This pipeline is configured to run on the IKMB MedCluster and DX Cluster.
To run this pipeline, use the following syntax:
nextflow run ikmb/hla --samples Samples.csv --tools 'xhla,hisat,optitype' -profile standard
This pipeline accepts input data in CSV format. The format should look as follows:
patient;sample;library;rgid;R1;R2
PatientA;Sample1;22Oct21_S3;C41232CXX.1.22Oct21_S3;/path/to/R1.fastq.gz;/path/to/R2.fastq.gz
This is the preferred input option as it provide more control over the naming and grouping of the data.
A simple ruby script is included with this pipeline to produce this file from a folder of FastQ files. However, please check the output to make sure that it correctly recognized the file names etc.
ruby samplesheet_from_folder.rb -f /path/to/data > Samples.csv
This can then be used as input like so:
nextflow run ikmb/hla --samples Samples.csv
Input folder containing paired-end fastQ files.
nextflow run ikmb/hla --folder '/path/to/folder'
A regular expression pointing to a set of paired-end fastQ files.
nextflow run ikmb/hla --reads '/path/to/*_R{1,2}_001.fastq.gz'
This pipeline supports several competing tool chains for HLA calling. Specify them with this option as a comma-separated list.
nextflow run ikmb/hla --samples Samples.csv --tools 'hisat,xhla,optitype'
Supported tools:
- xHLA (xhla)
- Hisat-genotype (hisat) Slow on anything other than targetted sequencing!
- Optitype (optitype)
- HLAscan (hlascan)
- HLA-HD (hlahd)
Please note: HLA-HD cannot be containerized due to licensing restrictions. It can thus only be made available as a local software module (MedCluster only!).
Provide a descriptive name for this analysis run.
Desired precision of the reported HLA calls. Default is '2' (i.e. HLA-A*01:01).
This pipeline has a built-in test. To run it, simply provide the appropriate profile and test config. On MedCluster, this would look like so:
nextflow run ikmb/hla -profile standard,test