From ecf1818c1e930701628beb3aafa8b65652580764 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 15 Mar 2016 12:44:40 +0100
Subject: [PATCH] Fixed docs
---
docs/pipelines/flexiprep.md | 4 ++--
docs/pipelines/mapping.md | 4 ++--
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 4 ++--
4 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/docs/pipelines/flexiprep.md b/docs/pipelines/flexiprep.md
index cd1e3f840..2140398ab 100644
--- a/docs/pipelines/flexiprep.md
+++ b/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 |
diff --git a/docs/pipelines/mapping.md b/docs/pipelines/mapping.md
index f04efebc6..79d2a5749 100644
--- a/docs/pipelines/mapping.md
+++ b/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 |
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 134fd13be..ab87244ee 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/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 */
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index c6d192cf2..fa1494e6c 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/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 */
--
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