Commit 9d748545 authored by bow's avatar bow
Browse files

Use file names for logging errors in Flexiprep Cutadapt wrapper instead of read names

parent d207b97f
......@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
* @param root: Configurable object from which this wrapper is initialized.
* @param fastqc: Fastqc wrapper that contains adapter information.
*/
class Cutadapt(root: Configurable, fastqc: Fastqc, readName: String) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
class Cutadapt(root: Configurable, fastqc: Fastqc) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
/** Clipped adapter names from FastQC */
protected def seqToName = fastqc.foundAdapters
......@@ -49,16 +49,16 @@ class Cutadapt(root: Configurable, fastqc: Fastqc, readName: String) extends nl.
// adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter
// sequences come from FastQC
case _ =>
throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in 'clipping_$readName'.")
throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in '$fastq_input'.")
}
}.toMap
// FastQC found no adapters
case otherwise =>
logger.info(s"No adapters found for summarizing in 'clipping_$readName'.")
logger.info(s"No adapters found for summarizing in '$fastq_input'.")
Map.empty[String, Map[String, Any]]
}
// "adapters" key not found ~ something went wrong in our part
case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry 'clipping_$readName'.")
case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry '$fastq_input'.")
}
initStats.updated("adapters", adapterCounts)
}
......
......@@ -93,7 +93,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
clip = if (!flexiprep.skipClip) {
val foundAdapters = fastqc.foundAdapters.map(_.seq)
if (foundAdapters.nonEmpty) {
val cutadapt = new Cutadapt(root, fastqc, read)
val cutadapt = new Cutadapt(root, fastqc)
cutadapt.fastq_input = seqtk.output
cutadapt.fastq_output = new File(output.getParentFile, input.getName + ".cutadapt.fq")
cutadapt.stats_output = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
......
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