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biopet.biopet
Commits
f7fb0c72
Commit
f7fb0c72
authored
Dec 20, 2016
by
Peter van 't Hof
Browse files
Fix comments on merge request
parent
3ba41502
Changes
2
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docs/pipelines/mapping.md
View file @
f7fb0c72
...
...
@@ -58,6 +58,7 @@ All other values should be provided in the config. Specific config values toward
| readgroup_sequencing_center | String (optional) | Read group sequencing center |
| readgroup_description | String (optional) | Read group description |
| predicted_insertsize | Integer (optional) | Read group predicted insert size |
| keep_final_bam_file | Boolean (default true) | when needed the pipeline can remove the bam file after it's not required anymore for other jobs |
It is possible to provide any config value as a command line argument as well, using the
`-cv`
flag.
E.g.
`-cv reference=<path/to/reference>`
would set value
`reference`
.
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
f7fb0c72
...
...
@@ -93,7 +93,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** Readgroup predicted insert size */
protected
var
predictedInsertsize
:
Option
[
Int
]
=
config
(
"predicted_insertsize"
)
val
keepFinalBamFile
:
Boolean
=
config
(
"keep_final_bamfile"
,
default
=
true
)
val
keepFinalBamFile
:
Boolean
=
config
(
"keep_final_bam
_
file"
,
default
=
true
)
protected
var
paired
:
Boolean
=
false
val
flexiprep
=
new
Flexiprep
(
this
)
...
...
@@ -276,8 +276,6 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
addSummaryQScript
(
bamMetrics
)
}
// add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, new File(outputDir, outputName + ".dedup.bam"), ".bam", ".bai")))
// add(Ln(this, bamFile, new File(outputDir, outputName + ".dedup.bam")))
outputFiles
+=
(
"finalBamFile"
->
finalBamFile
)
if
(
config
(
"unmapped_to_gears"
,
default
=
false
).
asBoolean
)
{
...
...
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