Commit f941cb35 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added md5 check to pipeline

parent b81ad8bb
package nl.lumc.sasc.biopet.pipelines.gears package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript } import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
import nl.lumc.sasc.biopet.extensions.tools.MergeOtuMaps import nl.lumc.sasc.biopet.extensions.tools.MergeOtuMaps
import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat, Ln } import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat, Ln }
...@@ -107,6 +108,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs ...@@ -107,6 +108,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
/** Function that add library jobs */ /** Function that add library jobs */
protected def addJobs(): Unit = { protected def addJobs(): Unit = {
inputFiles :+= InputFile(flexiprep.input_R1, config("R1_md5"))
flexiprep.input_R2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
add(flexiprep) add(flexiprep)
gs.fastqR1 = Some(flexiprep.fastqR1Qc) gs.fastqR1 = Some(flexiprep.fastqR1Qc)
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment