Commit 47c89884 authored by Cats's avatar Cats
Browse files

update CPAT to 3.0.4

parent 24a6f110
......@@ -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)
......
......@@ -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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