Commit 3c4a8dec authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'fix-bammetrics_summary' into 'develop'

Fix for #210

Fixes #210 

See merge request !242
parents 5555a57f 3c228abe
...@@ -243,7 +243,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S ...@@ -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") case _ => throw new IllegalStateException("Option aligner: '" + aligner + "' is not valid")
} }
if (chunking && numberChunks.getOrElse(1) > 1 && config("chunk_metrics", default = false)) 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) { if (!skipFlexiprep) {
flexiprep.runFinalize(fastq_R1_output, fastq_R2_output) flexiprep.runFinalize(fastq_R1_output, fastq_R2_output)
...@@ -264,7 +264,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S ...@@ -264,7 +264,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
} }
if (!skipMetrics) { 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) addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics) addSummaryQScript(bamMetrics)
} }
......
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