SCRIdb.upload_stats.stats

SCRIdb.upload_stats.stats(s3paths, sample_ids=None, sample_names=None, results_folder=None, cellranger=False, hash_tags=False)

The core method which collects stats from successfully processed scRNAseq samples.

Parameters

  • s3paths – Path/s to yaml or json file/s, or a single string to parent directory of project with samples listed in sample_names. For HASHTAGS: set this parameter to labels.json and hash_tags to True.

  • sample_ids (Optional[list]) – Sample ids from database for samples in project parent directory.

  • sample_names (Optional[list]) – Sample names in project parent directory.

  • results_folder (Union[str, list, None]) – Path to parent directory where outputs from processing pipeline are stored.

  • hash_tags (bool) – Hash tags stats format.

  • cellranger (bool) – Cell Ranger stats format.

Return type

tuple

Returns

tuple of stats and list of sample IDs