From 8a67021829b4e172529f47cde153d02ba81799f2 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Wed, 28 Jan 2015 16:11:37 +0100
Subject: [PATCH] Update on the pipeline, streamline and minimize the required
arguments taken from the commandline
---
.../extensions/conifer/ConiferAnalyze.scala | 24 -------------------
.../extensions/conifer/ConiferCall.scala | 4 ----
.../pipelines/kopisu/ConiferPipeline.scala | 4 ++--
.../pipelines/kopisu/ConiferSummary.scala | 6 ++---
4 files changed, 5 insertions(+), 33 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
index d18d682bf..7ce27881d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
@@ -39,30 +39,6 @@ class ConiferAnalyze(val root: Configurable) extends Conifer {
@Argument(doc = "Minimum population median RPKM per probe", required = false)
var min_rpkm: Option[Double] = config("min_rpkm")
- override def afterGraph: Unit = {
- super.afterGraph
- //
- // // create new RPKM_dir with the controls in it together with the subject
- // new_rpkm_dir = new File(this.output.getParent() + File.separator + "rpkm_tmp")
- // logger.info("Creating " + new_rpkm_dir.getAbsolutePath)
- // new_rpkm_dir.mkdir()
- //
- // for (f <- rpkm_dir.listFiles()) {
- // var target = new File(new_rpkm_dir + File.separator + f.getName)
- // if (!target.exists()) {
- // logger.info("Creating " + target.getAbsolutePath)
- // Ln(this, f, target, true).run
- // }
- // }
- // for (f <- rpkm_refdir.listFiles()) {
- // var target = new File(new_rpkm_dir + File.separator + f.getName)
- // if (!target.exists()) {
- // logger.info("Creating " + target.getAbsolutePath)
- // Ln(this, f, target, true).run
- // }
- // }
- }
-
override def cmdLine = super.cmdLine +
" analyze " +
" --probes" + required(probes) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
index 7404a9a1f..6583ed64e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
@@ -28,10 +28,6 @@ class ConiferCall(val root: Configurable) extends Conifer {
@Output(doc = "Output calls.txt", shortName = "out")
var output: File = _
- override def afterGraph {
- this.checkExecutable
- }
-
override def cmdLine = super.cmdLine +
" call " +
" --input" + required(input) +
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
index e4d8a0f3d..ec4464a57 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
@@ -84,7 +84,7 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
var target = new File(RPKMdir + File.separator + f.getName)
if (!target.exists()) {
logger.info("Creating " + target.getAbsolutePath)
- add(Ln(this, f, target, false))
+ add(Ln(this, f, target, true))
refRPKMlist :+= target
}
}
@@ -104,7 +104,7 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
summary.deps = List(coniferCall.output)
summary.label = sampleLabel
summary.calls = coniferCall.output
- summary.out = input2Calls(inputBam)
+ summary.out = new File(sampleDir + File.separator + input2Calls(inputBam))
add(summary)
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
index 04034a882..1691a19df 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
@@ -26,10 +26,10 @@ import scala.io.Source
class ConiferSummary(val root: Configurable) extends InProcessFunction with Configurable {
def filterCalls(callFile: File, outFile: File, sampleName: String): Unit = {
- val filename = callFile.getAbsolutePath
+ // val filename = callFile.getAbsolutePath
val writer = new BufferedWriter(new FileWriter(outFile))
- for (line <- Source.fromFile(filename).getLines()) {
+ for (line <- Source.fromFile(callFile).getLines()) {
line.startsWith(sampleName) || line.startsWith("sampleID") match {
case true => writer.write(line)
case _ =>
@@ -58,7 +58,7 @@ class ConiferSummary(val root: Configurable) extends InProcessFunction with Conf
override def run {
logger.debug("Start")
- filterCalls(out, calls, label)
+ filterCalls(calls, out, label)
logger.debug("Stop")
}
}
--
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