From 7aed677ae0cc08015953b968db223540cd6b45a3 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 9 Jan 2020 14:04:32 +0100
Subject: [PATCH] add parameter_meta for SplitNCigarReads,
ReorderGlobbedScatter and ScatterRegions
---
biopet/biopet.wdl | 25 +++++++++++++++++++++++++
gatk.wdl | 20 +++++++++++++++++++-
2 files changed, 44 insertions(+), 1 deletion(-)
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index 8cf2381..f91f93e 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -226,6 +226,12 @@ task ReorderGlobbedScatters {
# 4 gigs of memory to be able to build the docker image in singularity
memory: "4G"
}
+
+ parameter_meta {
+ scatters: {description: "The files which should be ordered.", category: "required"}
+ 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 ScatterRegions {
@@ -268,6 +274,25 @@ task ScatterRegions {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ scatterSize: {description: "Equivalent to biopet scatterregions' `-s` option.", category: "common"}
+ regions: {description: "The regions to be scattered.", category: "advanced"}
+ notSplitContigs: {description: "Equivalent to biopet scatterregions' `--notSplitContigs` flag.",
+ category: "advanced"}
+ bamFile: {description: "Equivalent to biopet scatterregions' `--bamfile` option.",
+ category: "advanced"}
+ bamIndex: {description: "The index for the bamfile given through bamFile.", category: "advanced"}
+
+ 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"}
+ 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 ValidateAnnotation {
diff --git a/gatk.wdl b/gatk.wdl
index 676f2fd..99b562b 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -113,7 +113,7 @@ task BaseRecalibrator {
inputBam: {description: "The BAM file to generate a BQSR report for.", category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
recalibrationReportPath: {description: "The location to write the BQSR report to.", category: "required"}
- sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advancded"}
+ sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"}
knownIndelsSitesVCFs: {description: "VCf files with known indels.", category: "advanced"}
knownIndelsSitesVCFIndexes: {description: "The indexed for the known variant VCFs.", category: "advanced"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
@@ -614,6 +614,24 @@ task SplitNCigarReads {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ inputBam: {description: "The BAM file for which spliced reads should be split.", category: "required"}
+ inputBamIndex: {description: "The input BAM file's index.", category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.",
+ category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ outputBam: {description: "The location the output BAM file should be written.", category: "required"}
+ intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
+
+ 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"}
+ 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 CombineVariants {
--
GitLab