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Add "sequencingCenter" and "platform" to file metadata to generalize and make migrations. #88

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allanbolipata opened this issue Jan 13, 2020 · 1 comment
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@allanbolipata
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https://github.com/mskcc/beagle/blob/develop/runner/operator/roslin_operator/bin/make_sample.py#L80-L81

At the moment we've only retrieved data from LIMS and have been hardcoding CN and PL to the values "MSKCC" and "Illumina", respectively, in the operators. Since we are going to begin importing data from non-MSKCC sources, we need to generalize those fields.

We must add "sequencingCenter" (which maps to CN) and "platform" (maps to PL) to the metadata. IGOLIMS data will always have "sequencingCenter" set to "MSKCC" and "platform" set to "Illumina", so we may need to make a migration to update existing files.

@allanbolipata
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I think this has been added

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