In https://github.com/AlexsLemonade/scpca-nf/pull/453, we are adding another term to scpca-meta.json files that are present in the checkpoints folder. Before we re-process samples to add in AnnData or cell typing, we will want to make sure the contents of scpca-meta.json for already processed samples match what's to be expected.
We already have a script, add-refs-scpca-meta.py, that reads in existing scpca-meta.json files and outpus a modified file with any new additions (currently just ref_mito and ref_fasta_index. We should be able to add a check for the presence of the assay_ontology_term_id and add it if it's not present.
allyhawkins
commented
10 months ago
In https://github.com/AlexsLemonade/scpca-nf/pull/453, we are adding another term to
scpca-meta.jsonfiles that are present in thecheckpointsfolder. Before we re-process samples to add in AnnData or cell typing, we will want to make sure the contents ofscpca-meta.jsonfor already processed samples match what's to be expected.We already have a script,
add-refs-scpca-meta.py, that reads in existingscpca-meta.jsonfiles and outpus a modified file with any new additions (currently justref_mitoandref_fasta_index. We should be able to add a check for the presence of theassay_ontology_term_idand add it if it's not present.