diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 944dee43fa5fae667cad5e08a05ae4ce9d5f8fbe..0dcf13eeab40c0f502a181b267da9dea9d3f3bb9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -207,6 +207,6 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
object BiopetCommandLineFunctionTrait {
import scala.collection.mutable.Map
private val versionCache: Map[String, String] = Map()
- private val executableMd5Cache: Map[String, String] = Map()
+ private[core] val executableMd5Cache: Map[String, String] = Map()
private val executableCache: Map[String, String] = Map()
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
index d71eaa1608feffffea1fe82537af02bda4e2257e..a1901ed793912f9e88056007479f9295145dae8f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
@@ -11,7 +11,7 @@ trait Summarizable extends Configurable {
def summaryFiles: Map[String, File]
- def summaryData: Map[String, Any]
+ def summaryStats: Map[String, Any]
/**
* This function is used to merge
@@ -20,5 +20,7 @@ trait Summarizable extends Configurable {
* @param key
* @return
*/
- def resolveSummaryConflict(v1: Any, v2: Any, key: String) = v1
+ def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
+ throw new IllegalStateException("Merge can not have same key by default")
+ }
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index 207acd79a3cfb67691d8342b3f8ae942df7f331c..fac1055e3b03699898e5ef4b36b1011ca3530133 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.{ FileInputStream, PrintWriter, File }
import java.security.MessageDigest
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunctionTrait, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.function.{ QFunction, InProcessFunction }
@@ -43,45 +44,72 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
}
def run(): Unit = {
- val map = (for (
+
+ val pipelineMap = {
+ val files = parseFiles(qscript.summaryFiles)
+ val settings = qscript.summarySettings
+ val executables = {
+ for ((name, (file, version)) <- qscript.executables) yield {
+ name -> Map("version" -> version, "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(file.getCanonicalPath, "N/A"))
+ }
+ }
+
+ val map = Map(qscript.summaryName -> ((if (settings.isEmpty) Map[String, Any]() else Map("settings" -> settings)) ++
+ (if (files.isEmpty) Map[String, Any]() else Map("files" -> Map("pipeline" -> files))) ++
+ (if (executables.isEmpty) Map[String, Any]() else Map("executables" -> executables.toMap))))
+
+ qscript match {
+ case tag: SampleLibraryTag => prefixSampleLibrary(map, tag.sampleId, tag.libId)
+ case _ => map
+ }
+ }
+
+ val jobsMap = (for (
((name, sampleId, libraryId), summarizables) <- qscript.summarizables;
summarizable <- summarizables
) yield {
- val map = Map(qscript.summaryName -> Map(name -> parseSummarizable(summarizable)))
+ val map = Map(qscript.summaryName -> parseSummarizable(summarizable, name))
- (sampleId match {
- case Some(sampleId) => Map("samples" -> Map(sampleId -> (libraryId match {
- case Some(libraryId) => Map("libraries" -> Map(libraryId -> map))
- case _ => map
- })))
- case _ => map
- }, (v1: Any, v2: Any, key: String) => summarizable.resolveSummaryConflict(v1, v2, key))
- }).foldRight(Map[String, Any]())((a, b) => ConfigUtils.mergeMaps(a._1, b, a._2))
+ (prefixSampleLibrary(map, sampleId, libraryId),
+ (v1: Any, v2: Any, key: String) => summarizable.resolveSummaryConflict(v1, v2, key))
+ }).foldRight(pipelineMap)((a, b) => ConfigUtils.mergeMaps(a._1, b, a._2))
val combinedMap = (for (qscript <- qscript.summaryQScripts) yield {
ConfigUtils.fileToConfigMap(qscript.summaryFile)
- }).foldRight(map)((a, b) => ConfigUtils.mergeMaps(a, b))
+ }).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b))
val writer = new PrintWriter(out)
writer.println(ConfigUtils.mapToJson(combinedMap).spaces4)
writer.close()
}
- def parseSummarizable(summarizable: Summarizable) = {
- val data = summarizable.summaryData
+ def prefixSampleLibrary(map: Map[String, Any], sampleId: Option[String], libraryId: Option[String]): Map[String, Any] = {
+ sampleId match {
+ case Some(sampleId) => Map("samples" -> Map(sampleId -> (libraryId match {
+ case Some(libraryId) => Map("libraries" -> Map(libraryId -> map))
+ case _ => map
+ })))
+ case _ => map
+ }
+ }
+
+ def parseSummarizable(summarizable: Summarizable, name: String) = {
+ val data = summarizable.summaryStats
val files = parseFiles(summarizable.summaryFiles)
- (if (data.isEmpty) Map[String, Any]() else Map("data" -> data)) ++
- (if (files.isEmpty) Map[String, Any]() else Map("files" -> files))
+ (if (data.isEmpty) Map[String, Any]() else Map("stats" -> Map(name -> data))) ++
+ (if (files.isEmpty) Map[String, Any]() else Map("files" -> Map(name -> files)))
}
def parseFiles(files: Map[String, File]): Map[String, Map[String, Any]] = {
- for ((key, file) <- files) yield {
- val map: mutable.Map[String, Any] = mutable.Map()
- map += "path" -> file.getAbsolutePath
- if (md5sum) map += "md5" -> parseChecksum(SummaryQScript.md5sumCache(file))
- key -> map.toMap
- }
+ for ((key, file) <- files) yield key -> parseFile(file)
+ }
+
+ def parseFile(file: File): Map[String, Any] = {
+ val map: mutable.Map[String, Any] = mutable.Map()
+ map += "path" -> file.getAbsolutePath
+ if (md5sum) map += "md5" -> parseChecksum(SummaryQScript.md5sumCache(file))
+ map.toMap
}
def parseChecksum(checksumFile: File): String = {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index ccf56efc8035eabba1c49dd9e2745de26f7efe30..fc90139f8db4dba65da7e7c90df8988f68bb87e7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -47,7 +47,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
if (config.contains("front")) for (adapter <- config("front").asList) opt_front += adapter.toString
var opt_discard: Boolean = config("discard", default = false)
- var opt_minimum_length: Option[Int] = config("minimum_length", 1)
+ var opt_minimum_length: Int = config("minimum_length", 1)
var opt_maximum_length: Option[Int] = config("maximum_length")
def cmdLine = required(executable) +
@@ -63,7 +63,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
required("--output", fastq_output) +
" > " + required(stats_output)
- def summaryData: Map[String, Any] = {
+ def summaryStats: Map[String, Any] = {
val trimR = """.*Trimmed reads: *(\d*) .*""".r
val tooShortR = """.*Too short reads: *(\d*) .*""".r
val tooLongR = """.*Too long reads: *(\d*) .*""".r
@@ -82,8 +82,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
}
}
- Map("version" -> getVersion,
- "num_reads_affected" -> stats("trimmed"),
+ Map("num_reads_affected" -> stats("trimmed"),
"num_reads_discarded_too_short" -> stats("tooshort"),
"num_reads_discarded_too_long" -> stats("toolong"),
"adapters" -> adapter_stats.toMap
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
index 556f8639f27b2d5d57c018ed9e31fb0195892a56..bb014d224c7a6c1ca9aeb7508538e288e88117cc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
@@ -45,7 +45,7 @@ class Seqstat(val root: Configurable) extends BiopetCommandLineFunction with Sum
def cmdLine = required(executable) + required(input) + " > " + required(output)
- def summaryData: Map[String, Any] = {
+ def summaryStats: Map[String, Any] = {
val map = ConfigUtils.fileToConfigMap(output)
ConfigUtils.any2map(map.getOrElse("stats", Map()))
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index 8a546534d305e8a8a36a69b6c94660d63abb9533..fae8c5802c3979af507421df955a91400d21923d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
@@ -81,7 +81,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
" > " + required(output_stats)
}
- def summaryData: Map[String, Any] = {
+ def summaryStats: Map[String, Any] = {
val pairKept = """FastQ paired records kept: (\d*) \((\d*) pairs\)""".r
val singleKept = """FastQ single records kept: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)""".r
val pairDiscarded = """FastQ paired records discarded: (\d*) \((\d*) pairs\)""".r
@@ -105,7 +105,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
}
}
- stats.toMap ++ Map("version" -> getVersion)
+ stats.toMap
}
override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index f691145215e6f6ccd54f4e72001165228672f6b9..53b109b8c4fc549924b8f494993f661ec09598ad 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -63,7 +63,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
def summaryFiles: Map[String, File] = Map()
- def summaryData: Map[String, Any] = {
+ def summaryStats: Map[String, Any] = {
val (header, content) = Picard.getMetrics(output)
(for (category <- 0 until content.size) yield {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index 9585491f971454ea2e0f4bb03b0c67b50aea8579..d5565316293e7af0460362064e39e713361a6b7c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -73,7 +73,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
def summaryFiles: Map[String, File] = Map("output_histogram" -> outputHistogram)
- def summaryData: Map[String, Any] = {
+ def summaryStats: Map[String, Any] = {
val (header, content) = Picard.getMetrics(output)
(for (i <- 0 to header.size if i < content.head.size)
yield (header(i).toLowerCase -> content.head(i))).toMap
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
index 9838040cc74a5da4cff3073ac0b2123b6de9e954..a3dc12182a8a236e3543f327adbd5f51c843b5d9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.extensions.seqtk
import java.io.File
+import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
@@ -23,7 +24,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
* Wrapper for the seqtk seq subcommand.
* Written based on seqtk version 1.0-r63-dirty.
*/
-class SeqtkSeq(val root: Configurable) extends Seqtk {
+class SeqtkSeq(val root: Configurable) extends Seqtk with Summarizable {
/** input file */
@Input(doc = "Input file (FASTQ or FASTA)")
@@ -81,6 +82,10 @@ class SeqtkSeq(val root: Configurable) extends Seqtk {
/** shift quality by '(-Q) - 33' */
var V: Boolean = config("V", default = false)
+ def summaryStats: Map[String, Any] = Map()
+
+ def summaryFiles: Map[String, File] = Map()
+
def cmdLine = {
required(executable) +
" seq " +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
index e866195ae4b9b132387809ed35ba2d78ac9098b1..48e1c36e1805dfa11b630618e002a7a1ba3f23e4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
@@ -44,7 +44,7 @@ class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFuncti
def summaryFiles: Map[String, File] = Map()
- def summaryData: Map[String, Any] = {
+ def summaryStats: Map[String, Any] = {
ConfigUtils.fileToConfigMap(summaryFile)
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index 32c0c5b1eb25ea43bcbfb211f3ea89bfabe60c0e..2b44e6300e844f9c0827901c66ff3cba464dcb4c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -64,7 +64,7 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction wi
def summaryFiles: Map[String, File] = Map()
- def summaryData: Map[String, Any] = {
+ def summaryStats: Map[String, Any] = {
val regex = new Regex("""Filtered (\d*) reads from first read file.
|Filtered (\d*) reads from second read file.
|Synced read files contain (\d*) reads.""".stripMargin,
@@ -82,8 +82,7 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction wi
}
} else (0, 0, 0)
- Map("version" -> BiopetExecutable.getVersion,
- "num_reads_discarded_R1" -> countFilteredR1,
+ Map("num_reads_discarded_R1" -> countFilteredR1,
"num_reads_discarded_R2" -> countFilteredR2,
"num_reads_kept" -> countRLeft
)
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
index 51139812f6169689a080aaf913c16b6ee2ae00fa..f46a9b91f6d82d90444700453ab9fdf1a32b723e 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
@@ -18,6 +18,6 @@ class CollectAlignmentSummaryMetricsTest extends TestNGSuite with Matchers {
val job = new CollectAlignmentSummaryMetrics(null)
job.output = file
- job.summaryData
+ job.summaryStats
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
index fc0c563e82a48aa3918ee5ad0913dd9a62e8d966..ffb5d528c1bf42044a5f61d282f6fe42aab11f1a 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
@@ -18,6 +18,6 @@ class CollectInsertSizeMetricsTest extends TestNGSuite with Matchers {
val job = new CollectInsertSizeMetrics(null)
job.output = file
- job.summaryData
+ job.summaryStats
}
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index cd9dd4ae019f2f61c88f7d95d9ab988d499efc8a..8946db96cfea9ff9637f5a88afaa9e733043ebb9 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -159,7 +159,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
outputFiles ++ Map("fastq_file" -> this.fastqfile)
}
- def summaryData: Map[String, Any] = Map("version" -> getVersion)
+ def summaryStats: Map[String, Any] = Map()
}
object Fastqc {