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add agat/spaddintrons #4650

Merged
merged 19 commits into from
Dec 27, 2023
Merged

add agat/spaddintrons #4650

merged 19 commits into from
Dec 27, 2023

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anoronh4
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@anoronh4 anoronh4 commented Dec 23, 2023 •
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PR checklist

Closes #4649

  • 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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@anoronh4 anoronh4 requested a review from a team as a code owner December 23, 2023 01:20
@anoronh4 anoronh4 self-assigned this Dec 23, 2023
sateeshperi
sateeshperi reviewed Dec 23, 2023
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anoronh4 and others added 7 commits December 27, 2023 10:39
@anoronh4 @sateeshperi
Update modules/nf-core/agat/spaddintrons/meta.yml
732f1c8 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@anoronh4 @sateeshperi
Update modules/nf-core/agat/spaddintrons/main.nf
511703d 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@anoronh4 @sateeshperi
Update modules/nf-core/agat/spaddintrons/environment.yml
77bbec5 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@anoronh4 @sateeshperi
Update modules/nf-core/agat/spaddintrons/environment.yml
b88e17d 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@anoronh4 @sateeshperi
Update modules/nf-core/agat/spaddintrons/meta.yml
540ddc6 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@anoronh4 @sateeshperi
Update modules/nf-core/agat/spaddintrons/meta.yml
9883b8a 
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
@anoronh4
Merge branch 'master' into agat/addspintrons
9f6f2ff
@sateeshperi sateeshperi added this pull request to the merge queue Dec 27, 2023
Merged via the queue into master with commit 6898156 Dec 27, 2023
11 checks passed
@sateeshperi sateeshperi deleted the agat/addspintrons branch December 27, 2023 19:30
lrauschning pushed a commit to lrauschning/modules that referenced this pull request Jan 17, 2024
@anoronh4 @sateeshperi @lrauschning
add agat/spaddintrons (nf-core#4650)
efd183e 
* add agat/spaddintrons

* fix linting error with prettier

* fix modules linting error in meta.yml

* Update modules/nf-core/agat/spaddintrons/meta.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/environment.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/environment.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/meta.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/meta.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* add meta map

* add meta to output and update snapshot

* add logic to use meta.id in determining output file name

* Update modules/nf-core/agat/spaddintrons/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* fix logic for output file name in stub

* remove trailing whitespace

* fix snapshot

---------

Co-authored-by: Anne Marie Noronha <anoronh4@users.noreply.github.com>
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Sateesh <perisateesh@gmail.com>
lrauschning pushed a commit to lrauschning/modules that referenced this pull request Jan 17, 2024
@anoronh4 @sateeshperi @lrauschning
add agat/spaddintrons (nf-core#4650)
184881c 
* add agat/spaddintrons

* fix linting error with prettier

* fix modules linting error in meta.yml

* Update modules/nf-core/agat/spaddintrons/meta.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/main.nf

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/environment.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/environment.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/meta.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/nf-core/agat/spaddintrons/meta.yml

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* add meta map

* add meta to output and update snapshot

* add logic to use meta.id in determining output file name

* Update modules/nf-core/agat/spaddintrons/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* fix logic for output file name in stub

* remove trailing whitespace

* fix snapshot

---------

Co-authored-by: Anne Marie Noronha <anoronh4@users.noreply.github.com>
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Sateesh <perisateesh@gmail.com>
@GallVp GallVp mentioned this pull request Nov 9, 2024
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@sateeshperi sateeshperi sateeshperi approved these changes

@Joon-Klaps Joon-Klaps Awaiting requested review from Joon-Klaps Joon-Klaps was automatically assigned from nf-core/nf-test

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new module: agat/spaddintrons
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