Commit 71b12276 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added option for metrics for each chunk

parent c43bfa2a
...@@ -186,6 +186,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript { ...@@ -186,6 +186,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
case "star-2pass" => addStar2pass(R1, R2, outputBam, deps) case "star-2pass" => addStar2pass(R1, R2, outputBam, deps)
case _ => throw new IllegalStateException("Option Alginer: '" + aligner + "' is not valid") case _ => throw new IllegalStateException("Option Alginer: '" + aligner + "' is not valid")
} }
if (config("chunk_metrics", default = false))
addAll(BamMetrics(this, outputBam, chunkDir + "metrics/").functions)
} }
if (!skipFlexiprep) { if (!skipFlexiprep) {
flexiprep.runFinalize(fastq_R1_output, fastq_R2_output) flexiprep.runFinalize(fastq_R1_output, fastq_R2_output)
...@@ -202,7 +204,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript { ...@@ -202,7 +204,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bamFile = mergeSamFile.output bamFile = mergeSamFile.output
} }
if (!skipMetrics) addAll(BamMetrics.apply(this, bamFile, outputDir + "metrics/").functions) if (!skipMetrics) addAll(BamMetrics(this, bamFile, outputDir + "metrics/").functions)
outputFiles += ("finalBamFile" -> bamFile) outputFiles += ("finalBamFile" -> bamFile)
} }
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