From 9c0d6b9525e0bf8cd934f7201f7e281094432a00 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 12 Dec 2019 15:39:52 +0100
Subject: [PATCH] consistent naming
---
bedtools.wdl | 43 +++++++++++++++++++++++++++++++++++--------
1 file changed, 35 insertions(+), 8 deletions(-)
diff --git a/bedtools.wdl b/bedtools.wdl
index 3c7a9b8..2e65c7d 100644
--- a/bedtools.wdl
+++ b/bedtools.wdl
@@ -23,20 +23,20 @@ version 1.0
task Complement {
input {
File genome
- File bedFile
+ File inputBed
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
- String outputFile = basename(bedFile, "\.bed") + ".complement.bed"
+ String outputBed = basename(inputBed, "\.bed") + ".complement.bed"
}
command {
bedtools complement \
-g ~{genome} \
- -i ~{bedFile} \
- > ~{outputFile}
+ -i ~{inputBed} \
+ > ~{outputBed}
}
output {
- File complementBed = outputFile
+ File complementBed = outputBed
}
runtime {
@@ -46,9 +46,9 @@ task Complement {
parameter_meta {
genome: {description: "Genome file with names and sizes",
category: "required"}
- bedFile: {description: "The bedfile to complement",
+ inputBed: {description: "The inputBed to complement",
category: "required"}
- outputFile: {description: "The path to write the output to",
+ outputBed: {description: "The path to write the output to",
category: "advanced"}
dockerImage: {
description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
@@ -93,6 +93,33 @@ task GetChromSizes {
}
}
+task Merge {
+ input {
+ Array[File]+ inputBed
+ String outputBed = "merged.bed"
+ String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
+ }
+
+ command {
+ bedtools merge -i ~{inputBed} > ~{outputBed}
+ }
+
+ output {
+ File mergedBed = outputBed
+ }
+
+ parameter_meta {
+ inputBed: {description: "The inputBed to complement",
+ category: "required"}
+ outputBed: {description: "The path to write the output to",
+ category: "advanced"}
+ dockerImage: {
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"
+ }
+ }
+}
+
task Sort {
input {
File inputBed
@@ -125,7 +152,7 @@ task Sort {
}
output {
- File bedFile = outputBed
+ File sortedBed = outputBed
}
runtime {
--
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