Paragraph: log to stderr instead of separate file

bbimber · bbimber · commit 11e89d358f62 · 2024-06-23T08:26:56.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java
@@ -187,9 +187,6 @@ else if (header.getReadGroups().size() > 1)
                     paragraphArgs.add(threads.toString());
                 }
 
-                paragraphArgs.add("--logfile");
-                paragraphArgs.add(new File("/work/paragraph.log").getPath());
-
                 dockerWrapper.executeWithDocker(paragraphArgs, ctx.getWorkingDirectory(), ctx.getFileManager());
 
                 File genotypes = new File(ctx.getWorkingDirectory(), "genotypes.vcf.gz");

Original file line number	Diff line number	Diff line change
`@@ -187,9 +187,6 @@ else if (header.getReadGroups().size() > 1)`
`187`	`187`	`paragraphArgs.add(threads.toString());`
`188`	`188`	`}`
`189`	`189`
`190`		`- paragraphArgs.add("--logfile");`
`191`		`- paragraphArgs.add(new File("/work/paragraph.log").getPath());`
`192`		`-`
`193`	`190`	`dockerWrapper.executeWithDocker(paragraphArgs, ctx.getWorkingDirectory(), ctx.getFileManager());`
`194`	`191`
`195`	`192`	`File genotypes = new File(ctx.getWorkingDirectory(), "genotypes.vcf.gz");`