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Dev remove getscale #94

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Dev remove getscale #94

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jianhong
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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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/hicar branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@jianhong
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@emiller88 Did I understand you correctly about this? Does subworkflow work?

@jianhong jianhong changed the title Dev remove getscale and the meta id issue Dev remove getscale Jul 14, 2023
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fc4b412

+| ✅ 153 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-14 11:52:01

@edmundmiller
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I was just asking whether it needed to be its own process. If it was computationally intensive or not (which it should just be some quick calculations), because that would be a lot of overhead in the cloud or just extra jobs to submit in slurm.

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I was just asking whether it needed to be its own process. If it was computationally intensive or not (which it should just be some quick calculations), because that would be a lot of overhead in the cloud or just extra jobs to submit in slurm.

I suppose the this subworkflow will not submit any job. Correct me if I mis-understand about this. I keep this sub-workflow because it will be called by several different steps.

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edmundmiller commented Aug 14, 2023 •
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I suppose the this subworkflow will not submit any job. Correct me if I mis-understand about this. I keep this sub-workflow because it will be called by several different steps.

Hmm, makes sense! Maybe it needs an executor 'local' defined in the process?

@jianhong jianhong closed this Jan 5, 2024
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@mirpedrol mirpedrol Awaiting requested review from mirpedrol

@edmundmiller edmundmiller Awaiting requested review from edmundmiller

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