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Add mafft guidetree #7097

Merged
merged 24 commits into from
Nov 27, 2024
Merged

Add mafft guidetree #7097

merged 24 commits into from
Nov 27, 2024

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luisas
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@luisas luisas commented Nov 26, 2024

Add the mode MAFFT_GUIDETREE

PR checklist

Closes #7096

  • 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

@luisas luisas mentioned this pull request Nov 27, 2024
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@mashehu mashehu requested a review from a team as a code owner November 27, 2024 09:53
mirpedrol
mirpedrol approved these changes Nov 27, 2024
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LGTM :)

@mashehu
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mashehu commented Nov 27, 2024

what about the failing pytests?

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luisas commented Nov 27, 2024

what about the failing pytests?

Working on it now :) they are legit errors

@luisas luisas added this pull request to the merge queue Nov 27, 2024
Merged via the queue into nf-core:master with commit 868cb0d Nov 27, 2024
27 checks passed
@luisas luisas deleted the add_mafft_guidetree branch November 27, 2024 15:35
LouisLeNezet pushed a commit to LouisLeNezet/modules that referenced this pull request Dec 4, 2024
@luisas @mashehu
Add mafft guidetree (nf-core#7097)
a0657ec 
* move mafft to mafft_align

* add mafft guidetree

* update mafft align

* add mafft guidetree tests

* fixes

* up

* update other mafft tests

* update mafft

* fix

* don't lint deleted files

* filter out main.nf.test and main.nf.snapshot

* try different strategy

* fix other

* fix other

* add tests

* remove pytest

* up

* update nftest

* fix

---------

Co-authored-by: mashehu <[email protected]>
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@mirpedrol mirpedrol mirpedrol approved these changes

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new module: MAFFT/GUIDETREE
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@luisas @mashehu @mirpedrol