From 2b439234de95cab10f9abe2affd08f492c71759b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 18 Sep 2018 09:31:56 +0200
Subject: [PATCH] added structs
---
biopet/bamstats.wdl | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/biopet/bamstats.wdl b/biopet/bamstats.wdl
index 8459ca4..df919ef 100644
--- a/biopet/bamstats.wdl
+++ b/biopet/bamstats.wdl
@@ -2,19 +2,19 @@ version 1.0
# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2018
+import "../common.wdl" as common
+
task Generate {
input {
String? preCommand
File? toolJar
- File bam
- File bamIndex
+ IndexedBamFile bam
File? bedFile
Boolean scatterMode = false
Boolean onlyUnmapped = false
Boolean tsvOutputs = false
String outputDir
- File? reference
- File? referenceDict
+ Reference? reference
Int memory = 4
Float memoryMultiplier = 2.0
}
@@ -23,14 +23,16 @@ task Generate {
then "java -Xmx" + memory + "G -jar " + toolJar
else "biopet-bamstats -Xmx" + memory + "G"
+ String refArg = if (defined(reference)) then "--reference " + select_first([reference]).fasta else ""
+
command {
set -e -o pipefail
~{preCommand}
mkdir -p ~{outputDir}
~{toolCommand} Generate \
- --bam ~{bam} \
+ --bam ~{bam.file} \
~{"--bedFile " + bedFile} \
- ~{"--reference " + reference} \
+ ~{refArg} \
~{true="--onlyUnmapped" false="" onlyUnmapped} \
~{true="--scatterMode" false="" scatterMode} \
~{true="--tsvOutputs" false="" tsvOutputs} \
--
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