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Add ribotricer/detectorfs #5112

Merged
merged 24 commits into from
Mar 14, 2024
Merged

Add ribotricer/detectorfs #5112

merged 24 commits into from
Mar 14, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Mar 13, 2024 •
edited

Adds the new Ribotricer 'detect orfs' module for ORF prediction from Riboseq data.

PR checklist

  • 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
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@pinin4fjords pinin4fjords requested a review from a team as a code owner March 13, 2024 12:04
@pinin4fjords pinin4fjords requested review from vagkaratzas and removed request for a team March 13, 2024 12:04
@pinin4fjords pinin4fjords marked this pull request as draft March 13, 2024 12:04
@pinin4fjords pinin4fjords marked this pull request as ready for review March 13, 2024 18:52
@pinin4fjords pinin4fjords changed the title [WIP] Add ribotricer/detectorfs Add ribotricer/detectorfs Mar 13, 2024
adamrtalbot
adamrtalbot reviewed Mar 14, 2024
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pinin4fjords and others added 2 commits March 14, 2024 09:52
@pinin4fjords @adamrtalbot
Apply suggestions from code review
649e5c3 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
@pinin4fjords @adamrtalbot
Update modules/nf-core/ribotricer/detectorfs/main.nf
c068c11 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
pinin4fjords and others added 2 commits March 14, 2024 09:59
@pinin4fjords
default -> filtered
2f7fbea
@pinin4fjords @adamrtalbot
Fix typo
94d3e4a 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
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Thanks @adamrtalbot !

@pinin4fjords pinin4fjords added this pull request to the merge queue Mar 14, 2024
Merged via the queue into master with commit eef39ec Mar 14, 2024
11 checks passed
@pinin4fjords pinin4fjords deleted the ribotricer/detectorfs branch March 14, 2024 15:29
jch-13 pushed a commit to jch-13/modules that referenced this pull request Mar 19, 2024
@pinin4fjords @adamrtalbot @jch-13
Add ribotricer/detectorfs (nf-core#5112)
0f7804c 
* Add ribotricer/detectorfs

* Don't snapshot PDFs

* Complete meta.yml

* Add test for --report_all, address linting things

* Fix tag, add stub tests

* Appease eclint

* Add missing configs

* Make ribotricer versioning more reliable in conda

* Conda differs in floating point precision

* Update nf-test.config

* Apply suggestions from code review

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

* Update modules/nf-core/ribotricer/detectorfs/main.nf

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

* Clarify language around strandedness inference

* default -> filtered

* Fix typo

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

* ifelse -> switch to appease @adamrtalbot

* variables need to be defined outsite switch

* unstranded is broken

* More tests

* Appease eclint

* Fix configs

---------

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
@pinin4fjords @adamrtalbot @jennylsmith
Add ribotricer/detectorfs (nf-core#5112)
1eff332 
* Add ribotricer/detectorfs

* Don't snapshot PDFs

* Complete meta.yml

* Add test for --report_all, address linting things

* Fix tag, add stub tests

* Appease eclint

* Add missing configs

* Make ribotricer versioning more reliable in conda

* Conda differs in floating point precision

* Update nf-test.config

* Apply suggestions from code review

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

* Update modules/nf-core/ribotricer/detectorfs/main.nf

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

* Clarify language around strandedness inference

* default -> filtered

* Fix typo

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

* ifelse -> switch to appease @adamrtalbot

* variables need to be defined outsite switch

* unstranded is broken

* More tests

* Appease eclint

* Fix configs

---------

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

@vagkaratzas vagkaratzas Awaiting requested review from vagkaratzas vagkaratzas is a code owner automatically assigned from nf-core/nf-test

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