From 8057d0792c8fa2721d0267a9ea699b5df3609aea Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 6 Sep 2019 14:41:50 +0200
Subject: [PATCH] cleanup bedtools.wdl
---
CHANGELOG.md | 1 +
bedtools.wdl | 13 ++++++-------
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 38163a8..b7b2b0d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
version 1.0.0-dev
---------------------------
++ All inputs to bedtools Sort are now reflected in the generated command
+ Add WDL task for TALON
+ Add WDL task for TranscriptClean
+ Fastqsplitter: fix mkdir command to work with biocontainer's busybox mkdir
diff --git a/bedtools.wdl b/bedtools.wdl
index 9ef29ad..f9859f9 100644
--- a/bedtools.wdl
+++ b/bedtools.wdl
@@ -30,7 +30,6 @@ task Sort {
Boolean chrThenScoreD = false
File? g
File? faidx
- Boolean header = false
String outputBed = "output.sorted.bed"
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
@@ -40,9 +39,11 @@ task Sort {
mkdir -p $(dirname ~{outputBed})
bedtools sort \
-i ~{inputBed} \
- ~{if sizeA then "-sizeA" else ""} \
- ~{if sizeD then "-sizeD" else ""} \
- ~{if chrThenSizeD then "-chrThenSizeD" else ""} \
+ ~{true="-sizeA" false="" sizeA} \
+ ~{true="-sizeD" false="" sizeD} \
+ ~{true="-chrThenScoreD" false="" chrThenScoreD} \
+ ~{"-g " + g} \
+ ~{"-faidx" + faidx} \
> ~{outputBed}
}
@@ -53,6 +54,4 @@ task Sort {
runtime {
docker: dockerImage
}
-
-
-}
\ No newline at end of file
+}
--
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