Update internal-instructions.md

Co-authored-by: Ally Hawkins <[email protected]>

internal-instructions.md

@@ -43,7 +43,8 @@ There are several flags and/or parameters which you may additionally wish to spe
   + `-resume`: Resume workflow from most recent checkpoint
   + `-with-tower`: Use `Nextflow Tower` to monitor workflow (requires separate [Nextflow Tower registration](https://tower.nf/))
 + Workflow parameters:
-  + `--run_ids list, of, ids`: A custom list of ids (run, library, sample or project) for this run.
+  + `--run_ids list, of, ids`: A custom comma-separated list of ids (run, library, or sample) for this run.
+  + `--project list,of, project_ids`: A custom comma-separated list of project ids for this run 
   [The default](config/profile_ccdl.config) run ids are `"SCPCR000001,SCPCS000101"`.
   + `--repeat_mapping`: Use this flag to repeat mapping, even if results already exist.
     + By default, the workflow checks whether each library has existing `alevin-fry` or `salmon` mapping results, and skips mapping for libraries with existing results.