/t1k_pipeline

Primary LanguageNextflow

T1K Nextflow pipeline

Reference files

Create reference files for HLA and KIR alleles along with gene coordinate file for BAM inputs.

git clone https://github.com/mourisl/T1K.git
cd T1K/

wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz | \
  gzip -cd > gencode.v41.annotation.gtf
perl t1k-build.pl -o kiridx --download IPD-KIR -g gencode.v41.annotation.gtf
perl t1k-build.pl -o hlaidx --download IPD-IMGT/HLA -g gencode.v41.annotation.gtf

Example run

Uses reference files generated above

nextflow run main.nf -params-file params.json