WDL wrapper for the pgsc_calc workflow
The first step of the workflow formats the input genomes in PLINK2 format.
The next step runs the pgsc_calc nextflow workflow inside a docker container.
| input | description |
|---|---|
| vcf | Array of VCF files |
| chromosome | Array of chromosome strings (1-22, X, Y) corresponding to vcf. If there is one VCF file with multiple chromosomes, this input should be an empty string ([""]) |
| target_build | "GRCh38" (default) or "GRCh37" |
| pgs_id | PGS catalog IDs to calculate (e.g. ["PGS001229", "PGS000802"]) |
| run_ancestry | true to perform ancestry adjustment using a reference panel, false to skip this step |
| ref_panel | Google bucket path of a reference panel file (e.g. "gs://fc-a8511200-791a-4375-bccf-fbe41ac3f9f6/pgsc_HGDP+1kGP_v1.tar.zst"); used if run_ancestry is true |
| sampleset_name | Name of the sampleset; used to construct output file names (default "cohort") |
| arguments | Additional arguments to pass to psgc_calc |
Output files from pgsc_calc are described here.