Commit ccd0ed71 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Aligner BWA typo and Mapping clean paths

parent 9d5bc538
......@@ -6,7 +6,11 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 1/16/15.
* BWA sampe wrapper
*
* based on executable verion 0.7.10-r789
*
* @param root Configurable
*/
class BwaSampe(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file R1", required = true)
......@@ -39,11 +43,14 @@ class BwaSampe(val root: Configurable) extends Bwa {
var r: String = _
def cmdLine = required(executable) +
required("samse") +
required("sampe") +
optional("-a", a) +
optional("-o", o) +
optional("-n", n) +
optional("-N", N) +
optional("-c", c) +
optional("-f", output) +
optional("-r", r) +
optional("-c", c) +
conditional(P, "-P") +
conditional(s, "-s") +
conditional(A, "-A") +
......
......@@ -123,7 +123,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def biopetScript() {
if (!skipFlexiprep) {
flexiprep.outputDir = outputDir + "flexiprep/"
flexiprep.outputDir = outputDir + "flexiprep" + File.separator
flexiprep.input_R1 = input_R1
if (paired) flexiprep.input_R2 = input_R2
flexiprep.sampleId = this.sampleId
......@@ -208,7 +208,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bamFile = mergeSamFile.output
}
if (!skipMetrics) addAll(BamMetrics(this, bamFile, outputDir + "metrics/").functions)
if (!skipMetrics) addAll(BamMetrics(this, bamFile, outputDir + "metrics" + File.separator).functions)
add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, finalBamFile, ".bam", ".bai")))
add(Ln(this, bamFile, finalBamFile))
......@@ -357,6 +357,4 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
}
object Mapping extends PipelineCommand {
}
object Mapping extends PipelineCommand
\ No newline at end of file
Supports Markdown
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