From 66a08a19a7684ac0f3267d8168557ff7b2dfe2f3 Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Tue, 27 Sep 2016 13:38:48 +0200 Subject: [PATCH] config save check --- .../nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala index b86224bbb..3ca6cf26c 100644 --- a/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala +++ b/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala @@ -92,10 +92,6 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum } else inputVcf if (enableScatter) { - val doNotRemove: Boolean = config("do_not_remove", default = false) - if (doNotRemove) { - logger.warn("Chunking combined with do_not_remove possibly leads to mangled CSQ fields") - } val outputVcfFiles = BedRecordList.fromReference(referenceFasta()) .scatter(config("bin_size", default = 50000000)) .allRecords.map { region => @@ -116,6 +112,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum runChunk(sv.out, chunkDir, chunkName) } + if (this.functions.filter(_.isInstanceOf[VepNormalizer]).exists(_.asInstanceOf[VepNormalizer].doNotRemove)) + logger.warn("Chunking combined with do_not_remove possibly leads to mangled CSQ fields") + val cv = new CatVariants(this) cv.variant = outputVcfFiles.toList cv.outputFile = outputVcf -- GitLab