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bwa.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 = "bwa"
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)", "$1")
Int totalMemMb = if inGiga then memoryValue*1024 else memoryValue
Int memoryByThreadsMb = floor(totalMemMb/threads)
command <<<
~{path_exe} 2>&1 | grep "Program\|Version\|Contact"
>>>
output {
String version = read_string(stdout())
}
runtime {
cpu: "~{threads}"
requested_memory_mb_per_core: "${memoryByThreadsMb}"
}
parameter_meta {
path_exe: {
description: 'Path used as executable [default: "bwa"]',
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'
}
}
}
# Options optimizations :
# - It seems that option "-V" didn't do anything
# - Since minimap2 replace BWA for long-reads it seems deprecated to use "-x"
# - It seems unnecessary to change all options in the human context
task memnosort {
meta {
author: "Olivier Ardouin"
email: "o-ardouin(at)chu-montpellier.fr"
version: "0.0.1"
date: "2021-11-23"
}
input {
String path_exe = "bwa"
String? outputPath
String? sample
String subString = "(_S[0-9]+)?(_L[0-9][0-9][0-9])?(_R[12])?(_[0-9][0-9][0-9])?.(fastq|fq)(.gz)?"
String subStringReplace = ""
File fastqR1
File? fastqR2
File refFasta
File refFai
File refAmb
File refAnn
File refBwt
File refPac
File refSa
String platformReads = "ILLUMINA"
Boolean markShorter = true
Int minScore = 30
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(sample) then sample else sub(basename(fastqR1),subString,subStringReplace)
String outputFile = if defined(outputPath) then "~{outputPath}/~{baseName}.sam" else "~{baseName}.sam"
command <<<
if [[ ! -d $(dirname ~{outputFile}) ]]; then
mkdir -p $(dirname ~{outputFile})
fi
~{path_exe} mem \
-R "@RG\tID:~{baseName}\tSM:~{baseName}\tPL:~{platformReads}" \
-T ~{minScore} \
~{true="-M" false="" markShorter} \
-t ~{threads} \
~{refFasta} \
~{fastqR1} ~{default="" fastqR2} \
>>>
output {
File outputFile = stdout()
}
runtime {
cpu: "~{threads}"
requested_memory_mb_per_core: "${memoryByThreadsMb}"
}
parameter_meta {
path_exe: {
description: 'Path used as executable [default: "bwa"]',
category: 'System'
}
sample: {
description: 'Sample name to use for output file name [default: sub(basename(fastqR1),subString,"")]',
category: 'Output path/name option'
}
subString: {
description: 'Substring to remove to get sample name [default: "(_S[0-9]+)?(_L[0-9][0-9][0-9])?(_R[12])?(_[0-9][0-9][0-9])?.(fastq|fq)(.gz)?"]',
category: 'Output path/name option'
}
subStringReplace: {
description: 'subString replace by this string [default: ""]',
category: 'Output path/name option'
}
fastqR1: {
description: 'Input file with reads 1 (fastq, fastq.gz, fq, fq.gz).',
category: 'Required'
}
fastqR2: {
description: 'Input file with reads 2 (fastq, fastq.gz, fq, fq.gz).',
category: 'Tool option'
}
refFasta: {
description: 'Path to the reference file (format: fasta)',
category: 'Required'
}
platformReads: {
description: 'Type of plateform that produce reads [default: ILLUMINA]',
category: 'Tool option'
}
markShorter: {
description: 'Mark shorter split hits as secondary (for Picard compatibility). [default: true]',
category: 'Tool option'
}
minScore: {
description: 'Don’t output alignment with score lower than this value. [default: 30]',
category: 'Tool 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 mem {
meta {
author: "Charles VAN GOETHEM"
email: "c-vangoethem(at)chu-montpellier.fr"
version: "0.0.2"
date: "2021-03-05"
}
input {
String path_exe = "bwa"
String path_exe_samtools = "samtools"
String? outputPath
String? sample
String subString = "(_S[0-9]+)?(_L[0-9][0-9][0-9])?(_R[12])?(_[0-9][0-9][0-9])?.(fastq|fq)(.gz)?"
String subStringReplace = ""
File fastqR1
File? fastqR2
File refFasta
File refFai
File refAmb
File refAnn
File refBwt
File refPac
File refSa
String platformReads = "ILLUMINA"
Boolean markShorter = true
Int minScore = 30
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(sample) then sample else sub(basename(fastqR1),subString,subStringReplace)
String outputFile = if defined(outputPath) then "~{outputPath}/~{baseName}.bam" else "~{baseName}.bam"
command <<<
if [[ ! -d $(dirname ~{outputFile}) ]]; then
mkdir -p $(dirname ~{outputFile})
fi
~{path_exe} mem \
-R "@RG\tID:~{baseName}\tSM:~{baseName}\tPL:~{platformReads}" \
-T ~{minScore} \
~{true="-M" false="" markShorter} \
-t ~{threads} \
~{refFasta} \
~{fastqR1} ~{default="" fastqR2} \
| ~{path_exe_samtools} sort -@ ~{threads-1} -m ~{memoryByThreadsMb}M -o ~{outputFile}
>>>
output {
File outputFile = outputFile
}
runtime {
cpu: "~{threads}"
requested_memory_mb_per_core: "${memoryByThreadsMb}"
}
parameter_meta {
path_exe: {
description: 'Path used as executable [default: "bwa"]',
category: 'System'
}
path_exe_samtools: {
description: 'Path used as executable [default: "samtools"]',
category: 'System'
}
outputPath: {
description: 'Output path where bam file was generated. [default: pwd()]',
category: 'Output path/name option'
}
sample: {
description: 'Sample name to use for output file name [default: sub(basename(fastqR1),subString,"")]',
category: 'Output path/name option'
}
subString: {
description: 'Substring to remove to get sample name [default: "(_S[0-9]+)?(_L[0-9][0-9][0-9])?(_R[12])?(_[0-9][0-9][0-9])?.(fastq|fq)(.gz)?"]',
category: 'Output path/name option'
}
subStringReplace: {
description: 'subString replace by this string [default: ""]',
category: 'Output path/name option'
}
fastqR1: {
description: 'Input file with reads 1 (fastq, fastq.gz, fq, fq.gz).',
category: 'Required'
}
fastqR2: {
description: 'Input file with reads 2 (fastq, fastq.gz, fq, fq.gz).',
category: 'Tool option'
}
refFasta: {
description: 'Path to the reference file (format: fasta)',
category: 'Required'
}
platformReads: {
description: 'Type of plateform that produce reads [default: ILLUMINA]',
category: 'Tool option'
}
markShorter: {
description: 'Mark shorter split hits as secondary (for Picard compatibility). [default: true]',
category: 'Tool option'
}
minScore: {
description: 'Don’t output alignment with score lower than this value. [default: 30]',
category: 'Tool 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 index {
meta {
author: "Charles VAN GOETHEM"
email: "c-vangoethem(at)chu-montpellier.fr"
version: "0.0.1"
date: "2020-07-30"
}
input {
String path_exe = "bwa"
File in
String? outputPath
String? algo
String? name
Int? blockSize
Boolean sixtyFour = false
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 basename(in)
String outputBaseName = if defined(outputPath) then "~{outputPath}/~{baseName}" else "~{baseName}"
command <<<
if [[ ! -d $(dirname ~{outputBaseName}) ]]; then
mkdir -p $(dirname ~{outputBaseName})
fi
~{path_exe} index \
~{default="" "-a " + algo} \
~{default="" "-b " + blockSize} \
~{true="-6" false="" sixtyFour} \
-p ~{outputBaseName} \
~{in}
>>>
output {
File refAmb = outputBaseName + ".amb"
File refAnn = outputBaseName + ".ann"
File refPac = outputBaseName + ".pac"
File refBwt = outputBaseName + ".bwt"
File refSa = outputBaseName + ".sa"
}
runtime {
cpu: "~{threads}"
requested_memory_mb_per_core: "${memoryByThreadsMb}"
}
parameter_meta {
path_exe: {
description: 'Path used as executable [default: "bwa"]',
category: 'System'
}
outputPath: {
description: 'Output path where bam file was generated. [default: pwd()]',
category: 'Output path/name option'
}
in: {
description: 'Fasta file to index by bwa.',
category: 'Required'
}
algo: {
description: 'BWT construction algorithm: bwtsw, is or rb2 [auto]',
category: 'Tool option'
}
name: {
description: 'Prefix of the index files names [fasta name]',
category: 'Tool option'
}
blockSize: {
description: 'Block size for the bwtsw algorithm (effective with algo: bwtsw)',
category: 'Tool option'
}
sixtyFour: {
description: 'Index files named as <in.fasta>.64.* instead of <in.fasta>.*',
category: 'Tool 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'
}
}
}