Commit 0efd042b authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'fix-BIOPET-425' into 'develop'

Fix biopet 425

Fixes BIOPET-425 and BIOPET-426

See merge request !483
parents 1337c894 643b1d89
......@@ -112,6 +112,7 @@ object KopisuTest {
Files.touch(new File(controlDir, "test.txt"))
val config = Map(
"skip_write_dependencies" -> true,
"name_prefix" -> "test",
"output_dir" -> outputDir,
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
......
......@@ -128,6 +128,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
}
val executables = Map(
"skip_write_dependencies" -> true,
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"db" -> "test",
"bowtie_index" -> (outputDir + File.separator + "ref"),
......
......@@ -184,6 +184,7 @@ object MultisampleMappingTestTrait {
copyFile("empty.sam")
val config = Map(
"skip_write_dependencies" -> true,
"name_prefix" -> "test",
"cache" -> true,
"dir" -> "test",
......
......@@ -131,6 +131,7 @@ object SageTest {
copyFile("ref.fa.fai")
val config: Map[String, Any] = Map(
"skip_write_dependencies" -> true,
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"output_dir" -> outputDir.getAbsolutePath,
"fastqc" -> Map("exe" -> "test"),
......
......@@ -104,14 +104,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
def summarySettings = Map("sv_callers" -> configCallers.toList)
/** Files for the summary */
def summaryFiles: Map[String, File] = {
val callers: Set[String] = configCallers
//callersList.filter(x => callers.contains(x.name)).map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
Map(
"final_mergedvcf" -> outputMergedVCF
)
}
def summaryFiles: Map[String, File] = Map("final_mergedvcf" -> outputMergedVCF)
}
object ShivaSvCalling extends PipelineCommand
\ No newline at end of file
......@@ -36,7 +36,8 @@ class Bcftools(val root: Configurable) extends Variantcaller {
bt.v = true
bt.c = true
add(mp | new FixMpileup(this) | bt > outputFile)
val pipe = mp | new FixMpileup(this) | bt > outputFile
add(pipe)
add(Tabix(this, outputFile))
}
}
......@@ -38,7 +38,8 @@ class BcftoolsSingleSample(val root: Configurable) extends Variantcaller {
bt.c = true
bt.output = new File(outputDir, sample + ".vcf.gz")
add(mp | new FixMpileup(this) | bt)
val pipe = mp | new FixMpileup(this) | bt
add(pipe)
add(Tabix(this, bt.output))
bt.output
}
......
......@@ -28,7 +28,8 @@ class Freebayes(val root: Configurable) extends Variantcaller {
val fb = new nl.lumc.sasc.biopet.extensions.Freebayes(this)
fb.bamfiles = inputBams.values.toList
fb.outputVcf = new File(outputDir, namePrefix + ".freebayes.vcf")
add(fb | new Bgzip(this) > outputFile)
val pipe = fb | new Bgzip(this) > outputFile
add(pipe)
add(Tabix.apply(this, outputFile))
}
......
......@@ -40,7 +40,8 @@ class RawVcf(val root: Configurable) extends Variantcaller {
val m2v = new MpileupToVcf(this)
m2v.inputBam = bamFile
m2v.output = new File(outputDir, sample + ".raw.vcf")
add(mp | m2v)
val pipe = mp | m2v
add(pipe)
val vcfFilter = new VcfFilter(this) {
override def configNamespace = "vcffilter"
......
......@@ -198,6 +198,7 @@ object ShivaSvCallingTest {
copyFile("ref.fa.fai")
val config = Map(
"skip_write_dependencies" -> true,
"name_prefix" -> "test",
"output_dir" -> outputDir,
"cache" -> true,
......
......@@ -191,6 +191,7 @@ object ShivaTest {
copyFile("ref.fa.fai")
val config = Map(
"skip_write_dependencies" -> true,
"name_prefix" -> "test",
"cache" -> true,
"dir" -> "test",
......
......@@ -230,6 +230,7 @@ object ShivaVariantcallingTest {
copyFile("ref.fa.fai")
val config = Map(
"skip_write_dependencies" -> true,
"name_prefix" -> "test",
"output_dir" -> outputDir,
"cache" -> true,
......
......@@ -119,6 +119,7 @@ object TinyCapTest {
Files.touch(annotationRefflat)
val config = Map(
"skip_write_dependencies" -> true,
"output_dir" -> outputDir,
"reference_fasta" -> (referenceFasta.getAbsolutePath),
"bowtie_index" -> (bowtieIndex.getAbsolutePath),
......
......@@ -107,6 +107,7 @@ object ToucanTest {
exacVcfFile.deleteOnExit()
val config = Map(
"skip_write_dependencies" -> true,
"reference_fasta" -> resourcePath("/fake_chrQ.fa"),
"output_dir" -> outputDir,
"gatk_jar" -> "test",
......
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