Declare inputs in ParagraphStep

bbimber · bbimber · commit d2a0fe9e5ef0 · 2024-12-03T16:53:41.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java
@@ -281,7 +281,7 @@ else if (!svVcf.exists())
                     paragraphArgs.add(threads.toString());
                 }
 
-                dockerWrapper.executeWithDocker(paragraphArgs, ctx.getWorkingDirectory(), ctx.getFileManager());
+                dockerWrapper.executeWithDocker(paragraphArgs, ctx.getWorkingDirectory(), ctx.getFileManager(), Arrays.asList(so.getFile(), genomeFasta, svVcf));
 
                 File genotypes = new File(paragraphOutDir, "genotypes.vcf.gz");
                 if (!genotypes.exists())

Original file line number	Diff line number	Diff line change
`@@ -281,7 +281,7 @@ else if (!svVcf.exists())`
`281`	`281`	`paragraphArgs.add(threads.toString());`
`282`	`282`	`}`
`283`	`283`
`284`		`- dockerWrapper.executeWithDocker(paragraphArgs, ctx.getWorkingDirectory(), ctx.getFileManager());`
	`284`	`+ dockerWrapper.executeWithDocker(paragraphArgs, ctx.getWorkingDirectory(), ctx.getFileManager(), Arrays.asList(so.getFile(), genomeFasta, svVcf));`
`285`	`285`
`286`	`286`	`File genotypes = new File(paragraphOutDir, "genotypes.vcf.gz");`
`287`	`287`	`if (!genotypes.exists())`