From 357e43000f2e16e62927dd72cb1f36da24f384a5 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Fri, 21 Jun 2019 11:22:50 +0200
Subject: [PATCH] add SV task: clever.wdl
---
clever.wdl | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 74 insertions(+)
create mode 100644 clever.wdl
diff --git a/clever.wdl b/clever.wdl
new file mode 100644
index 0000000..b6eabd0
--- /dev/null
+++ b/clever.wdl
@@ -0,0 +1,74 @@
+version 1.0
+
+import "common.wdl"
+import "bwa.wdl"
+task Prediction {
+ input {
+ IndexedBamFile bamFile
+ BwaIndex bwaIndex
+ String outputPath
+ Int threads = 10
+ }
+
+
+ command <<<
+ set -e
+ mkdir -p $(dirname ~{outputPath})
+ clever \
+ -T ~{threads} \
+ --use_mapq \
+ --sorted \
+ -f \
+ ~{bamFile.file} \
+ ~{bwaIndex.fastaFile} \
+ ~{outputPath}
+ >>>
+
+ output {
+ File predictions = "~{outputPath}/predictions.vcf"
+ }
+
+ runtime {
+ cpu: threads
+ docker: "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
+ }
+
+}
+
+task Mateclever {
+ input {
+ IndexedBamFile bamFile
+ BwaIndex bwaIndex
+ File predictions
+ String outputPath
+ Int threads = 10
+ Int cleverMaxDelLength = 100000
+ Int maxLengthDiff= 30
+ Int maxOffset = 150
+ }
+
+ command <<<
+ set -e
+ mkdir -p $(dirname ~{outputPath})
+ echo ~{outputPath} ~{bamFile.file} ~{predictions} none > predictions.list
+ mateclever \
+ -T ~{threads} \
+ -k \
+ -f \
+ -M ~{cleverMaxDelLength} \
+ -z ~{maxLengthDiff} \
+ -o ~{maxOffset} \
+ ~{bwaIndex.fastaFile} \
+ predictions.list \
+ ~{outputPath}
+ >>>
+
+ output {
+ File matecleverVcf = "~{outputPath}/deletions.vcf"
+ }
+
+ runtime {
+ cpu: threads
+ docker: "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
+ }
+}
--
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