github.com/UW-GAC/pgsc_calc_wdl/pgsc_calc_prepare_genomes

# pgsc_calc_wdl WDL wrapper for the [pgsc_calc](https://pgsc-calc.readthedocs.io/en/latest/) workflow The first step of the workflow [formats the input genomes](https://pgsc-calc.readthedocs.io/en/latest/how-to/prepare.html) in PLINK2 format. The next step [runs the pgsc_calc nextflow workflow](https://pgsc-calc.readthedocs.io/en/latest/getting-started.html) inside a docker container. input | description --- | --- vcf | Array of VCF files. If provided, will be converted to pgen/pvar/psam. If not provided, use pgen/pvar/psam inpute instead pgen | Array of pgen files pvar | Array of pvar files psam | Array of psam files chromosome | Array of chromosome strings (1-22, X, Y) corresponding to `vcf` or `pgen/pvar/psam`. If there is one 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](https://pgsc-calc.readthedocs.io/en/latest/explanation/geneticancestry.html) 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](https://pgsc-calc.readthedocs.io/en/latest/reference/params.html#param-ref) to pass to psgc_calc Output files from pgsc_calc are described [here](https://pgsc-calc.readthedocs.io/en/latest/explanation/output.html#interpret).