Ensure pgsc_calc works with FID & IID columns

[smlmbrt]

I switched to singularity with your modification and was able to get past the sorting issue. After rerunning, I was receiving this error with FRAPOSA:

Jan-29 13:08:17.508 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT (PGSPOPsFetal)'

Caused by:
  Process `PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT (PGSPOPsFetal)` terminated with an error exit status (1)

Command executed:

  fraposa GRCh38_reference_ALL_extracted         --method oadp         --dim_ref 10         --stu_filepref GRCh38_PGSPOPsFetal_ALL_oriented         --stu_filt_iid <(cut -f1 splitfamaa)         --out GRCh38_PGSPOPsFetal_ALL_oriented_splitfamaa
  
  cat <<-END_VERSIONS > versions.yml
  FRAPOSA_PROJECT:
      fraposa: TODO
  END_VERSIONS

Command exit status:
  1

Command output:
  FRAPOSA started.
  Reference data: GRCh38_reference_ALL_extracted
  Study data: GRCh38_PGSPOPsFetal_ALL_oriented
  Output prefix: GRCh38_PGSPOPsFetal_ALL_oriented_splitfamaa
  Method: oadp
  Reference dimension: 10
  Study dimension: 20
  Online SVD dimension: 40
  2024-01-29 13:08:12.774600
  Attemping to load saved reference PCA result...
  Warning: If you have changed the parameter settings, please delete GRCh38_reference_ALL_extracted_*.dat and GRCh38_reference_ALL_extracted.pcs then rerun FRAPOSA.
  Reference PCA result successfully loaded.
  2024-01-29 13:08:13.534661
  Loading study data...
  ERROR: 0 / 3486 ids in filter list match the study dataset

To fix the error, I edited the fraposa_project.nf module to modify the ID file to reflect both the FID and IID columns for my sample:
cut -f1,f2 splitfamaa

After this fix, I was receiving an error related to this issue: #235. I edited the configuration file to include my appropriate paths, and I have the ancestry-adjusted score files now.

Originally posted by @jasamack in #234 (reply in thread)

[nebfield]

Now available in v2.0.0-beta.2 🥳