergeTasks(SequenceOutputHandler.JobContext ctx, Pi
         {
             job.getLogger().debug("Merging track: " + trackName);
             List<File> toConcat = orderedJobDirs.stream().map(dirName -> {
-                File f = getOutputVcf(trackName, new File(ctx.getWorkingDirectory(), dirName));
+                File f = getOutputVcf(trackName, new File(ctx.getSourceDirectory(), dirName));
                 if (!f.exists())
                 {
                     throw new IllegalStateException("Missing file: " + f.getPath());

Original file line number	Diff line number	Diff line change
`@@ -430,7 +430,7 @@ public void performAdditionalMergeTasks(SequenceOutputHandler.JobContext ctx, Pi`
`430`	`430`	`{`
`431`	`431`	`job.getLogger().debug("Merging track: " + trackName);`
`432`	`432`	`List<File> toConcat = orderedJobDirs.stream().map(dirName -> {`
`433`		`- File f = getOutputVcf(trackName, new File(ctx.getWorkingDirectory(), dirName));`
	`433`	`+ File f = getOutputVcf(trackName, new File(ctx.getSourceDirectory(), dirName));`
`434`	`434`	`if (!f.exists())`
`435`	`435`	`{`
`436`	`436`	`throw new IllegalStateException("Missing file: " + f.getPath());`