From f25df1aeb3fb07a166e3a5b3029537da28c25b3a Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 6 Feb 2020 14:14:44 +0100
Subject: [PATCH] scatterregions always outputs ordered scatters
---
biopet/biopet.wdl | 25 ++++++++++++++++++++++---
1 file changed, 22 insertions(+), 3 deletions(-)
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index f91f93e..4760682 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -254,7 +254,7 @@ task ScatterRegions {
# linking does not work.
String outputDirPath = "scatters"
- command {
+ command <<<
set -e -o pipefail
mkdir -p ~{outputDirPath}
biopet-scatterregions -Xmx~{javaXmx} \
@@ -264,10 +264,29 @@ task ScatterRegions {
~{"-L " + regions} \
~{"--bamFile " + bamFile} \
~{true="--notSplitContigs" false="" notSplitContigs}
- }
+
+ # Glob messes with order of scatters (10 comes before 1), which causes
+ # problems at gatherGvcfs
+ # Therefore we reorder the scatters with python.
+ # Copy all the scatter files to the CWD so the output matches paths in
+ # the cwd.
+ for file in ~{outputDirPath}/*
+ do cp $file .
+ done
+ python << CODE
+ import os
+ scatters = os.listdir("~{outputDirPath}")
+ splitext = [ 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 = ["{}-{}.{}".format(x[0],x[1],x[2]) for x in ordered]
+ for x in merged:
+ print(x)
+ CODE
+ >>>
output {
- Array[File] scatters = glob(outputDirPath + "/scatter-*.bed")
+ Array[File] scatters = read_lines(stdout())
}
runtime {
--
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