Skip to content
Snippets Groups Projects
Commit d09f9f9d authored by sajvanderzeeuw's avatar sajvanderzeeuw
Browse files

make intermediate fastq

parent 3f86e487
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+ 3
− 2
View file @ d09f9f9d
...@@ -171,8 +171,9 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri ...@@ -171,8 +171,9 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if (!bamFile.exists) throw new IllegalStateException("Bam in config does not exist, file: " + bamFile) if (!bamFile.exists) throw new IllegalStateException("Bam in config does not exist, file: " + bamFile)
if (config("bam_to_fastq", default = false).getBoolean) { if (config("bam_to_fastq", default = false).getBoolean) {
val samToFastq = SamToFastq(this, bamFile, runDir + sampleID + "-" + runID + ".R1.fastq", runDir + sampleID + "-" + runID + ".R2.fastq") val samToFastq = SamToFastq(this, bamFile, runDir + sampleID + "-" + runID + ".R1.fastq",
add(samToFastq) runDir + sampleID + "-" + runID + ".R2.fastq")
add(samToFastq, isIntermediate = true)
val mapping = Mapping.loadFromLibraryConfig(this, runConfig, sampleConfig, runDir, startJobs = false) val mapping = Mapping.loadFromLibraryConfig(this, runConfig, sampleConfig, runDir, startJobs = false)
mapping.input_R1 = samToFastq.fastqR1 mapping.input_R1 = samToFastq.fastqR1
mapping.input_R2 = samToFastq.fastqR2 mapping.input_R2 = samToFastq.fastqR2
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment