From 6e463326b94866f3eaced9fb23d84deceea207c2 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 23 May 2019 13:05:16 +0200
Subject: [PATCH] add bedtools sort
---
LICENSE | 2 +-
bedtools.wdl | 58 ++++++++++++++++++++++++++++++++++++++++++++++++++++
wiseguy.wdl | 2 +-
3 files changed, 60 insertions(+), 2 deletions(-)
create mode 100644 bedtools.wdl
diff --git a/LICENSE b/LICENSE
index e580f6d..37eeade 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
MIT License
-Copyright (c) 2018 Leiden University Medical Center
+Copyright (c) 2017 Leiden University Medical Center
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
diff --git a/bedtools.wdl b/bedtools.wdl
new file mode 100644
index 0000000..acc8132
--- /dev/null
+++ b/bedtools.wdl
@@ -0,0 +1,58 @@
+version 1.0
+
+# Copyright (c) 2017 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task sort {
+ input {
+ File inputBed
+ Boolean sizeA = false
+ Boolean sizeD = false
+ Boolean chrThenSizeA = false
+ Boolean chrThenSizeD = false
+ 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"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputBed})
+ bedtools sort \
+ -i ~{inputBed} \
+ ~{if sizeA then "-sizeA" else ""} \
+ ~{if sizeD then "-sizeD" else ""} \
+ ~{if chrThenSizeD then "-chrThenSizeD" else ""} \
+ > ~{outputBed}
+ }
+
+ output {
+ File bedFile = outputBed
+ }
+
+ runtime {
+ docker: dockerImage
+ }
+
+
+}
\ No newline at end of file
diff --git a/wiseguy.wdl b/wiseguy.wdl
index 5accca5..c5e8b17 100644
--- a/wiseguy.wdl
+++ b/wiseguy.wdl
@@ -1,6 +1,6 @@
version 1.0
-# Copyright (c) 2018 Leiden University Medical Center
+# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
--
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