Commit a06766d9 authored by Sander Bollen's avatar Sander Bollen

use output dir for varda intermediates

parent 035f43f7
......@@ -123,7 +123,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val filteredVcfs = splits.map(x => {
val filter = new VcfFilter(this)
filter.inputVcf = x.output
filter.outputVcf = swapExt(x.output, ".vcf.gz", ".filtered.vcf.gz")
filter.outputVcf = swapExt(outputDir, x.output, ".vcf.gz", ".filtered.vcf.gz")
filter.minGenomeQuality = minGQ
add(filter)
filter
......@@ -132,7 +132,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val bedTracks = filteredVcfs.map(x => {
val bed = new GvcfToBed(this)
bed.inputVcf = x.outputVcf
bed.outputBed = swapExt(x.outputVcf, ".vcf.gz", ".bed")
bed.outputBed = swapExt(outputDir, x.outputVcf, ".vcf.gz", ".bed")
add(bed)
bed
})
......@@ -140,7 +140,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val zippedBedTracks = bedTracks.map(x => {
val gzip = new Gzip(this)
gzip.input = List(x.outputBed)
gzip.output = swapExt(x.outputBed, ".bed", ".bed.gz")
gzip.output = swapExt(outputDir, x.outputBed, ".bed", ".bed.gz")
add(gzip)
gzip
})
......@@ -149,11 +149,11 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
annotate.vcf = vcf
annotate.queries = annotationQueries
annotate.waitToComplete = true
annotate.output = swapExt(vcf, ".vcf.gz", ".tmp.annot")
annotate.output = swapExt(outputDir, vcf, ".vcf.gz", ".tmp.annot")
add(annotate)
val annotatedVcf = new ManweDownloadAfterAnnotate(this, annotate)
annotatedVcf.output = swapExt(annotate.output, ".tmp.annot", "tmp.annot.vcf.gz")
annotatedVcf.output = swapExt(outputDir, annotate.output, ".tmp.annot", "tmp.annot.vcf.gz")
add(annotatedVcf)
val imports = for (
......@@ -164,7 +164,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
importing.vcfs = List(vcf.outputVcf)
importing.name = Some(sample)
importing.waitToComplete = true
importing.output = swapExt(vcf.outputVcf, ".vcf.gz", ".tmp.import")
importing.output = swapExt(outputDir, vcf.outputVcf, ".vcf.gz", ".tmp.import")
importing.public = isPublic
add(importing)
importing
......@@ -172,7 +172,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val activates = imports.map(x => {
val active = new ManweActivateAfterAnnotImport(this, annotate, x)
active.output = swapExt(x.output, ".tmp.import", ".tmp.activated")
active.output = swapExt(outputDir, x.output, ".tmp.import", ".tmp.activated")
add(active)
active
})
......@@ -180,7 +180,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val finalLn = new Ln(this)
activates.foreach(x => finalLn.deps :+= x.output)
finalLn.input = annotatedVcf.output
finalLn.output = swapExt(annotatedVcf.output, "tmp.annot.vcf.gz", ".varda_annotated.vcf.gz")
finalLn.output = swapExt(outputDir, annotatedVcf.output, "tmp.annot.vcf.gz", ".varda_annotated.vcf.gz")
finalLn.relative = true
add(finalLn)
......
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