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Add custom/tabulartogseacls #2606

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merged 19 commits into from
Dec 8, 2022

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pinin4fjords
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@pinin4fjords pinin4fjords commented Dec 2, 2022

Creates a module for building .cls files of the type consumed by GSEA from sample metadata tables in either CSV or TSV format, with output like:

6 2 1
#mCherry hND6
mCherry mCherry mCherry hND6 hND6 hND6

This is essentially a description of the classes in a column of a sample sheet so that differential gene set analysis can be undertaken.

The necessary column(variable) is currently taken from the meta (which will gel with efforts in the differentialabundance workflow), but it can be passed outside the meta if that would be preferable.

The module does not currently consume the matrix itself, but the samples metadata file which assumed to be in synch with the appropriate matrices (which we separately ensure in the differential abundance workflow).

PR checklist

  • This comment contains a description of changes (with reason).
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@nvnieuwk thanks for the review- think we should be good here too now :-)

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Looks good here too! 🚀

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@jfy133 jfy133 left a comment

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Docs people! Docs!

modules/nf-core/custom/tabulartogseacls/main.nf Outdated Show resolved Hide resolved
modules/nf-core/custom/tabulartogseacls/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/custom/tabulartogseacls/meta.yml Outdated Show resolved Hide resolved
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pinin4fjords commented Dec 7, 2022

Docs people! Docs!

@jfy133 Ok, no cookies for me. But docs fixed! Thanks for the review.

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Almost there, but I would still allow complete flexibility by not requiring a specific meta element

(You can blame @FriederikeHanssen for this, I used to be more flexible with metas but she's convinced me now ;) )

modules/nf-core/custom/tabulartogseacls/meta.yml Outdated Show resolved Hide resolved
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Jonathan Manning and others added 3 commits December 7, 2022 22:15
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Appreciate the review @jfy133

@pinin4fjords pinin4fjords merged commit 3dcd7a7 into nf-core:master Dec 8, 2022
@pinin4fjords pinin4fjords deleted the custom/tsvtogseacls branch December 8, 2022 17:42
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3 participants