From 508945fbfb9fcd0aa890097572da8044605cedc0 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 17 Oct 2018 14:47:04 +0200
Subject: [PATCH] add scatter reorder task
---
biopet/biopet.wdl | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index c732d9c..867859e 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -200,6 +200,34 @@ task FastqSync {
}
}
+task ReorderGlobbedScatters {
+ input {
+ Array[File]+ scatters
+ String scatterDir
+ }
+
+ command <<<
+ python << CODE
+ from os.path import basename
+ scatters = ['~{sep="','" scatters}']
+ splitext = [basename(x).split(".") for x in scatters]
+ splitnum = [x.split("-") + [y] for x,y in splitext]
+ ordered = sorted(splitnum, key=lambda x: int(x[1]))
+ merged = ["~{scatterDir}/{}-{}.{}".format(x[0],x[1],x[2]) for x in ordered]
+ for x in merged:
+ print(x)
+ CODE
+ >>>
+
+ output {
+ Array[String] reorderedScatters = read_lines(stdout())
+ }
+
+ runtime {
+ memory: 1
+ }
+}
+
task ScatterRegions {
input {
String? preCommand
--
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