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biopet.biopet
Commits
ecf1818c
Commit
ecf1818c
authored
Mar 15, 2016
by
Peter van 't Hof
Browse files
Fixed docs
parent
00a24e74
Changes
4
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Inline
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docs/pipelines/flexiprep.md
View file @
ecf1818c
...
...
@@ -44,8 +44,8 @@ Command line flags for Flexiprep are:
| Flag (short)| Flag (long) | Type | Function |
| ------------ | ----------- | ---- | -------- |
| -R1 | --input
_r
1 | Path (
**required**
) | Path to input fastq file |
| -R2 | --input
_r
2 | Path (optional) | Path to second read pair fastq file. |
| -R1 | --input
R
1 | Path (
**required**
) | Path to input fastq file |
| -R2 | --input
R
2 | 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
View file @
ecf1818c
...
...
@@ -28,8 +28,8 @@ Command line flags for the mapping pipeline are:
| Flag (short)| Flag (long) | Type | Function |
| ------------ | ----------- | ---- | -------- |
| -R1 | --input
_r
1 | Path (
**required**
) | Path to input fastq file |
| -R2 | --input
_r
2 | Path (optional) | Path to second read pair fastq file. |
| -R1 | --input
R
1 | Path (
**required**
) | Path to input fastq file |
| -R2 | --input
R
2 | 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
View file @
ecf1818c
...
...
@@ -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
View file @
ecf1818c
...
...
@@ -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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