From 2050f3fed42c63381cd6b5d0f7ae88f0ca3e838f Mon Sep 17 00:00:00 2001
From: cedrick <cagaser@outlook.com>
Date: Mon, 10 Feb 2020 16:32:58 +0100
Subject: [PATCH] update parameters meta
---
clever.wdl | 4 ++++
delly.wdl | 1 +
manta.wdl | 2 ++
picard.wdl | 2 ++
survivor.wdl | 7 +++++++
5 files changed, 16 insertions(+)
diff --git a/clever.wdl b/clever.wdl
index 863bf7e..e1b1777 100644
--- a/clever.wdl
+++ b/clever.wdl
@@ -41,6 +41,8 @@ task Prediction {
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"}
bwaIndex: {description: "The BWA index files.", category: "required"}
+ memory: {description: "The memory required to run the programs", category: "common"}
+ threads: {description: "The the number of threads required to run a program", category: "common"}
}
}
@@ -94,5 +96,7 @@ task Mateclever {
category: "advanced"}
bwaIndex: {description: "The BWA index files.", category: "required"}
predictions: {description: "The predicted deletions (VCF) from clever.", category: "required"}
+ memory: {description: "The memory required to run the programs", category: "common"}
+ threads: {description: "The the number of threads required to run a program", category: "common"}
}
}
diff --git a/delly.wdl b/delly.wdl
index baaef56..940b5d3 100644
--- a/delly.wdl
+++ b/delly.wdl
@@ -39,5 +39,6 @@ task CallSV {
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
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"}
+ memory: {description: "The memory required to run the programs", category: "common"}
}
}
diff --git a/manta.wdl b/manta.wdl
index d44ff0a..9c79786 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -128,6 +128,8 @@ task Germline {
callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
+ memoryGb: {description: "The memory required to run the manta", category: "common"}
+ cores: {description: "The the number of cores required to run a program", category: "common"}
}
}
diff --git a/picard.wdl b/picard.wdl
index 5b3c3c6..6f85bfd 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -647,6 +647,8 @@ task RenameSample {
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
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"}
+ javaXmx: {description: "The max. memory allocated for JAVA", category: "common"}
+ memory: {description: "The memory required to run the programs", category: "common"}
}
}
diff --git a/survivor.wdl b/survivor.wdl
index 8763053..bf14781 100644
--- a/survivor.wdl
+++ b/survivor.wdl
@@ -47,5 +47,12 @@ task Merge {
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
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"}
+ minSize: {description: "The mimimum size of SV to be merged", category: "required"}
+ distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size", category: "required"}
+ strandType: {description: "A boolean to include strand type of an SV to be merged", category: "required"}
+ svType: {description: "A boolean to include the type SV to be merged", category: "required"}
+ suppVecs: {description: "The minimum number of SV callers to support the merging", category: "required"}
+ breakpointDistance: {description: "The distance between pairwise breakpoints between SVs", category: "required"}
+ memory: {description: "The memory required to run the programs", category: "common"}
}
}
--
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