Seq Lab: Fix bug where Index data is not being created / added in Manual Library Pooling

[tim-snyder-wustl]

Index fields are hidden in the 'SEQ Lab: Create Illumina Library Pools' but are needed in the Illumina Sequencing Setup protocols, so not sure what's going on here. Will need to reach out to @mcordes-gtac for clarification.

Should these field not be hidden? Should they pull in index data from parent entities? If so, how?

[tim-snyder-wustl]

@mcordes-gtac Can you provide some clarification here?

Do the new pools need to pull in index data from their parents here? If so, how? This is a 'fan-in' protocol, so which of the parent entities should the new pools inherit this data from?

[mcordes-gtac]

Yes, pools should pull in the index data from their parents, and I think this is related to dilutions maintaining metadata from libraries? Pools can contain Libraries, Dilutions and/or other Pools. Within those, we should be able to track back to the index metadata from the original library. This information will obviously be critical for run sheet creation as the run sheet will contain library metadata for everything within the pool being sequence. I hope that all makes sense??

On 6/19/23, 11:08 AM, "Tim Snyder" @.***> wrote:

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@mcordes-gtachttps://github.com/mcordes-gtac Can you provide some clarification here?

Do the new pools need to pull in index data from their parents here? If so, how? This is a 'fan-in' protocol, so which of the parent entities should the new pools inherit this data from?

— Reply to this email directly, view it on GitHubhttps://github.com/GTAC-MGI/GTAC-ESP-LIMS/issues/259#issuecomment-1597440917, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZGEF3VDCG5YCGJIYM3TLNDXMB2OFANCNFSM6AAAAAAY2DM7DE. You are receiving this because you were mentioned.Message ID: @.***>

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[tim-snyder-wustl]

@mcordes-gtac

Where I am confused is this - a pool has the following properties:

        - Index Name:
            rule: text
        - i5 Index Name:
            rule: text
        - i7 Index Sequence:
            rule: text
        - i5 Index Sequence:
            rule: text

but if a pool is a collection / combination of other pools, libraries, or dilutions, how would a pool have one i7 and one i5 field? Are these fields even applicable to Pools?

If so, how does this work:

If I'm building a pool from 3 different libraries, those libraries will all have unique indexes, correct? From which library will the pool inherit these values from? Or should it be a list of values in these pool fields containing all the values from the parents?

[mcordes-gtac]

I see what you are saying. This field would not be applicable to a pool unless, as you suggest, listing all of the values from the parent. I think we can easily see all of the parent values by selecting the pool entity or hovering over it, so there wouldn’t be much use in providing this list as a value of the pool.

On 6/19/23, 11:26 AM, "Tim Snyder" @.***> wrote:

• External Email - Caution *

@mcordes-gtachttps://github.com/mcordes-gtac

Where I am confused is this - a pool has the following properties:

    - Index Name:

        rule: text

    - i5 Index Name:

        rule: text

    - i7 Index Sequence:

        rule: text

    - i5 Index Sequence:

        rule: text

but if a pool is a collection / combination of other pools, libraries, or dilutions, how would a pool have one i7 and one i5 field? Are these fields even applicable to Pools?

If so, how does this work:

If I'm building a pool from 3 different libraries, those libraries will all have unique indexes, correct? From which library will the pool inherit these values from? Or should it be a list of values in these pool fields containing all the values from the parents?

— Reply to this email directly, view it on GitHubhttps://github.com/GTAC-MGI/GTAC-ESP-LIMS/issues/259#issuecomment-1597461495, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZGEF3WEI4C4LAJE4V4O47LXMB4TTANCNFSM6AAAAAAY2DM7DE. You are receiving this because you were mentioned.Message ID: @.***>

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[tim-snyder-wustl]

@mcordes-gtac Ok, I'll remove these values from the Pool entity.