Commit 4e1cada3 authored by bow's avatar bow
Browse files

Merge branch 'feature-typofixes' into 'develop'

Feature typofixes

Some small fixes..

Wrapper update *(bwa) and Mapping pipeline..

See merge request !78
parents 9d5bc538 e0cd4cdd
...@@ -6,7 +6,11 @@ import nl.lumc.sasc.biopet.core.config.Configurable ...@@ -6,7 +6,11 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input } import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/** /**
* Created by pjvan_thof on 1/16/15. * BWA sampe wrapper
*
* based on executable version 0.7.10-r789
*
* @param root Configurable
*/ */
class BwaSampe(val root: Configurable) extends Bwa { class BwaSampe(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file R1", required = true) @Input(doc = "Fastq file R1", required = true)
...@@ -39,11 +43,14 @@ class BwaSampe(val root: Configurable) extends Bwa { ...@@ -39,11 +43,14 @@ class BwaSampe(val root: Configurable) extends Bwa {
var r: String = _ var r: String = _
def cmdLine = required(executable) + def cmdLine = required(executable) +
required("samse") + required("sampe") +
optional("-a", a) +
optional("-o", o) +
optional("-n", n) + optional("-n", n) +
optional("-N", N) +
optional("-c", c) +
optional("-f", output) + optional("-f", output) +
optional("-r", r) + optional("-r", r) +
optional("-c", c) +
conditional(P, "-P") + conditional(P, "-P") +
conditional(s, "-s") + conditional(s, "-s") +
conditional(A, "-A") + conditional(A, "-A") +
......
...@@ -123,7 +123,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript { ...@@ -123,7 +123,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def biopetScript() { def biopetScript() {
if (!skipFlexiprep) { if (!skipFlexiprep) {
flexiprep.outputDir = outputDir + "flexiprep/" flexiprep.outputDir = outputDir + "flexiprep" + File.separator
flexiprep.input_R1 = input_R1 flexiprep.input_R1 = input_R1
if (paired) flexiprep.input_R2 = input_R2 if (paired) flexiprep.input_R2 = input_R2
flexiprep.sampleId = this.sampleId flexiprep.sampleId = this.sampleId
...@@ -208,7 +208,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript { ...@@ -208,7 +208,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bamFile = mergeSamFile.output 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, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, finalBamFile, ".bam", ".bai")))
add(Ln(this, bamFile, finalBamFile)) add(Ln(this, bamFile, finalBamFile))
...@@ -357,6 +357,4 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript { ...@@ -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
}
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