Fixed docs

docs/pipelines/flexiprep.md

@@ -44,8 +44,8 @@ Command line flags for Flexiprep are:
 
 | Flag  (short)| Flag (long) | Type | Function |
 | ------------ | ----------- | ---- | -------- |
-| -R1 | --input_r1 | Path (**required**) | Path to input fastq file |
-| -R2 | --input_r2 | Path (optional) | Path to second read pair fastq file. |
+| -R1 | --inputR1 | Path (**required**) | Path to input fastq file |
+| -R2 | --inputR2 | Path (optional) | Path to second read pair fastq file. |
 | -sample | --sampleid | String (**required**) | Name of sample |
 | -library | --libid | String (**required**) | Name of library |
 

docs/pipelines/mapping.md

@@ -28,8 +28,8 @@ Command line flags for the mapping pipeline are:
 
 | Flag  (short)| Flag (long) | Type | Function |
 | ------------ | ----------- | ---- | -------- |
-| -R1 | --input_r1 | Path (**required**) | Path to input fastq file |
-| -R2 | --input_r2 | Path (optional) | Path to second read pair fastq file. |
+| -R1 | --inputR1 | Path (**required**) | Path to input fastq file |
+| -R2 | --inputR2 | Path (optional) | Path to second read pair fastq file. |
 | -sample | --sampleid | String (**required**) | Name of sample |
 | -library | --libid | String (**required**) | Name of library |
 

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -27,10 +27,10 @@ import org.broadinstitute.gatk.queue.QScript
 class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
   def this() = this(null)
 
-  @Input(doc = "R1 fastq file (gzipped allowed)", shortName = "R1", required = true)
+  @Input(doc = "R1 fastq file (gzipped allowed)", shortName = "R1", fullName = "inputR1", required = true)
   var inputR1: File = _
 
-  @Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", required = false)
+  @Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", fullName = "inputR2", required = false)
   var inputR2: Option[File] = None
 
   /** Skip Trim fastq files */

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -41,10 +41,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
 
   def this() = this(null)
 
-  @Input(doc = "R1 fastq file", shortName = "R1", required = true)
+  @Input(doc = "R1 fastq file", shortName = "R1", fullName = "inputR1", required = true)
   var inputR1: File = _
 
-  @Input(doc = "R2 fastq file", shortName = "R2", required = false)
+  @Input(doc = "R2 fastq file", shortName = "R2", fullName = "inputR2", required = false)
   var inputR2: Option[File] = None
 
   /** Output name */