From 8c8bb2f3af7f5adecdebdee615742e4e5312c40b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 6 Aug 2014 14:17:47 +0200
Subject: [PATCH] Removed old summary and fix file name for new summary
---
.../biopet/pipelines/flexiprep/Flexiprep.scala | 15 +--------------
1 file changed, 1 insertion(+), 14 deletions(-)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 3b87c042d..b88e6aaaa 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -70,7 +70,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
R2_name = R2_name.substring(0, R2_name.lastIndexOf(R2_ext))
}
- summary.out = outputDir + "new.flexiprep.summary.json"
+ summary.out = outputDir + sampleName + "-" + libraryName + ".qc.summary.json"
}
def biopetScript() {
@@ -276,19 +276,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
}
}
- if (!skipSummary) {
- val summarize = new Summarize(this)
- summarize.runDir = outputDir
- summarize.samplea = R1_name
- if (paired) summarize.sampleb = R2_name
- summarize.samplename = R1_name
- summarize.clip = !skipClip
- summarize.trim = !skipTrim
- summarize.out = new File(outputDir + summarize.samplename + "." + this.getClass.getSimpleName + ".summary.json")
- for ((k, v) <- outputFiles) summarize.deps +:= v
- add(summarize)
- }
-
add(summary)
}
--
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