simulation failing with upcoming release

[jashapiro]

When preparing for the 2024-11-25 data release, the workflow for simulating data failed. I suspect this had to do with genes that now have all zero values, but I will have to investigate and update the workflow to handle this error.

The error message is listed below.

Command executed:

  mkdir SCPCS000257
  simulate-sce.R       --sample_dir input       --metadata_file single_cell_metadata.tsv       --output_dir SCPCS000257

Command exit status:
  1

Command output:
  Error in computing default starting values.

Command error:
  Error in `map()`:
  ℹ In index: 3.
  Caused by error in `manageparam()`:
  ! Error in if (any(x < 0)) stop("values must be positive to fit an gamma  distribution") : 
    missing value where TRUE/FALSE needed
  Backtrace:
       ▆
    1. ├─purrr::walk(...)
    2. │ └─purrr::map(.x, .f, ..., .progress = .progress)
    3. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
    4. │     ├─purrr:::with_indexed_errors(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     ├─purrr:::call_with_cleanup(...)
    7. │     └─global .f(.x[[i]], ...)
    8. │       └─global simulate_sce(real_sce, opts$ncells, replacement_metadata, processed = is_processed)
    9. │         ├─splatter::simpleEstimate(as.matrix(counts(sce_sim)))
   10. │         └─splatter:::simpleEstimate.matrix(as.matrix(counts(sce_sim))) at splatter/R/simple-estimate.R:28:5
   11. │           └─fitdistrplus::fitdist(means, "gamma", method = "mme") at splatter/R/simple-estimate.R:53:5
   12. │             └─fitdistrplus:::manageparam(...)
   13. │               └─base::stop(trystart)
   14. └─base::.handleSimpleError(...)
   15.   └─purrr (local) h(simpleError(msg, call))
   16.     └─cli::cli_abort(...)
   17.       └─rlang::abort(...)
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[jashapiro]

closed by #898