Commit f7fb0c72 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix comments on merge request

parent 3ba41502
......@@ -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`.
......
......@@ -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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