Commit 7f36c0c0 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Update yamsvp pipeline, link files

parent 482ffc59
......@@ -76,12 +76,11 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
val bamFile: File =
if (libraryBamfiles.size == 1) {
// When the sample has only 1 run, make a link in the main alignment directory
val alignmentlink = Ln( root, libraryBamfiles.head,
alignmentDir + sampleID + ".merged.bam", true )
val alignmentlink = Ln(root, libraryBamfiles.head,
alignmentDir + sampleID + ".merged.bam", true)
add(alignmentlink, isIntermediate = true)
alignmentlink.out
}
else if (libraryBamfiles.size > 1) {
} else if (libraryBamfiles.size > 1) {
val mergeSamFiles = new SambambaMerge(root)
mergeSamFiles.input = libraryBamfiles
mergeSamFiles.output = alignmentDir + sampleID + ".merged.bam"
......@@ -92,10 +91,6 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
val bamMarkDup = SambambaMarkdup(root, bamFile)
add(bamMarkDup)
// val analysisBam: File = bamMarkDup.output
// val analysisBamIndex = SambambaIndex(root, analysisBam)
// add(analysisBamIndex)
/// bamfile will be used as input for the SV callers. First run Clever
// val cleverVCF : File = sampleDir + "/" + sampleID + ".clever.vcf"
......
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