From f2645096efbdf32d6f9c0292e15f0cf54c7e8a9e Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Mon, 8 Jun 2015 13:06:14 +0200 Subject: [PATCH] Fix insertsize table --- .../nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp index d67bd4efd..266c63876 100644 --- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp +++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp @@ -45,7 +45,7 @@ Sample #if (!sampleLevel) Library #end #for (field <- fields) - ${field} + ${field.replaceAll("_", " ")} #end @@ -65,7 +65,7 @@ val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats") val fieldValues = for (field <- fields) yield { - summary.getValue((prefixPath ::: List(metricsTag, "stats", "insert_size_metrics", field)):_*) + summary.getValue((prefixPath ::: List("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil) } }# #for (value <- fieldValues) -- GitLab