You can use cbTool metaCat to merge the meta.tsv files from different pipelines (cbScanpy, cbSeurat, etc) into a single one, like this:
cbTool metaCat myMeta.tsv seuratOut/meta.tsv scanpyOut/meta.tsv ./newMeta.tsv --fixDot
The option –fixDot will work around R’s strange habit of replacing special characters in the cell identifiers with “.”. Directories created with ExportToCellbrowser() from R should not have this problem, but others may.
You can start with one of the auto-generated cellbrowser.conf files or start from a fresh one with cbBuild –init. In this cellbrowser.conf, add all the coordinates files from all your pipelines.