Commit 5d5c30c1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed summary files of flexiprep

parent a7da2f6a
......@@ -47,11 +47,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Returns files to store in summary */
def summaryFiles: Map[String, File] = {
if (!skipTrim || !skipClip)
Map("input_R1" -> input_R1, "output_R1" -> outputFiles("output_R1_gzip")) ++
(if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> outputFiles("output_R2_gzip")) else Map())
else Map("input_R1" -> input_R1) ++
(if (paired) Map("input_R2" -> input_R2.get) else Map())
Map("input_R1" -> input_R1, "output_R1" -> fastqR1Qc) ++
(if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> fastqR2Qc.get) else Map())
}
/** returns settings to store in summary */
......@@ -112,8 +109,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def biopetScript() {
runInitialJobs()
val out = if (paired) runTrimClip(outputFiles("fastq_input_R1"), Some(outputFiles("fastq_input_R2")), outputDir)
else runTrimClip(outputFiles("fastq_input_R1"), outputDir)
val out = if (paired) runTrimClip(input_R1, input_R2, outputDir)
else runTrimClip(input_R1, outputDir)
val R1_files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
val R2_files = for ((k, v) <- outputFiles if k.endsWith("output_R2")) yield v
......
......@@ -196,7 +196,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
extractIfNeeded(input_R1, flexiprep.outputDir),
if (paired) Some(extractIfNeeded(input_R2.get, outputDir)) else None)
)
} else Map(outputDir -> (flexiprep.outputFiles("fastq_input_R1"), flexiprep.outputFiles.get("fastq_input_R2")))
} else Map(outputDir -> (flexiprep.fastqR1Qc, flexiprep.fastqR2Qc))
}
if (chunking) {
......
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