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Run 8 parallel alignment processes by default #418

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Run 8 parallel alignment processes by default #418

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fellen31
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@fellen31 fellen31 commented Oct 8, 2024 •
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Closes #376, by setting --parallel_alignments to 8 by default. This is a reasonable default.

Instead of running one test with parallel alignment, this test is not run without parallel alignment (--parallel_alignments 1).

Blocked: fellen31/splitubam#5

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 Oct 8, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 612e415

+| ✅ 169 tests passed       |+
#| ❔  20 tests were ignored |#

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/README.md
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-10-08 11:01:17

@fellen31 fellen31 force-pushed the split-alignment-by-default branch 2 times, most recently from ec7eedf to 27e4858 Compare October 10, 2024 08:07
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Split alignment by default
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