diff --git a/internal-instructions.md b/internal-instructions.md index 55cdd36a..4a4d146f 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -47,12 +47,12 @@ There are several flags and/or parameters which you may additionally wish to spe [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. - + Using this flag will override that default behavior and repeat mapping even if the given library's results exist. + Using this flag will override that default behavior and repeat mapping even if the given library's results exist. + + For more implementation details, please refer to the [external instructions](external-instructions.md#repeating-mapping-steps). + `--perform_celltyping`: Use this flag to perform cell type annotation, which is turned off by default. + `--repeat_celltyping`: Use this flag to repeat cell type annotation, even if results already exist. - For more information, please refer to the [external instructions](external-instructions.md#repeating-mapping-steps). + By default, the workflow checks whether each library has existing cell type annotation results for `SingleR` and/or `CellAssign` (depending on references for that library). - + Using this flag will override that default behavior and repeat cell type annotation even if the given library's results exist. + Using this flag will override that default behavior and repeat cell type annotation even if the given library's results exist. + This flag is _only considered_ if `--perform_celltyping` is also used. Please refer to [`nextflow.config`](nextflow.config) and [other configuration files](config/) for other parameters which can be modified.