Record platform of sequencer in database rather than hard-coding as "Illumina"

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#507 opened on May 9, 2019 0 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 5/5
Estimated time: Over a week
Newbie friendliness: 30/100

Issue type: Feature
Clarity: Mostly clear
Activity status: Stale
Tech stack: python
Domain: backend, databases

Research direction

Start by reviewing how sequencer records and prep sheets are represented, then read related issues #266 and #430 before proposing the database change. Done means the platform is stored per sequencer and the prep sheet uses that value instead of hard-coded "Illumina", while accounting for the related lane-count and vocabulary work.

Written by the indexing model from the issue text.

Description

enhancement scope:medium

The platform of the particular sequencer used for a run is output in the prep sheet. Currently, that value is hard-coded as Illumina, but since the lab also uses other kinds of sequencers (Nanopore, PacBio, etc), this is not adequate. This info needs to be recorded per-sequencer somewhere--preferably the database.

Note that this should almost certainly be done at the same time as #266 Move definition of number of lanes per sequencer into database from SequencingProcess and #430 Instrument_model is a standard vocabulary in EBI .

Dominant language: Python
Stars: 2
Forks: 15
PR merge metrics: No merged PRs in 30d

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