Commit cb6f9998 authored by Sander Bollen's avatar Sander Bollen
Browse files

fixing missing cutadapt mock values

parent a7b54487
......@@ -39,7 +39,7 @@ class CarpTest extends TestNGSuite with Matchers {
def testCarp(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean, threatment: Boolean, control: Boolean): Unit = {
val map = {
var m = ConfigUtils.mergeMaps(Map("output_dir" -> CarpTest.outputDir
), CarpTest.excutables)
), CarpTest.executables)
if (sample1) m = ConfigUtils.mergeMaps(CarpTest.sample1, m.toMap)
if (sample2) m = ConfigUtils.mergeMaps(CarpTest.sample2, m.toMap)
......@@ -82,12 +82,13 @@ class CarpTest extends TestNGSuite with Matchers {
object CarpTest {
val outputDir = Files.createTempDir()
val excutables = Map(
val executables = Map(
"reference" -> "test",
"seqstat" -> Map("exe" -> "test"),
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
"sickle" -> Map("exe" -> "test"),
"cutadapt" -> Map("exe" -> "test"),
"bwa" -> Map("exe" -> "test"),
"samtools" -> Map("exe" -> "test"),
"macs2" -> Map("exe" -> "test"),
......
......@@ -48,7 +48,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir,
"skip_trim" -> skipTrim,
"skip_clip" -> skipClip
), Map(FlexiprepTest.excutables.toSeq: _*))
), Map(FlexiprepTest.executables.toSeq: _*))
val flexiprep: Flexiprep = initPipeline(map)
flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq" + (if (zipped) ".gz" else ""))
......@@ -79,10 +79,11 @@ class FlexiprepTest extends TestNGSuite with Matchers {
object FlexiprepTest {
val outputDir = Files.createTempDir()
val excutables = Map(
val executables = Map(
"seqstat" -> Map("exe" -> "test"),
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
"sickle" -> Map("exe" -> "test")
"sickle" -> Map("exe" -> "test"),
"cutadapt" -> Map("exe" -> "test")
)
}
\ No newline at end of file
......@@ -57,7 +57,7 @@ class MappingTest extends TestNGSuite with Matchers {
"number_chunks" -> chunks,
"skip_markduplicates" -> skipMarkDuplicate,
"skip_flexiprep" -> skipFlexiprep
), Map(MappingTest.excutables.toSeq: _*))
), Map(MappingTest.executables.toSeq: _*))
val mapping: Mapping = initPipeline(map)
mapping.input_R1 = new File(mapping.outputDir, "bla_R1.fq")
......@@ -107,12 +107,13 @@ class MappingTest extends TestNGSuite with Matchers {
object MappingTest {
val outputDir = Files.createTempDir()
val excutables = Map(
val executables = Map(
"reference" -> "test",
"seqstat" -> Map("exe" -> "test"),
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
"sickle" -> Map("exe" -> "test"),
"cutadapt" -> Map("exe" -> "test"),
"bwa" -> Map("exe" -> "test"),
"star" -> Map("exe" -> "test"),
"bowtie" -> Map("exe" -> "test"),
......
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