From 47c89884e700c1c7ad11ba26e195d7812a6f1fac Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 30 Jun 2021 14:27:10 +0200
Subject: [PATCH] update CPAT to 3.0.4
---
CHANGELOG.md | 2 ++
CPAT.wdl | 17 +++++++++--------
2 files changed, 11 insertions(+), 8 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 28e998e..112b8f0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,8 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
++ Update CPAT to version 3.0.4.
+ + Changed the `outFilePath` input to `outputPrefix`.
+ GffCompare: Make the `referenceAnnotation` input optional.
+ Stringtie: Add the `minimumCoverage` input.
+ UMI-tools: update default dockerImage to use umitools v1.1.1 with correct samtools version (1.10)
diff --git a/CPAT.wdl b/CPAT.wdl
index afb6785..b3414bc 100644
--- a/CPAT.wdl
+++ b/CPAT.wdl
@@ -23,7 +23,7 @@ version 1.0
task CPAT {
input {
File gene
- String outFilePath
+ String outputPrefix
File hex
File logitModel
@@ -35,7 +35,7 @@ task CPAT {
Array[String]? stopCodons
Int timeMinutes = 10 + ceil(size(gene, "G") * 30)
- String dockerImage = "biocontainers/cpat:v1.2.4_cv1"
+ String dockerImage = "biocontainers/cpat:3.0.4--py39hcbe4a3b_0"
}
# Some WDL magic in the command section to properly output the start and
@@ -47,7 +47,7 @@ task CPAT {
mkdir -p "$(dirname ~{outFilePath})"
cpat.py \
--gene ~{gene} \
- --outfile ~{outFilePath} \
+ --outfile ~{outputPrefix} \
--hex ~{hex} \
--logitModel ~{logitModel} \
~{"--ref " + referenceGenome} \
@@ -56,7 +56,11 @@ task CPAT {
}
output {
- File outFile = outFilePath
+ File orfSeqs = "~{outputPrefix}.ORF_seqs.fa"
+ File orfProb = "~{outputPrefix}.ORF_prob.tsv"
+ File orfProbBest = "~{outputPrefix}.ORF_prob.best.tsv"
+ File noOrf = "~{outputPrefix}.no_ORF.txt"
+ File rScript = "~{outputPrefix}.r"
}
runtime {
@@ -67,7 +71,7 @@ task CPAT {
parameter_meta {
# inputs
gene: {description: "Equivalent to CPAT's `--gene` option.", category: "required"}
- outFilePath: {description: "Equivalent to CPAT's `--outfile` option.", category: "required"}
+ outputPrefix: {description: "Equivalent to CPAT's `--outfile` option.", category: "required"}
hex: {description: "Equivalent to CPAT's `--hex` option.", category: "required"}
logitModel: {description: "Equivalent to CPAT's `--logitModel` option.", category: "required"}
referenceGenome: {description: "Equivalent to CPAT's `--ref` option.", category: "advanced"}
@@ -76,9 +80,6 @@ task CPAT {
stopCodons: {description: "Equivalent to CPAT's `--stop` 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"}
-
- # outputs
- outFile: {description: "CPAT logistic regression model."}
}
}
--
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