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check --profile is well formatted #4794

Merged
merged 1 commit into from
Jan 24, 2024
Merged

check --profile is well formatted #4794

merged 1 commit into from
Jan 24, 2024

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mirpedrol
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Add the changes introduced to the pipeline template with nf-core/tools#2678

PR checklist

Closes #XXX

  • 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

maxulysse
maxulysse reviewed Jan 24, 2024
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subworkflows/nf-core/initialise/main.nf
Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
}
if (args[0]) {
log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
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why such a big indentation?

@maxulysse maxulysse added this pull request to the merge queue Jan 24, 2024
Merged via the queue into nf-core:master with commit 980fbd9 Jan 24, 2024
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jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@mirpedrol @jennylsmith
check --profile is well formatted (nf-core#4794)
9406b31
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@maxulysse maxulysse maxulysse approved these changes

@mashehu mashehu mashehu approved these changes

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot

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3 participants
@mirpedrol @maxulysse @mashehu