This directory contains information and metadata about references used in the scpca-nf workflow.

If you are a Data Lab member looking for more information about maintaining or adding additional references, please refer to internal-instructions.md.

These files are used by build-index.nf to generate transcriptome reference files.

• ref-metadata.tsv provides transcriptome reference metadata for organisms considered in the scpca-nf workflow. This file is used by build-infex.nf to generate transcriptome references.
• scpca-refs.json contains the relative paths of the default reference files for mapping and quantification provided by the Data Lab, and is used for the scpca-nf workflow configuration parameter ref_json. The base location for the reference files is given by the configuration parameter ref_rootdir. This file is produced by scripts/create-reference-json.R.

These files are used by build-celltype-ref.nf to generate cell type annotation reference files.

• celltype-reference-metadata.tsv provides information about the name, source, and contents of cell type annotation references established by the Data Lab for use with SingleR and CellAssign.
• PanglaoDB_markers_<date>.tsv is the full set of marker genes exported from PanglaoDB, versioned at the given date.