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icgc-dcc / egasub

EGASub - ICGC EGA Submission CLI
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Allow additional information be provided as tag-value pairs via 'attributes' #67

Open lheisler opened 7 years ago

lheisler commented 7 years ago

EGA allows additional information to be provided when registering objects, outside of what is indicated in the yaml templates for analysis and run objects and explained in the SOP.

for example, I've added the following lines to my analysis.yaml, to provide some detail on how the analysis was done

analysis_attributes: analysis_attribute: tag: aligner value: bwa analysis_attribute: tag: aligner_ver value: 0.6.2 analysis_attribute: tag: mark_duplicates value: picard analysis_attribute: tag: mark_duplicates_ver value: 1.90

This was info i had provided previously when using XML through the rest server

It would be good to indicate that this is possile in the SOP.

junjun-zhang commented 7 years ago

Yes, EGA metadata XML (SRA XML in general) allows submitter to add custom key-value pair. We plan to support that by adding sample.attributes, experiment.attributes and analysis.attributes to the metadata YAML. It will be necessary to preserve some keys, eg, icgc_sample_id which we use to add ICGC Sample ID as custom key-value attribute for sample object.