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add regressive, fix tcoffee and consensus #6802

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merged 6 commits into from
Oct 18, 2024
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@luisas luisas commented Oct 18, 2024

PR checklist

Add regressive module
Update T-coffee module - remove the fix that was implemented for the regressive for compression, since now it is its own module.

Update consensus module to also provide evaluation outputs

  • 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

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Minor comments

def prefix = task.ext.prefix ?: "${meta.id}"
def tree_args = tree ? "-regtree $tree" : ""
def template_args = template ? "-template_file $template" : ""
def outfile = compress ? "stdout" : "${prefix}.aln"
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Equal sign alignment

modules/nf-core/tcoffee/regressive/meta.yml Outdated Show resolved Hide resolved
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LGTM, just fix the CI issues

@luisas luisas enabled auto-merge October 18, 2024 14:02
@luisas luisas added this pull request to the merge queue Oct 18, 2024
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Oct 18, 2024
@luisas luisas added this pull request to the merge queue Oct 18, 2024
Merged via the queue into nf-core:master with commit 66b2256 Oct 18, 2024
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@luisas luisas deleted the regressive branch October 18, 2024 15:04
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2 participants