From 840a37d19727ee6edb790287cfd447e9964ce669 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Fri, 30 Oct 2020 17:39:16 +0100
Subject: [PATCH] Fix a third Travis error.
---
deepvariant.wdl | 2 +-
gffcompare.wdl | 44 +++++++++++++++++++++++---------------------
gffread.wdl | 2 +-
3 files changed, 25 insertions(+), 23 deletions(-)
diff --git a/deepvariant.wdl b/deepvariant.wdl
index 20bf8e2..8b08e11 100644
--- a/deepvariant.wdl
+++ b/deepvariant.wdl
@@ -81,7 +81,7 @@ task RunDeepVariant {
modelType: {description: "<WGS|WES|PACBIO>. Type of model to use for variant calling. Each model_type has an associated default model, which can be overridden by the --customized_model flag.", category: "required"}
outputVcf: {description: "Path where we should write VCF file.", category: "required"}
postprocessVariantsExtraArgs: {description: "A comma-separated list of flag_name=flag_value. 'flag_name' has to be valid flags for calpostprocess_variants.py.", category: "advanced"}
- customizedModel: {description: "A path to a model checkpoint to load for the `call_variants` step. If not set, the default for each --model_type will be used"., category: "advanced"}
+ customizedModel: {description: "A path to a model checkpoint to load for the `call_variants` step. If not set, the default for each --model_type will be used.", category: "advanced"}
numShards: {description: "Number of shards for make_examples step.", category: "common"}
outputGVcf: {description: "Path where we should write gVCF file.", category: "common"}
regions: {description: "List of regions we want to process, in BED/BEDPE format.", category: "advanced"}
diff --git a/gffcompare.wdl b/gffcompare.wdl
index 5d80f61..8bd5309 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -22,16 +22,11 @@ version 1.0
task GffCompare {
input {
- File? inputGtfList
Array[File] inputGtfFiles
File referenceAnnotation
- String? outputDir
- String outPrefix = "gffcmp" # gffcmp is the default used by the program as well. This
- # needs to be defined in order for the output values to be consistent and correct.
- File? genomeSequences
- Int? maxDistanceFreeEndsTerminalExons
- Int? maxDistanceGroupingTranscriptStartSites
- String? namePrefix
+ # gffcmp is the default used by the program as well. This needs to be
+ # defined in order for the output values to be consistent and correct.
+ String outPrefix = "gffcmp"
Boolean C = false
Boolean A = false
Boolean X = false
@@ -44,15 +39,22 @@ task GffCompare {
Boolean verbose = false
Boolean debugMode = false
+ File? inputGtfList
+ String? outputDir
+ File? genomeSequences
+ Int? maxDistanceFreeEndsTerminalExons
+ Int? maxDistanceGroupingTranscriptStartSites
+ String? namePrefix
+
Int timeMinutes = 1 + ceil(size(inputGtfFiles, "G") * 30)
String dockerImage = "quay.io/biocontainers/gffcompare:0.10.6--h2d50403_0"
# This workaround only works in the input section.
- # Issue addressed at https://github.com/openwdl/wdl/pull/263
+ # Issue addressed at https://github.com/openwdl/wdl/pull/263.
File? noneFile # This is a wdl workaround. Please do not assign!
}
- # This allows for the creation of output directories
+ # This allows for the creation of output directories.
String dirPrefix = if defined(outputDir)
then select_first([outputDir]) + "/"
else ""
@@ -93,22 +95,22 @@ task GffCompare {
then "annotated"
else "combined"
- # Check if a redundant .gtf will be created
+ # Check if a redundant .gtf will be created.
Boolean createRedundant = C || A || X
output {
+ # noneFile is not stable. Please replace this as soon as wdl spec allows.
File annotated = totalPrefix + "." + annotatedName + ".gtf"
File loci = totalPrefix + ".loci"
File stats = totalPrefix + ".stats"
File tracking = totalPrefix + ".tracking"
- # noneFile is not stable. Please replace this as soon as wdl spec allows
+ Array[File] allFiles = select_all([annotated, loci, stats, tracking, redundant, missedIntrons])
File? redundant = if createRedundant
then totalPrefix + ".redundant.gtf"
else noneFile
File? missedIntrons = if debugMode
then totalPrefix + ".missed_introns.gtf"
else noneFile
- Array[File] allFiles = select_all([annotated, loci, stats, tracking, redundant, missedIntrons])
}
runtime {
@@ -117,15 +119,10 @@ task GffCompare {
}
parameter_meta {
- inputGtfList: {description: "Equivalent to gffcompare's `-i` option.", category: "advanced"}
+ # inputs
inputGtfFiles: {description: "The input GTF files.", category: "required"}
referenceAnnotation: {description: "The GTF file to compare with.", category: "required"}
- outputDir: {description: "The location the output should be written.", category: "common"}
outPrefix: {description: "The prefix for the output.", category: "advanced"}
- genomeSequences: {description: "Equivalent to gffcompare's `-s` option.", category: "advanced"}
- maxDistanceFreeEndsTerminalExons: {description: "Equivalent to gffcompare's `-e` option.", category: "advanced"}
- maxDistanceGroupingTranscriptStartSites: {description: "Equivalent to gffcompare's `-d` option.", category: "advanced"}
- namePrefix: {description: "Equivalent to gffcompare's `-p` option.", category: "advanced"}
C: {description: "Equivalent to gffcompare's `-C` flag.", category: "advanced"}
A: {description: "Equivalent to gffcompare's `-A` flag.", category: "advanced"}
X: {description: "Equivalent to gffcompare's `-X` flag.", category: "advanced"}
@@ -137,9 +134,14 @@ task GffCompare {
noTmap: {description: "Equivalent to gffcompare's `-T` flag.", category: "advanced"}
verbose: {description: "Equivalent to gffcompare's `-V` flag.", category: "advanced"}
debugMode: {description: "Equivalent to gffcompare's `-D` flag.", category: "advanced"}
+ inputGtfList: {description: "Equivalent to gffcompare's `-i` option.", category: "advanced"}
+ outputDir: {description: "The location the output should be written.", category: "common"}
+ genomeSequences: {description: "Equivalent to gffcompare's `-s` option.", category: "advanced"}
+ maxDistanceFreeEndsTerminalExons: {description: "Equivalent to gffcompare's `-e` option.", category: "advanced"}
+ maxDistanceGroupingTranscriptStartSites: {description: "Equivalent to gffcompare's `-d` option.", category: "advanced"}
+ namePrefix: {description: "Equivalent to gffcompare's `-p` option.", 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"}
+ 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"}
}
meta {
diff --git a/gffread.wdl b/gffread.wdl
index d83e4d7..76ee20d 100644
--- a/gffread.wdl
+++ b/gffread.wdl
@@ -79,4 +79,4 @@ task GffRead {
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
+}
--
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