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Add tx2gene module (formerly local to rnaseq)#4854

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pinin4fjords merged 10 commits intomasterfrom
tximport
Feb 6, 2024
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Add tx2gene module (formerly local to rnaseq)#4854
pinin4fjords merged 10 commits intomasterfrom
tximport

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@pinin4fjords pinin4fjords commented Feb 5, 2024

nf-core/test-datasets#1083 should be merged first, and appropriate adjustments made here.

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  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
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@pinin4fjords pinin4fjords requested review from a team and kpadm February 5, 2024 22:04
@pinin4fjords pinin4fjords marked this pull request as draft February 5, 2024 22:04
@pinin4fjords pinin4fjords marked this pull request as ready for review February 5, 2024 22:29
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Want me to wait for nf-core/test-datasets#1083 before reviewing?

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Want me to wait for nf-core/test-datasets#1083 before reviewing?

No, go right ahead. I'll update the test data reference, but everything else should be good

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I don't like how the error is handled, but since this is a port I think we should go with it and add an additional test in future.

pinin4fjords and others added 2 commits February 6, 2024 13:33
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
@pinin4fjords pinin4fjords added this pull request to the merge queue Feb 6, 2024
Merged via the queue into master with commit c884823 Feb 6, 2024
@pinin4fjords pinin4fjords deleted the tximport branch February 6, 2024 13:59
adamrtalbot added a commit to adamrtalbot/modules that referenced this pull request Feb 6, 2024
* Add test data link

* Add tx2gene

* Fix linting, update snapshots

* path -> directory

* Correct conda setup

* Correct conda setup

* Update test data reference

* Apply minor suggestions from code review

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Error out at point of failure in determining transcript attribute

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
jch-13 pushed a commit to jch-13/modules that referenced this pull request Mar 19, 2024
* Add test data link

* Add tx2gene

* Fix linting, update snapshots

* path -> directory

* Correct conda setup

* Correct conda setup

* Update test data reference

* Apply minor suggestions from code review

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Error out at point of failure in determining transcript attribute

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
* Add test data link

* Add tx2gene

* Fix linting, update snapshots

* path -> directory

* Correct conda setup

* Correct conda setup

* Update test data reference

* Apply minor suggestions from code review

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Error out at point of failure in determining transcript attribute

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
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2 participants