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mpa.wdl
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mpa.wdl
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version 1.0
# MobiDL 2.0 - MobiDL 2 is a collection of tools wrapped in WDL to be used in any WDL pipelines.
# Copyright (C) 2021 MoBiDiC
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
task get_version {
meta {
author: "Charles VAN GOETHEM"
email: "c-vangoethem(at)chu-montpellier.fr"
version: "0.0.1"
date: "2020-11-20"
}
input {
String path_exe = "mpa"
Int threads = 1
Int memoryByThreads = 768
String? memory
}
String totalMem = if defined(memory) then memory else memoryByThreads*threads + "M"
Boolean inGiga = (sub(totalMem,"([0-9]+)(M|G)", "$2") == "G")
Int memoryValue = sub(totalMem,"([0-9]+)(M|G)", "$1")
Int totalMemMb = if inGiga then memoryValue*1024 else memoryValue
Int memoryByThreadsMb = floor(totalMemMb/threads)
command <<<
~{path_exe} --version
>>>
output {
String version = read_string(stdout())
}
runtime {
cpu: "~{threads}"
requested_memory_mb_per_core: "${memoryByThreadsMb}"
}
parameter_meta {
path_exe: {
description: 'Path used as executable [default: "mpa"]',
category: 'System'
}
threads: {
description: 'Sets the number of threads [default: 1]',
category: 'System'
}
memory: {
description: 'Sets the total memory to use ; with suffix M/G [default: (memoryByThreads*threads)M]',
category: 'System'
}
memoryByThreads: {
description: 'Sets the total memory to use (in M) [default: 768]',
category: 'System'
}
}
}
task mpa {
meta {
author: "Charles VAN GOETHEM"
email: "c-vangoethem(at)chu-montpellier.fr"
version: "0.0.1"
date: "2020-10-07"
}
input {
String path_exe = "mpa"
File in
String? outputPath
String? name
String suffix = ".mpa"
String subString = ""
String subStringReplace = ""
Int threads = 1
Int memoryByThreads = 768
String? memory
}
String totalMem = if defined(memory) then memory else memoryByThreads*threads + "M"
Boolean inGiga = (sub(totalMem,"([0-9]+)(M|G)", "$2") == "G")
Int memoryValue = sub(totalMem,"([0-9]+)(M|G)", "$1")
Int totalMemMb = if inGiga then memoryValue*1024 else memoryValue
Int memoryByThreadsMb = floor(totalMemMb/threads)
String baseName = if defined(name) then name else sub(basename(in),subString,subStringReplace)
String outputFile = if defined(outputPath) then "~{outputPath}/~{baseName}~{suffix}.vcf" else "~{baseName}~{suffix}.vcf"
command <<<
if [[ ! -d $(dirname ~{outputFile}) ]]; then
mkdir -p $(dirname ~{outputFile})
fi
~{path_exe} \
--input ~{in} \
--output ~{outputFile}
>>>
output {
File outputFile = outputFile
}
runtime {
cpu: "~{threads}"
requested_memory_mb_per_core: "${memoryByThreadsMb}"
}
parameter_meta {
path_exe: {
description: 'Path used as executable [default: "mpa"]',
category: 'System'
}
outputPath: {
description: 'Output path where files were generated. [default: pwd()]',
category: 'Output path/name option'
}
name: {
description: 'Name to use for output file name [default: sub(basename(in),subString,subStringReplace)]',
category: 'Output path/name option'
}
in: {
description: 'Input vcf',
category: 'Required'
}
suffix: {
description: 'Suffix to add to the output [default: .adaptersTrim]',
category: 'Output path/name option'
}
subString: {
description: 'Extension to remove from the input file [default: ""]',
category: 'Output path/name option'
}
subStringReplace: {
description: 'subString replace by this string [default: ""]',
category: 'Output path/name option'
}
threads: {
description: 'Sets the number of threads [default: 1]',
category: 'System'
}
memory: {
description: 'Sets the total memory to use ; with suffix M/G [default: (memoryByThreads*threads)M]',
category: 'System'
}
memoryByThreads: {
description: 'Sets the total memory to use (in M) [default: 768]',
category: 'System'
}
}
}