From 96a896c956584d98da46b483b4685a8457996a03 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 23 Jan 2020 11:48:33 +0100
Subject: [PATCH] add intersect bed task
---
bedtools.wdl | 46 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/bedtools.wdl b/bedtools.wdl
index 50f9f92..6ae3b3c 100644
--- a/bedtools.wdl
+++ b/bedtools.wdl
@@ -164,3 +164,49 @@ task Sort {
docker: dockerImage
}
}
+
+task Intersect {
+ input {
+ File regionsA
+ File regionsB
+ # Giving a faidx file will set the sorted option.
+ File? faidx
+ String outputBed = "intersect.bed"
+ String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
+ }
+ Boolean sorted = defined(faidx)
+
+ command {
+ set -e
+ ~{"cut -f1,2 " + faidx} ~{true="> sorted.genome" false ="" sorted}
+ bedtools intersect \
+ -a ~{regionsA} \
+ -b ~{regionsB} \
+ ~{true="--sorted" false="" sorted} \
+ ~{true="-g sorted.genome" false="" sorted} \
+ > ~{outputBed}
+ }
+
+ output {
+ File intersectedBed = outputBed
+ }
+
+ runtime {
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ faidx: {description: "The fasta index (.fai) file that is used to create the genome file required for sorted output. Implies sorted option.",
+ category: "common"}
+ regionsA: {description: "Region file a to intersect",
+ category: "required"}
+ regionsB: {description: "Region file b to intersect",
+ 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"
+ }
+ }
+}
--
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