Add wrapper function for running internal references

[sjspielman]

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Part of #1080

Describe the goals of the changes to the analysis module.

In #1126, a function was added to the infercnv-consensus-cell-type module to prepare internal normal references, i.e. a normal reference that uses cells only from the given library. The function was implemented to be specific to ewings data from SCPCP000015.

In the future if we want to run other projects with internal references, we will need to update this code to include project-specific functions and an overall wrapper function to call from the inferCNV script.

---

Here are the relevant sections of code with TODOs:

OpenScPCA-analysis/analyses/infercnv-consensus-cell-type/scripts/01_run-infercnv.R

Lines 240 to 250 in e540d82

	# TODO: Currently this function is specific to SCPCP000015
	# In the future this may need to be updated as a wrapper function to call individual project functions
	prepare_internal_reference_annotations(
	opts$reference_celltype_group, # cell type groups to include in reference
	opts$reference_celltype_tsv, # map between reference groups and consensus cell types
	opts$celltype_tsv, # consensus cell type annotations
	opts$annotation_file, # annotations file to export
	library_id, # SCE of interest library id
	opts$testing # logical if we're running with test data
	)
	}

OpenScPCA-analysis/analyses/infercnv-consensus-cell-type/scripts/utils.R

Lines 23 to 24 in e540d82

	# TODO: currently the code assumes this contains columns `ewing_annotation` and `consensus_annotation`
	celltype_df <- readr::read_tsv(celltype_tsv)

OpenScPCA-analysis/analyses/infercnv-consensus-cell-type/scripts/utils.R

Lines 38 to 47 in e540d82

	annotation_df <- celltype_df |>
	# add indicator for cell types intended for the reference
	dplyr::mutate(annotation = ifelse(
	# TODO: If we want to use non-ewings projects in this script, this will NOT WORK.
	# We may need project-specific helper functions for this spot in the code if/when the time comes.
	consensus_annotation %in% reference_celltypes & !stringr::str_detect(ewing_annotation, "tumor"),
	"reference",
	"unknown"
	))
	}

What will your pull request contain?

Re-organized functions

Will you require additional software beyond what is already in the analysis module?

No, only renv

Will you require different computational resources beyond what the analysis module already uses?

No

If known, when do you expect to file the pull request?

This PR will be filed as needed.