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Remove title from cell metadata and move schema to object metadata #473

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merged 3 commits into from
Oct 9, 2023
Merged

Remove title from cell metadata and move schema to object metadata #473

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ca866d7
remove title and move schema
allyhawkins Sep 28, 2023
efff12a
Merge remote-tracking branch 'origin/development' into allyhawkins/sc…
allyhawkins Oct 9, 2023
8ca63c3
move schema version to first step
allyhawkins Oct 9, 2023
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10 changes: 5 additions & 5 deletions bin/sce_to_anndata.R
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,10 @@ if (!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))) {
# sure that the sce that is getting converted to AnnData is compliant with CZI
# CZI 3.0.0 requirements: https://github.com/chanzuckerberg/single-cell-curation/blob/b641130fe53b8163e50c39af09ee3fcaa14c5ea7/schema/3.0.0/schema.md
format_czi <- function(sce) {

# add schema version
metadata(sce)$schema_version = "3.0.0"

# add library_id as an sce colData column
# need this column to join in the sample metadata with the colData
sce$library_id <- metadata(sce)$library_id
Expand All @@ -71,12 +75,8 @@ format_czi <- function(sce) {
# create columns for assay and suspension ontology terms
assay_ontology_term_id = metadata(sce)$assay_ontology_term_id,
suspension_type = metadata(sce)$seq_unit,
# move project id to title slot in metadata list
title = metadata(sce)$project_id,
# add is_primary_data column; only needed for anndata objects
is_primary_data = FALSE,
# add schema version
schema_version = "3.0.0"
is_primary_data = FALSE
)

# add colData back to sce object
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