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nanorepeat.wdl
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nanorepeat.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 nanorepeat {
meta {
author: "Charles VAN GOETHEM"
email: "c-vangoethem(at)chu-montpellier.fr"
version: "0.0.1"
date: "2023-10-18"
}
input {
String path_exe = "nanoRepeat.py"
File bamFile
File bamFileIndex
File refGenome
File refGenomeIndex
File? bedFile
String outputPath
String dataType = "ont"
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 <<<
if [[ ! -d $(dirname ~{outputPath}) ]]; then
mkdir -p $(dirname ~{outputPath})
fi
~{path_exe} \
--input ~{bamFile} \
--type bam \
--ref_fasta ~{refGenome} \
--repeat_region_bed ~{bedFile} \
--out_prefix ~{outputPath} \
--data_type ~{dataType} \
--num_cpu ~{threads}
>>>
runtime {
cpu: "~{threads}"
requested_memory_mb_per_core: "${memoryByThreadsMb}"
}
parameter_meta {
path_exe: {
description: 'Path used as executable [default: "nanoRepeat.py"]',
category: 'System'
}
outputPath: {
description: 'Output path where files were generated.',
category: 'Output'
}
bamFile: {
description: 'BAM input file.',
category: 'Required'
}
bamFileIndex: {
description: 'BAM index',
category: 'Required'
}
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'
}
}
}