From a772e3773feedcb22f7e18f8a1f0130fd9b3cf0c Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 16 Oct 2020 15:08:33 +0200
Subject: [PATCH] add gripss, timeMinutes for gridss, fix typos
---
bcftools.wdl | 2 +-
gridss.wdl | 7 ++-
gripss.wdl | 117 +++++++++++++++++++++++++++++++++++++++++++++++++++
snpeff.wdl | 2 +-
4 files changed, 124 insertions(+), 4 deletions(-)
create mode 100644 gripss.wdl
diff --git a/bcftools.wdl b/bcftools.wdl
index 0be3be9..e68e527 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -150,7 +150,7 @@ task Filter {
~{vcf} \
-O z \
-o ~{outputPath}
- bctools index --tbi ~{outputPath}
+ bcftools index --tbi ~{outputPath}
}
output {
diff --git a/gridss.wdl b/gridss.wdl
index 44b9e9f..7516553 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -1,6 +1,6 @@
version 1.0
-# Copyright (c) 2017 Leiden University Medical Center
+# Copyright (c) 2020 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -34,7 +34,8 @@ task GRIDSS {
String outputPrefix = "gridss"
Int jvmHeapSizeGb = 30
- Int threads = 1
+ Int threads = 2
+ Int timeMinutes = ceil(1440 / threads) + 10
String dockerImage = "quay.io/biocontainers/gridss:2.9.4--0"
}
@@ -64,6 +65,7 @@ task GRIDSS {
runtime {
cpu: threads
memory: "~{jvmHeapSizeGb + 1}G"
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -79,6 +81,7 @@ task GRIDSS {
threads: {description: "The number of the threads to use.", category: "advanced"}
jvmHeapSizeGb: {description: "The size of JVM heap for assembly and variant calling",category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
\ No newline at end of file
diff --git a/gripss.wdl b/gripss.wdl
new file mode 100644
index 0000000..6ed0bcf
--- /dev/null
+++ b/gripss.wdl
@@ -0,0 +1,117 @@
+version 1.0
+
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task ApplicationKt {
+ input {
+ File inputVcf
+ String outputPath = "gripss.vcf.gz"
+ File referenceFasta
+ File breakpointHotspot
+ File breakendPon
+ File breakpointPon
+
+ String memory = "25G"
+ String javaXmx = "24G"
+ Int timeMinutes = 60
+ String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.8--0"
+ }
+
+ command {
+ java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -cp /usr/local/share/hmftools-gripss-1.8-0/gripss.jar \
+ com.hartwig.hmftools.gripss.GripssApplicationKt \
+ -ref_genome ~{referenceFasta} \
+ -breakpoint_hotspot ~{breakpointHotspot} \
+ -breakend_pon ~{breakendPon} \
+ -breakpoint_pon ~{breakpointPon} \
+ -input_vcf ~{inputVcf} \
+ -output_vcf ~{outputPath}
+ }
+
+ output {
+ File outputVcf = outputPath
+ File outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ inputVcf: {description: "The input VCF.", category: "required"}
+ outputPath: {description: "The path where th eoutput VCF will be written.", category: "common"}
+ referenceFasta: {description: "The reference fasta file.", category: "advanced"}
+ breakpointHotspot: {description: "Equivalent to the `-breakpoint_hotspot` option.", category: "required"}
+ breakendPon: {description: "Equivalent to the `-breakend_pon` option.", category: "required"}
+ breakpointPon: {description: "Equivalent to the `breakpoint_pon` option.", category: "required"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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 HardFilterApplicationKt {
+ input {
+ File inputVcf
+ String outputPath = "gripss_hard_filter.vcf.gz"
+
+ String memory = "25G"
+ String javaXmx = "24G"
+ Int timeMinutes = 60
+ String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.8--0"
+ }
+
+ command {
+ java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -cp /usr/local/share/hmftools-gripss-1.8-0/gripss.jar \
+ com.hartwig.hmftools.gripss.GripssHardFilterApplicationKt \
+ -input_vcf ~{inputVcf} \
+ -output_vcf ~{outputPath}
+ }
+
+ output {
+ File outputVcf = outputPath
+ File outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ inputVcf: {description: "The input VCF.", category: "required"}
+ outputPath: {description: "The path where th eoutput VCF will be written.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ }
+}
\ No newline at end of file
diff --git a/snpeff.wdl b/snpeff.wdl
index 079a720..d639a03 100644
--- a/snpeff.wdl
+++ b/snpeff.wdl
@@ -24,7 +24,7 @@ task SnpEff {
set -e
mkdir -p "$(dirname ~{outputPath})"
unzip ~{datadirZip}
- snpEff -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ snpEff -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-v \
~{genomeVersion} \
-noDownload \
--
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