From 8bf162ad0ba7a632218c8263d47e3364c66d3f35 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 15 Oct 2015 13:26:31 +0200
Subject: [PATCH] Remove "reference" from testing
---
.../nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala | 1 -
.../pipelines/gatk/ShivaVariantcallingTest.scala | 1 -
.../picard/CollectAlignmentSummaryMetrics.scala | 10 ++++++++--
.../extensions/picard/CollectInsertSizeMetrics.scala | 6 ++++--
.../nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala | 1 -
.../sasc/biopet/pipelines/gentrap/GentrapTest.scala | 1 -
.../lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala | 1 -
.../pipelines/shiva/ShivaVariantcallingTest.scala | 1 -
8 files changed, 12 insertions(+), 10 deletions(-)
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
index 66f0bfcc5..f03a5ca26 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
@@ -115,7 +115,6 @@ object ShivaTest {
"dir" -> "test",
"vep_script" -> "test",
"output_dir" -> outputDir,
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
index 8e8a1eddf..1740b33ac 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
@@ -131,7 +131,6 @@ object ShivaVariantcallingTest {
"cache" -> true,
"dir" -> "test",
"vep_script" -> "test",
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index ff19efe11..b2fb2097e 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -17,12 +17,13 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
+import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard CollectAlignmentSummaryMetrics */
-class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
+class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
javaMainClass = new picard.analysis.CollectAlignmentSummaryMetrics().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
@@ -41,7 +42,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
var output: File = _
@Argument(doc = "Reference file", required = false)
- var reference: File = config("reference")
+ var reference: File = _
@Argument(doc = "ASSUME_SORTED", required = false)
var assumeSorted: Boolean = config("assumeSorted", default = true)
@@ -52,6 +53,11 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
@Argument(doc = "STOP_AFTER", required = false)
var stopAfter: Option[Long] = config("stopAfter")
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ if (reference == null) reference = referenceFasta()
+ }
+
/** Returns command to execute */
override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index 3c4693b5e..88d2eab60 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
+import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
@@ -24,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import scala.collection.immutable.Nil
/** Extension for picard CollectInsertSizeMetrics */
-class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable {
+class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
javaMainClass = new picard.analysis.CollectInsertSizeMetrics().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
@@ -37,7 +38,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
protected var outputHistogram: File = null
@Argument(doc = "Reference file", required = false)
- var reference: File = config("reference")
+ var reference: File = _
@Argument(doc = "DEVIATIONS", required = false)
var deviations: Option[Double] = config("deviations")
@@ -59,6 +60,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
override def beforeGraph() {
outputHistogram = new File(output + ".pdf")
+ if (reference == null) reference = referenceFasta()
}
/** Returns command to execute */
diff --git a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
index 1f5efdc2f..da5d79939 100644
--- a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+++ b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
@@ -116,7 +116,6 @@ object CarpTest {
copyFile("ref.fa.fai")
val executables = Map(
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
diff --git a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 37deb389e..575b20b3e 100644
--- a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -196,7 +196,6 @@ object GentrapTest {
copyFile("ref.fa.fai")
val executables = Map(
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"refFlat" -> "test",
"annotation_gtf" -> "test",
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
index 53286ecde..31777668d 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
@@ -109,7 +109,6 @@ object ShivaTest {
"cache" -> true,
"dir" -> "test",
"vep_script" -> "test",
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index caeea0326..dae0b9743 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -112,7 +112,6 @@ object ShivaVariantcallingTest {
"cache" -> true,
"dir" -> "test",
"vep_script" -> "test",
- "reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
--
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