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Fixed mistake in last fix #305

Merged
merged 2 commits into from
Dec 12, 2024
Merged

Fixed mistake in last fix #305

merged 2 commits into from
Dec 12, 2024

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erikrikarddaniel
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@erikrikarddaniel erikrikarddaniel commented Dec 12, 2024 •
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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/metatdenovo 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>).
  • 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).

A directory I relied on in #304 is missing when Eukulele doesn't produce the count, which made my fix fail.

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github-actions bot commented Dec 12, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit b35f4b2

+| ✅ 206 tests passed       |+
!| ❗   7 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable (incorrectly) found: params.max_cpus
  • nextflow_config - Config variable (incorrectly) found: params.max_memory
  • nextflow_config - Config variable (incorrectly) found: params.max_time
  • nextflow_config - Old lines for loading custom profiles found. File should contain: ```groovy
    // Load nf-core custom profiles from different Institutions
    includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - .gitignore does not match the template
  • actions_awsfulltest - .github/workflows/awsfulltest.yml is not triggered correctly

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
  • nextflow_config - Config manifest.version should end in dev: 1.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]
  • nfcore_yml - nf-core version in .nf-core.yml is not set to the latest version. Should be 3.0.2 but was 2.14.1

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-12 08:47:15

@erikrikarddaniel erikrikarddaniel merged commit 8630dd9 into nf-core:dev Dec 12, 2024
7 of 8 checks passed
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@danilodileo danilodileo Awaiting requested review from danilodileo

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