nanoplot.wdl

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 = "NanoPlot"

		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: "NanoPlot"]',
			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 nanoplot_summary {
	meta {
		author: "Charles VAN GOETHEM"
		email: "c-vangoethem(at)chu-montpellier.fr"
		version: "0.0.1"
		date: "2020-10-07"
	}

	input {
		String path_exe = "NanoPlot"

		File in
		String? name
		String? outputPath

		Boolean N50 = true
		Int? dpi

		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 ~{outputFile}) ]]; then
			mkdir -p $(dirname ~{outputFile})
		fi

		~{path_exe} \
			--threads ~{threads} \
			~{true="--N50" false="--no-N50" N50} \
			~{default="" "--dpi " + dpi} \
			--outdir ~{outputPath} \
			~{default="" "--prefix " + name} \
			--summary ~{in}

	>>>

	output {
		File outputFile = outputFile
	}

	runtime {
		cpu: "~{threads}"
		requested_memory_mb_per_core: "${memoryByThreadsMb}"
	}

	parameter_meta {
		path_exe: {
			description: 'Path used as executable [default: "NanoPlot"]',
			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 summary file from guppy.',
			category: 'Required'
		}
		N50: {
			description: 'Show the N50 mark in the read length histogram (default: true)',
			category: 'Option'
		}
		dpi: {
			description: 'Set the dpi for saving images',
			category: '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'
		}
	}
}

task nanoplot_fastq {
	meta {
		author: "Charles VAN GOETHEM"
		email: "c-vangoethem(at)chu-montpellier.fr"
		version: "0.0.1"
		date: "2020-10-07"
	}

	input {
		String path_exe = "NanoPlot"

		File in
		String? name
		String? outputPath

		Boolean N50 = true
		Int? dpi

		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 ~{outputFile}) ]]; then
			mkdir -p $(dirname ~{outputFile})
		fi

		~{path_exe} \
			--threads ~{threads} \
			~{true="--N50" false="--no-N50" N50} \
			~{default="" "--dpi " + dpi} \
			--outdir ~{outputPath} \
			~{default="" "--prefix " + name} \
			--fastq ~{in}

	>>>

	output {
		File outputFile = outputFile
	}

	runtime {
		cpu: "~{threads}"
		requested_memory_mb_per_core: "${memoryByThreadsMb}"
	}

	parameter_meta {
		path_exe: {
			description: 'Path used as executable [default: "NanoPlot"]',
			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 fastq file.',
			category: 'Required'
		}
		N50: {
			description: 'Show the N50 mark in the read length histogram (default: true)',
			category: 'Option'
		}
		dpi: {
			description: 'Set the dpi for saving images',
			category: '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'
		}
	}
}