workflow_notes.md

Workflow Notes

These R Markdown files are kept on the workflows branch as GitHub-only workflow templates. They are not package vignettes.

Best starting points

• hcocena_main.Rmd: closest to the current object-passing workflow
• hcocena_satellite.Rmd: useful for optional analysis ideas
• hcocena_main_seq_only.Rmd: useful if a single-modality example is needed

Other files in git history

The Git history still contains older STAR protocol and earlier workflow variants, but they are intentionally not part of this GitHub workflow set.

Workflow direction

When updating these workflow files, prefer:

• explicit object-passing with hc <- ...
• current exported package functions
• current hc@satellite / satellite_outputs storage conventions
• examples that match the current S4/container workflow

Wrapper status

The restored workflows now use current hc_* wrappers consistently, including for helpers that previously required manual object bridging:

• hc_import_clusters()
• hc_user_specific_cluster_profiling()
• hc_col_anno_numerical()
• hc_meta_correlation_num()
• hc_cut_hclust()

Practical recommendation

If these documents are updated further, keep them on this GitHub-only workflows branch or move them into a separate companion repository such as hcocena-workflows. Avoid adding them back to the Bioconductor submission branch unless they are intentionally converted into maintained package vignettes.