Commit ecf1818c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed docs

parent 00a24e74
......@@ -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 |
......
......@@ -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 |
......
......@@ -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 */
......
......@@ -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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