OptiType does HLA genotyping producing 4-digit HLA genotyping predictions from NGS data and selects major/minor HLA Class I alleles. The workflow pre-filters input fastq reads by aligning to and HLA fasta reference based on library type (dna|rna) using RazerS3, as suggested in the tool documentation.
- optiType 1.3.1
- razers3 3.5.8
- slicer 0.3.0
- gsi software modules : optitype 1.3.1 slicer 0.3.0
- gsi software module dependencies : singularity 3.9.4 razers 3.5.8 samtools 1.16.1
java -jar cromwell.jar run optitype.wdl --inputs inputs.json
| Parameter | Value | Description |
|---|---|---|
fastqR1 |
File | Fastq file for read 1 |
fastqR2 |
File | Fastq file for read 2 |
outputFileNamePrefix |
String | Prefix for output files |
libtype |
String | the type of library, which will determine the hla reference to use. dna |
| Parameter | Value | Default | Description |
|---|---|---|---|
numChunks |
Int | 1 | Number of chunks to split fastq file [1, no splitting] |
numReads |
Int? | None | Number of reads |
| Parameter | Value | Default | Description |
|---|---|---|---|
countChunkSize.modules |
String | "python/3.7" | name and version of modules |
countChunkSize.jobMemory |
Int | 16 | Memory allocated for this job |
countChunkSize.timeout |
Int | 48 | Hours before task timeout |
slicerR1.modules |
String | "slicer/0.3.0" | Required environment modules |
slicerR1.jobMemory |
Int | 16 | Memory allocated for this job |
slicerR1.timeout |
Int | 48 | Hours before task timeout |
slicerR2.modules |
String | "slicer/0.3.0" | Required environment modules |
slicerR2.jobMemory |
Int | 16 | Memory allocated for this job |
slicerR2.timeout |
Int | 48 | Hours before task timeout |
HLAReadsR1.modules |
String | "optitype/1.3.1" | Required environment modules |
HLAReadsR1.jobMemory |
Int | 16 | Memory allocated for this job |
HLAReadsR1.timeout |
Int | 48 | Hours before task timeout |
HLAReadsR2.modules |
String | "optitype/1.3.1" | Required environment modules |
HLAReadsR2.jobMemory |
Int | 16 | Memory allocated for this job |
HLAReadsR2.timeout |
Int | 48 | Hours before task timeout |
concatR1.jobMemory |
Int | 16 | Memory allocated for this job |
concatR1.timeout |
Int | 48 | Hours before task timeout |
concatR2.jobMemory |
Int | 16 | Memory allocated for this job |
concatR2.timeout |
Int | 48 | Hours before task timeout |
run_optitype.modules |
String | "optitype/1.3.1" | Required environment modules |
run_optitype.jobMemory |
Int | 16 | Memory allocated for this job |
run_optitype.timeout |
Int | 48 | Hours before task timeout |
| Output | Type | Description |
|---|---|---|
optitypeResults |
File | {'description': 'Results of optitype', 'vidarr_label': 'optitypeResults'} |
optitypePlot |
File | {'description': 'Plots of optitype', 'vidarr_label': 'optitypePlot'} |
This section lists command(s) run by Optitype workflow
- Running Optitype
set -euo pipefail
if [ -z "~{numReads}" ]; then
totalLines=$(zcat ~{fastqR1} | wc -l)
else totalLines=$((~{numReads}*4))
fi
python3 -c "from math import ceil; print (int(ceil(($totalLines/4.0)/~{numChunks})*4))"
set -euo pipefail
module load slicer/0.3.0
slicer -i ~{fastqR} -l ~{chunkSize} --gzip
set -euo pipefail
razers3 -i 95 -m 1 -dr 0 -o HLA.bam ~{hlaref} ~{fastq}
samtools bam2fq HLA.bam > HLA.fastq
set -euo pipefail
cat ~{sep=" " fastq} > hlareads.fastq
module load optitype
optitype -i ~{fastqR1} ~{fastqR2} --~{libtype} -v -o . --prefix ~{prefix}
For support, please file an issue on the Github project or send an email to [email protected] .
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