Commit 3c228abe authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix for #210

(cherry picked from commit 910074b8)
parent 5555a57f
......@@ -243,7 +243,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
case _ => throw new IllegalStateException("Option aligner: '" + aligner + "' is not valid")
}
if (chunking && numberChunks.getOrElse(1) > 1 && config("chunk_metrics", default = false))
addAll(BamMetrics(this, outputBam, new File(chunkDir, "metrics")).functions)
addAll(BamMetrics(this, outputBam, new File(chunkDir, "metrics"), sampleId, libId).functions)
}
if (!skipFlexiprep) {
flexiprep.runFinalize(fastq_R1_output, fastq_R2_output)
......@@ -264,7 +264,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
if (!skipMetrics) {
val bamMetrics = BamMetrics(this, bamFile, new File(outputDir, "metrics"))
val bamMetrics = BamMetrics(this, bamFile, new File(outputDir, "metrics"), sampleId, libId)
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment