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No need to check outdir for existence - Nextflow can create it on demand #319

Merged
merged 1 commit into from
Jul 7, 2023
Merged

No need to check outdir for existence - Nextflow can create it on demand #319

merged 1 commit into from
Jul 7, 2023

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robsyme
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@robsyme robsyme commented Jul 7, 2023

At the moment, we check the outdir parameter for existence, but many users will want to write results to a directory that doesn't currently exist. Removing params.outdir from the checkPathParamList will allow users to write to new directories.

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/taxprofiler 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).

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github-actions bot commented Jul 7, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 347d341

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-07 19:14:25

@robsyme robsyme merged commit 9fbab80 into dev Jul 7, 2023
20 checks passed
@robsyme robsyme deleted the new-outdir-fix branch July 7, 2023 20:32
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@maxulysse maxulysse maxulysse approved these changes

@jfy133 jfy133 jfy133 approved these changes

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@robsyme @maxulysse @jfy133