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This workflow uses BWA mem to map DNA sequencing data to a reference genome.
Usage
You can run the workflow using Cromwell:
java -jar cromwell-<version>.jar run -i inputs.json align-bwamem.wdl
Inputs
Inputs are provided through a JSON file. The minimally required inputs are described below and a template containing all possible inputs can be generated using Womtool as described in the WOMtool documentation. See this page for some additional general notes and information about pipeline inputs.
{
"AlignBwaMem.library": "A identifier for the sequencing library",
"AlignBwaMem.sample": "A identifier for the sample",
"AlignBwaMem.readgroup": "A identifier for the readgroup (eg. sequencing lane)",
"AlignBwaMem.inputFastq": {
"R1": "The path to the first-end fastq file",
"R2": "The second-end fastq file. This input may be ignored for single-end sequencing experiments"
},
"AlignBwaMem.bwaIndex": {
"fastaFile": "A path to the fasta file from the bwa index",
"indexFiles": "A list containing the other bwa index files"
},
"AlignBwaMem.outputDir": "The path to the output directory"
}
Some additional inputs which may be of interest are:
{
"AlignBwaMem.platform": "The sequencing platform used, this defaults to 'illumina'",
"AlignBwaMem.bwaMem.threads": "The number of threads to be used by BWA mem, this defaults to 2",
}
Example
{
"AlignBwaMem.library": "lib1",
"AlignBwaMem.sample": "s1",
"AlignBwaMem.readgroup": "lane1",
"AlignBwaMem.inputFastq": {
"R1": "/home/user/data/patient1/R1.fq.gz"
},
"AlignBwaMem.bwaIndex": {
"fastaFile": "/home/user/genomes/human/bwa/GRCh38.fasta",
"indexFiles": [
"/home/user/genomes/human/bwa/GRCh38.fasta.sa",
"/home/user/genomes/human/bwa/GRCh38.fasta.amb",
"/home/user/genomes/human/bwa/GRCh38.fasta.ann",
"/home/user/genomes/human/bwa/GRCh38.fasta.bwt",
"/home/user/genomes/human/bwa/GRCh38.fasta.pac"
]
},
"AlignBwaMem.outputDir": "/home/user/mapping/results",
"AlignBwaMem.bwaMem.threads": 8
}
output
This workflow produces a directory containing a coordinate-sorted BAM file and its index.