Unverified Commit a2655eb2 authored by Ruben Vorderman's avatar Ruben Vorderman Committed by GitHub
Browse files

Merge branch 'develop' into rhpvorderman-patch-1

parents f3ac5431 4e0ab25e
......@@ -10,6 +10,9 @@ 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`.
+ Survivor: Change integer to string literal in boolean parameters.
+ Samtools: Add mkdir line to `Fastq` task.
+ Add new parameters from CCS version 6.0.0 and add two new outputs:
`ccs_report.txt` & `zmw_metrics.json.gz`.
......
......@@ -23,7 +23,7 @@ version 1.0
task CPAT {
input {
File gene
String outFilePath
String outputPrefix
File hex
File logitModel
......@@ -36,7 +36,7 @@ task CPAT {
String memory = "4G"
Int timeMinutes = 10 + ceil(size(gene, "G") * 30)
String dockerImage = "biocontainers/cpat:v1.2.4_cv1"
String dockerImage = "quay.io/biocontainers/cpat:3.0.4--py39hcbe4a3b_0"
}
# Some WDL magic in the command section to properly output the start and
......@@ -45,10 +45,10 @@ task CPAT {
# to non-optionals.
command {
set -e
mkdir -p "$(dirname ~{outFilePath})"
mkdir -p "$(dirname ~{outputPrefix})"
cpat.py \
--gene ~{gene} \
--outfile ~{outFilePath} \
--outfile ~{outputPrefix} \
--hex ~{hex} \
--logitModel ~{logitModel} \
~{"--ref " + referenceGenome} \
......@@ -57,7 +57,11 @@ 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 {
......@@ -69,7 +73,7 @@ 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"}
......@@ -79,9 +83,6 @@ task CPAT {
memory: {description: "The amount of memory available to the job.", 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."}
}
}
......
......@@ -116,8 +116,8 @@ task GffCompare {
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
......
......@@ -44,9 +44,9 @@ task Merge {
fileList \
~{breakpointDistance} \
~{suppVecs} \
~{true=1 false=0 svType} \
~{true=1 false=0 strandType} \
~{true=1 false=0 distanceBySvSize} \
~{true='1' false='0' svType} \
~{true='1' false='0' strandType} \
~{true='1' false='0' distanceBySvSize} \
~{minSize} \
~{outputPath}
}
......
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