From 0162556c3cf51117bcaa5a6bec309a8247ea05dd Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 12 Dec 2019 16:16:01 +0100
Subject: [PATCH] make complement simpler by using fasta index
---
bedtools.wdl | 46 +++++++---------------------------------------
1 file changed, 7 insertions(+), 39 deletions(-)
diff --git a/bedtools.wdl b/bedtools.wdl
index 3e847d2..d775a4b 100644
--- a/bedtools.wdl
+++ b/bedtools.wdl
@@ -22,15 +22,19 @@ version 1.0
task Complement {
input {
- File genome
+ File faidx
File inputBed
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
String outputBed = basename(inputBed, "\.bed") + ".complement.bed"
}
+ # Use a fasta index file to get the genome sizes. And convert that to the
+ # bedtools specific "genome" format.
command {
+ set -e
+ cut -f1,2 ~{faidx} > sizes.genome
bedtools complement \
- -g ~{genome} \
+ -g sizes.genome \
-i ~{inputBed} \
> ~{outputBed}
}
@@ -44,7 +48,7 @@ task Complement {
}
parameter_meta {
- genome: {description: "Genome file with names and sizes",
+ faidx: {description: "The fasta index (.fai) file from which to extract the genome sizes",
category: "required"}
inputBed: {description: "The inputBed to complement",
category: "required"}
@@ -57,42 +61,6 @@ task Complement {
}
}
-# Technically not a bedtools task, but needed for bedtools complement.
-task GetChromSizes {
- input {
- File faidx
- # Debian for proper GNU Coreutils. Busybox sucks!
- String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
- String outputFile = basename(faidx, "\.fai") + ".genome"
- }
-
- # Get first two columns from the fasta index which note name and size.
- command {
- cut -f1,2 ~{faidx} \
- > ~{outputFile}
- }
-
- output {
- File chromSizes = outputFile
- }
-
- runtime {
- docker: dockerImage
- }
-
- parameter_meta {
- faidx: {description: "The fasta index (.fai) file from which to extract the genome sizes",
- category: "required"}
- outputFile: {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 Merge {
input {
File inputBed
--
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