From e7f818e20d78bbb70ec0b4639a30da98e11b3b66 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 28 Jul 2014 14:07:09 +0200
Subject: [PATCH] Switch to functions
---
.../flexiprep/FlexiprepSummary.scala | 126 +++++++-----------
1 file changed, 51 insertions(+), 75 deletions(-)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
index 3ff41f674..43ef401b7 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
@@ -1,9 +1,14 @@
package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.function.Sha1sum
+import nl.lumc.sasc.biopet.function.fastq.Cutadapt
import nl.lumc.sasc.biopet.function.fastq.Fastqc
+import nl.lumc.sasc.biopet.function.fastq.Sickle
+import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.FastqSync
+import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.Seqstat
import org.broadinstitute.gatk.queue.function.InProcessFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
import argonaut._, Argonaut._
import scalaz._, Scalaz._
@@ -11,59 +16,59 @@ import scalaz._, Scalaz._
class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Configurable {
this.analysisName = getClass.getSimpleName
- @Input(doc = "Seq stat files R1", required=true)
- var seqstatR1: List[File] = Nil
+ @Input(doc="deps")
+ var deps: List[File] = Nil
- @Input(doc = "Seq stat files R2", required=false)
- var seqstatR2: List[File] = Nil
-
- @Input(doc = "Seq stat files R1 after", required=false)
- var seqstatR1after: List[File] = Nil
-
- @Input(doc = "Seq stat files R2 after", required=false)
- var seqstatR2after: List[File] = Nil
-
- @Input(doc = "sha1 files R1", required=true)
- var sha1R1: File = _
-
- @Input(doc = "sha1 files R2", required=false)
- var sha1R2: File = _
+ @Output(doc = "Summary output", required=true)
+ var out: File = _
- @Input(doc = "sha1 files R1 after", required=false)
- var sha1R1after: File = _
+ class Chunk {
+ var seqstatR1: Seqstat = _
+ var seqstatR2: Seqstat = _
+ var seqstatR1after: Seqstat = _
+ var seqstatR2after: Seqstat = _
+
+ var cutadaptR1: Cutadapt = _
+ var cutadaptR2: Cutadapt = _
+
+ var fastqSync: FastqSync = _
+
+ var sickle: Sickle = _
+ }
- @Input(doc = "sha1 files R2 after", required=false)
- var sha1R2after: File = _
+ var chunks: Map[String, Chunk] = Map()
- @Input(doc = "Clip stat files R1", required=false)
- var clipstatR1: List[File] = Nil
+ def addSeqstat(seqstat:Seqstat, R2:Boolean = false, after:Boolean = false, chunk:String=""): Seqstat = {
+ if (!chunks.contains(chunk)) chunks += (chunk -> new Chunk)
+ if (!R2 && !after) chunks(chunk).seqstatR1 = seqstat
+ else if (!R2 && after) chunks(chunk).seqstatR1after = seqstat
+ else if (R2 && !after) chunks(chunk).seqstatR2 = seqstat
+ else if (R2 && after) chunks(chunk).seqstatR2after = seqstat
+ deps ::= seqstat.out
+ return seqstat
+ }
- @Input(doc = "Clip stat files R2", required=false)
- var clipstatR2: List[File] = Nil
+ def addCutadapt(cutadapt:Cutadapt, R2:Boolean = false, chunk:String=""): Cutadapt = {
+ if (!chunks.contains(chunk)) chunks += (chunk -> new Chunk)
+ if (!R2) chunks(chunk).cutadaptR1 = cutadapt
+ else chunks(chunk).cutadaptR2 = cutadapt
+ //TODO: stats file of cutadapt
+ return cutadapt
+ }
- @Input(doc = "Trim stat files", required=false)
- var trimstats: List[File] = Nil
- @Input(doc = "Sync stat files", required=false)
- var syncstats: List[File] = Nil
- @Output(doc = "Summary output", required=true)
- var out: File = _
+ var sha1R1: Sha1sum = _
+ var sha1R2: Sha1sum = _
+ var sha1R1after: Sha1sum = _
+ var sha1R2after: Sha1sum = _
- @Argument(doc = "fastqc files R1", required=true)
var fastqcR1: Fastqc = _
-
- @Argument(doc = "fastqc files R2", required=false)
var fastqcR2: Fastqc = _
-
- @Argument(doc = "fastqc files R1 after", required=false)
var fastqcR1after: Fastqc = _
-
- @Argument(doc = "fastqc files R2 after", required=false)
var fastqcR2after: Fastqc = _
- @Argument(doc = "Flexiprep Pipeline", required=true)
- var flexiprep: Flexiprep = _
+ var flexiprep: Flexiprep = root.asInstanceOf[Flexiprep]
var clipping = true
var trimming = true
@@ -74,58 +79,29 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
trimming = !flexiprep.skipTrim
paired = flexiprep.paired
- fastqcSummary(fastqcR1)
- if (paired) fastqcSummary(fastqcR2)
-
- sha1Summary(sha1R1)
- if (paired) sha1Summary(sha1R2)
-
- seqstatSummary(seqstatR1)
- if (paired) seqstatSummary(seqstatR2)
-
- if (clipping) {
- clipstatSummary(clipstatR1)
- if (paired) {
- clipstatSummary(clipstatR2)
- syncstatSummary(syncstats)
- }
- }
-
- if (trimming) trimstatSummary(trimstats)
-
- if (clipping || trimming) {
- fastqcSummary(fastqcR1after)
- if (paired) fastqcSummary(fastqcR2after)
-
- sha1Summary(sha1R1after)
- if (paired) sha1Summary(sha1R2after)
-
- seqstatSummary(seqstatR1after)
- if (paired) seqstatSummary(seqstatR2after)
- }
}
- def seqstatSummary(files: List[File]): Json = {
+ def seqstatSummary(): Json = {
//TODO
return null
}
- def sha1Summary(file:File): Json = {
+ def sha1Summary(): Json = {
//TODO
return null
}
- def fastqcSummary(fastqc:Fastqc): Json = {
+ def fastqcSummary(): Json = {
//TODO
return null
}
- def clipstatSummary(files: List[File]): Json = {
+ def clipstatSummary(): Json = {
//TODO
return null
}
- def syncstatSummary(files: List[File]): Json = {
+ def syncstatSummary(): Json = {
//TODO
return null
}
- def trimstatSummary(files: List[File]): Json = {
+ def trimstatSummary(): Json = {
//TODO
return null
}
--
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