From 197360002b63fc330b67a6978ee8d7a234c73de9 Mon Sep 17 00:00:00 2001
From: cedrick <cagaser@outlook.com>
Date: Thu, 13 Feb 2020 10:33:28 +0100
Subject: [PATCH] modify outputPath category from required to common
---
bcftools.wdl | 2 +-
clever.wdl | 2 +-
delly.wdl | 2 +-
manta.wdl | 2 +-
picard.wdl | 2 +-
samtools.wdl | 2 +-
survivor.wdl | 2 +-
7 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/bcftools.wdl b/bcftools.wdl
index 866a310..122fcdd 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -45,7 +45,7 @@ task Bcf2Vcf {
parameter_meta {
bcf: {description: "The generated BCF from an SV caller", category: "required"}
- outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+ 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"}
}
}
diff --git a/clever.wdl b/clever.wdl
index ca28336..33ac26f 100644
--- a/clever.wdl
+++ b/clever.wdl
@@ -119,7 +119,7 @@ task Prediction {
bamFile: {description: "The bam file to process.", category: "required"}
bamIndex: {description: "The index bam file.", category: "required"}
bwaIndex: {description: "The BWA index files.", category: "required"}
- outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
threads: {description: "The the number of threads required to run a program", category: "advanced"}
memory: {description: "The memory required to run the programs", 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"}
diff --git a/delly.wdl b/delly.wdl
index fab0637..ad8f18d 100644
--- a/delly.wdl
+++ b/delly.wdl
@@ -58,7 +58,7 @@ task CallSV {
bamIndex: {description: "The index bam file.", category: "required"}
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
- outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
memory: {description: "The memory required to run the programs", 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"}
}
diff --git a/manta.wdl b/manta.wdl
index cd869bb..5006a01 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -68,7 +68,7 @@ task Germline {
bamIndex: {description: "The index bam file.", category: "required"}
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
- runDir: {description: "The directory to use as run/output directory.", category: "required"}
+ runDir: {description: "The directory to use as run/output directory.", category: "common"}
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"}
diff --git a/picard.wdl b/picard.wdl
index 88ea3a2..7df96aa 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -671,7 +671,7 @@ task RenameSample {
parameter_meta {
# inputs
inputVcf: {description: "The VCF file to process.", category: "required"}
- outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
newSampleName: {description: "A string to replace the old sample name.", category: "required"}
memory: {description: "The memory required to run the programs", category: "advanced"}
javaXmx: {description: "The max. memory allocated for JAVA", category: "advanced"}
diff --git a/samtools.wdl b/samtools.wdl
index b04dd11..de7f2a3 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -425,7 +425,7 @@ task FilterShortReadsBam {
parameter_meta {
bamFile: {description: "The bam file to process.", category: "required"}
- outputPathBam: {description: "The filtered bam file.", category: "required"}
+ outputPathBam: {description: "The filtered bam file.", 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"}
}
}
diff --git a/survivor.wdl b/survivor.wdl
index 15bff09..ded11d7 100644
--- a/survivor.wdl
+++ b/survivor.wdl
@@ -69,7 +69,7 @@ task Merge {
strandType: {description: "A boolean to include strand type of an SV to be merged", category: "advanced"}
distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size", category: "advanced"}
minSize: {description: "The mimimum size of SV to be merged", category: "advanced"}
- outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
memory: {description: "The memory required to run the programs", 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"}
}
--
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