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Introduction
nf-core/hlatyping is a bioinformatics best-practice analysis pipeline for Precision HLA typing from next-generation sequencing data. The pipeline does next-generation sequencing-based Human Leukozyte Antigen (HLA) typing using OptiType . OptiType is a HLA genotyping algorithm based on integer linear programming. Reads of whole exome/genome/transcriptome sequencing data are mapped against a reference of known MHC class I alleles. To produce accurate 4-digit HLA genotyping predictions, all major and minor HLA-I loci are considered simultaneously to find an allele combination that maximizes the number of explained reads.
The pipeline is built using Nextflow , a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the nf-core website .
Pipeline summary
-
Read QC (
FastQC
) -
Generate reference indices (
yara
) -
Map reads to reference (
yara
) -
Run HLA typing (
OptiType
) -
Present QC for raw reads (
MultiQC
)
Quick Start
-
Install
Nextflow
(>=21.10.3
) -
Install any of
Docker
,Singularity
(you can follow this tutorial ),Podman
,Shifter
orCharliecloud
for full pipeline reproducibility (you can useConda
both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs ) . -
Download the pipeline and test it on a minimal dataset with a single command:
nextflow run nf-core/hlatyping -profile test,YOURPROFILE --outdir <OUTDIR>
Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (
YOURPROFILE
in the example command above). You can chain multiple config profiles in a comma-separated string.-
The pipeline comes with config profiles called
docker
,singularity
,podman
,shifter
,charliecloud
andconda
which instruct the pipeline to use the named tool for software management. For example,-profile test,docker
. -
Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use
-profile <institute>
in your command. This will enable eitherdocker
orsingularity
and set the appropriate execution settings for your local compute environment. -
If you are using
singularity
, please use thenf-core download
command to download images first, before running the pipeline. Setting theNXF_SINGULARITY_CACHEDIR
orsingularity.cacheDir
Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. -
If you are using
conda
, it is highly recommended to use theNXF_CONDA_CACHEDIR
orconda.cacheDir
settings to store the environments in a central location for future pipeline runs.
-
-
Start running your own analysis!
nextflow run nf-core/hlatyping --input samplesheet.csv --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
Documentation
The nf-core/hlatyping pipeline comes with documentation about the pipeline usage , parameters and output .
Credits
nf-core/hlatyping was originally written by Christopher Mohr from Medical Data Integration Center and Quantitative Biology Center , Alexander Peltzer from Boehringer Ingelheim , and Sven Fillinger from Quantitative Biology Center .
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines .
For further information or help, don't hesitate to get in touch on the
Slack
#hlatyping
channel
(you can join with
this invite
).
Citations
If you use nf-core/hlatyping for your analysis, please cite it using the following doi: 10.5281/zenodo.1401039
An extensive list of references for the tools used by the pipeline can be found in the
CITATIONS.md
file.
You can cite the
nf-core
publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x .
Code Snippets
18 19 20 21 22 23 24 25 26 27 28 29 | """ if [ \$({ samtools view -H $input -@$task.cpus ; samtools view $input -@$task.cpus | head -n1000; } | samtools view -c -f 1 -@$task.cpus ) -gt 0 ]; then echo false > is_singleend.txt else echo true > is_singleend.txt fi cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ |
17 18 19 20 21 22 23 24 25 26 | """ check_samplesheet.py \\ $samplesheet \\ samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml "${task.process}": python: \$(python --version | sed 's/Python //g') END_VERSIONS """ |
26 27 28 29 30 31 32 33 34 | """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz fastqc $args --threads $task.cpus ${prefix}.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) END_VERSIONS """ |
36 37 38 39 40 41 42 43 44 45 | """ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) END_VERSIONS """ |
50 51 52 53 54 55 56 57 58 | """ touch ${prefix}.html touch ${prefix}.zip cat <<-END_VERSIONS > versions.yml "${task.process}": fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) END_VERSIONS """ |
23 24 25 26 27 28 29 30 31 32 33 | """ gunzip \\ -f \\ $args \\ $archive cat <<-END_VERSIONS > versions.yml "${task.process}": gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') END_VERSIONS """ |
37 38 39 40 41 42 43 | """ touch $gunzip cat <<-END_VERSIONS > versions.yml "${task.process}": gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') END_VERSIONS """ |
28 29 30 31 32 33 34 35 36 37 38 39 40 | """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ . cat <<-END_VERSIONS > versions.yml "${task.process}": multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) END_VERSIONS """ |
43 44 45 46 47 48 49 50 51 52 | """ touch multiqc_data touch multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml "${task.process}": multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) END_VERSIONS """ |
25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | """ # Create a config for OptiType on a per sample basis with task.ext.args2 #Doing it old school now echo "[mapping]" > config.ini echo "razers3=razers3" >> config.ini echo "threads=$task.cpus" >> config.ini echo "[ilp]" >> config.ini echo "$args2" >> config.ini echo "threads=1" >> config.ini echo "[behavior]" >> config.ini echo "deletebam=true" >> config.ini echo "unpaired_weight=0" >> config.ini echo "use_discordant=false" >> config.ini # Run the actual OptiType typing with args OptiTypePipeline.py -i ${bam} -c config.ini --${meta.seq_type} $args --prefix $prefix --outdir $prefix #Couldn't find a nicer way of doing this cat <<-END_VERSIONS > versions.yml "${task.process}": optitype: \$(cat \$(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g") END_VERSIONS """ |
26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 | """ samtools collate \\ $args \\ --threads $task.cpus \\ -O \\ $input \\ . | samtools fastq \\ $args2 \\ --threads $task.cpus \\ -1 ${prefix}_1.fq.gz \\ -2 ${prefix}_2.fq.gz \\ -0 ${prefix}_other.fq.gz \\ -s ${prefix}_singleton.fq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ |
38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 | """ samtools \\ view \\ --threads ${task.cpus-1} \\ ${reference} \\ ${readnames} \\ $args \\ -o ${prefix}.${file_type} \\ $input \\ $args2 cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ |
57 58 59 60 61 62 63 64 65 | """ touch ${prefix}.bam touch ${prefix}.cram cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ |
23 24 25 26 27 28 29 30 31 32 | """ yara_indexer \\ $fasta \\ -o ${fasta} cat <<-END_VERSIONS > versions.yml "${task.process}": yara: \$(echo \$(yara_indexer --version 2>&1) | sed 's/^.*yara_indexer version: //; s/ .*\$//') END_VERSIONS """ |
27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | """ yara_mapper \\ $args \\ -t $task.cpus \\ -f bam \\ ${index_prefix} \\ $reads | samtools view -@ $task.cpus -hb -F4 | samtools sort -@ $task.cpus > ${prefix}.mapped.bam samtools index -@ $task.cpus ${prefix}.mapped.bam cat <<-END_VERSIONS > versions.yml "${task.process}": yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ |
44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | """ yara_mapper \\ $args \\ -t $task.cpus \\ -f bam \\ ${index_prefix} \\ ${reads[0]} \\ ${reads[1]} > output.bam samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_1.mapped.bam samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_2.mapped.bam samtools index -@ $task.cpus ${prefix}_1.mapped.bam samtools index -@ $task.cpus ${prefix}_2.mapped.bam cat <<-END_VERSIONS > versions.yml "${task.process}": yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ |
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