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updates modules to remove enable_conda #284

Merged
merged 4 commits into from
Feb 16, 2023
Merged

updates modules to remove enable_conda #284

merged 4 commits into from
Feb 16, 2023

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jemten
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@jemten jemten commented Feb 15, 2023

This PR updates the modules to remove enable_conda, which has been deprecated.

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/raredisease 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> -stub).
  • Ensure the test suite passes (nextflow run . -profile test2samples,docker --outdir <OUTDIR> -stub).
  • 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 Feb 15, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8955858

+| ✅ 152 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  15 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • 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.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in test2samples.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • 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: .github/PULL_REQUEST_TEMPLATE.md
  • 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 2.7.2
  • Run at 2023-02-16 08:13:52

@jemten jemten marked this pull request as ready for review February 15, 2023 10:08
Lucpen
Lucpen reviewed Feb 16, 2023
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LGTM

@jemten jemten merged commit 7a0d47a into nf-core:dev Feb 16, 2023
@jemten jemten deleted the remove_enable_conda branch February 16, 2023 09:15
@jemten jemten mentioned this pull request Apr 4, 2023
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@Lucpen Lucpen Lucpen approved these changes

@ramprasadn ramprasadn Awaiting requested review from ramprasadn

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@jemten @Lucpen