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Commit c3255755 authored by JasperBoom's avatar JasperBoom
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Update gffcompare.

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biopet/bamstats.wdl deleted 100644 → 0
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version 1.0
# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import "../common.wdl" as common
task Generate {
input {
IndexedBamFile bam
Boolean scatterMode = false
Boolean onlyUnmapped = false
Boolean tsvOutputs = false
String outputDir
String? preCommand
File? toolJar
File? bedFile
Reference? reference
String javaXmx = "8G"
String memory = "9G"
}
File referenceFasta = if defined(reference) then select_first([reference]).fasta else ""
String toolCommand = if defined(toolJar)
then "java -Xmx~{javaXmx} -jar " + toolJar
else "biopet-bamstats -Xmx~{javaXmx}"
command {
set -e -o pipefail
~{preCommand}
mkdir -p ~{outputDir}
~{toolCommand} Generate \
--bam ~{bam.file} \
~{"--bedFile " + bedFile} \
~{true="--reference" false="" defined(reference)} ~{referenceFasta} \
~{true="--onlyUnmapped" false="" onlyUnmapped} \
~{true="--scatterMode" false="" scatterMode} \
~{true="--tsvOutputs" false="" tsvOutputs} \
--outputDir ~{outputDir}
}
output {
File json = outputDir + "/bamstats.json"
File summaryJson = outputDir + "/bamstats.summary.json"
}
runtime {
memory: memory
}
}
biopet/biopet.wdl deleted 100644 → 0
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− 552
View file @ 7aea19d5
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biopet/sampleconfig.wdl deleted 100644 → 0
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View file @ 7aea19d5
version 1.0
# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import "../common.wdl" as common
task SampleConfig {
input {
Array[File]+ inputFiles
String keyFilePath
File? toolJar
String? preCommand
String? sample
String? library
String? readgroup
String? jsonOutputPath
String? tsvOutputPath
String javaXmx = "16G"
String memory = "17G"
}
String toolCommand = if defined(toolJar)
then "java -Xmx~{javaXmx} -jar " + toolJar
else "biopet-sampleconfig -Xmx~{javaXmx}"
command {
set -e -o pipefail
~{preCommand}
mkdir -p . ~{"$(dirname " + jsonOutputPath + ")"} ~{"$(dirname " + tsvOutputPath + ")"}
~{toolCommand} \
-i ~{sep="-i " inputFiles} \
~{"--sample " + sample} \
~{"--library " + library} \
~{"--readgroup " + readgroup} \
~{"--jsonOutput " + jsonOutputPath} \
~{"--tsvOutput " + tsvOutputPath} \
> ~{keyFilePath}
}
output {
File keysFile = keyFilePath
File? jsonOutput = jsonOutputPath
File? tsvOutput = tsvOutputPath
}
runtime {
memory: memory
}
}
task SampleConfigCromwellArrays {
input {
Array[File]+ inputFiles
String outputPath
File? toolJar
String? preCommand
String javaXmx = "4G"
String memory = "5G"
}
String toolCommand = if defined(toolJar)
then "java -Xmx~{javaXmx} -jar " + toolJar
else "biopet-sampleconfig -Xmx~{javaXmx}"
command {
set -e -o pipefail
~{preCommand}
mkdir -p $(dirname ~{outputPath})
~{toolCommand} CromwellArrays \
-i ~{sep="-i " inputFiles} \
~{"-o " + outputPath}
}
output {
File outputFile = outputPath
}
runtime {
memory: memory
}
}
task CaseControl {
input {
Array[File]+ inputFiles
Array[File]+ inputIndexFiles
Array[File]+ sampleConfigs
String outputPath
String controlTag = "control"
File? toolJar
String? preCommand
String javaXmx = "4G"
String memory = "5G"
}
String toolCommand = if defined(toolJar)
then "java -Xmx~{javaXmx} -jar " + toolJar
else "biopet-sampleconfig -Xmx~{javaXmx}"
command {
set -e -o pipefail
~{preCommand}
mkdir -p $(dirname ~{outputPath})
~{toolCommand} CaseControl \
-i ~{sep=" -i " inputFiles} \
-s ~{sep=" -s " sampleConfigs} \
~{"-o " + outputPath} \
~{"--controlTag " + controlTag}
}
output {
File outputFile = outputPath
CaseControls caseControls = read_json(outputFile)
}
runtime {
memory: memory
}
}
biopet/seqstat.wdl deleted 100644 → 0
+ 0
− 64
View file @ 7aea19d5
version 1.0
# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import "../common.wdl" as common
task Generate {
input {
FastqPair fastq
String outputFile
String sample
String library
String readgroup
String? preCommand
File? toolJar
String javaXmx = "4G"
String memory = "5G"
}
String toolCommand = if defined(toolJar)
then "java -Xmx~{javaXmx} -jar " + toolJar
else "biopet-seqstat -Xmx~{javaXmx}"
command {
set -e -o pipefail
~{preCommand}
mkdir -p $(dirname ~{outputFile})
~{toolCommand} Generate \
--fastqR1 ~{fastq.R1} \
~{"--fastqR2 " + fastq.R2} \
--output ~{outputFile} \
~{"--sample " + sample} \
~{"--library " + library } \
~{"--readgroup " + readgroup }
}
output {
File json = outputFile
}
runtime {
memory: memory
}
}
gffcompare.wdl
+ 3
− 3
View file @ c3255755
......@@ -145,10 +145,10 @@ task GffCompare {
# outputs
annotated: {description: "Annotated GTF file."}
loci: {description: ""}
loci: {description: "File describing the processed loci."}
stats: {description: "Various statistics related to the “accuracy” (or a measure of agreement) of the input transcripts when compared to reference annotation data."}
tracking: {description: "File matching transcripts up between samples."}
allFiles: {description: "A collection of all outputs files."}
tracking: {description: "File matching up transcripts between samples."}
allFiles: {description: "A collection of all output files."}
redundant: {description: "File containing duplicate/redundant transcripts."}
missedIntrons: {description: "File denoting missed introns."}
}
......
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