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Template update for nf-core/tools version 2.13.1 #3

Merged
merged 7 commits into from
May 8, 2024
Merged

Template update for nf-core/tools version 2.13.1 #3

merged 7 commits into from
May 8, 2024

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adamrtalbot
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@adamrtalbot adamrtalbot commented May 2, 2024 •
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Updates the pipeline repo to show recent changes in nf-core, including using nf-schema instead of a Python script. Should reduce the overheads of running Dragen considerably.

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/dragen 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).
  • 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 May 2, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 580901a

+| ✅ 142 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  16 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • files_exist - File not found: LICENSE or LICENSE.md or LICENCE or LICENCE.md

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • 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 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 output.md: Write this documentation describing your workflow's output
  • 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in dragen.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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
  • pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
  • schema_description - No description provided in schema for parameter: dragen_index

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nf-dragen_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nf-dragen_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nf-dragen_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
  • 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 does not exist: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-nf-dragen_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nf-dragen_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nf-dragen_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-dragen/nf-dragen/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-02 17:31:39

maxulysse
maxulysse reviewed May 3, 2024
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CHANGELOG.md Outdated Show resolved Hide resolved
maxulysse
maxulysse reviewed May 3, 2024
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assets/email_template.txt
Comment on lines -1 to -8
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~\\
|\\ | |__ __ / ` / \\ |__) |__ } {
| \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,
`._,._,'
nf-core/dragen v${version}
----------------------------------------------------
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we don't have a ASCII version of Seqera?

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Hmm not in the template. Is this important?

maxulysse
maxulysse reviewed May 3, 2024
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assets/sendmail_template.txt
Content-Transfer-Encoding: base64
Content-ID: <nfcorepipelinelogo>
Content-Disposition: inline; filename="nf-core-dragen_logo_light.png"
Content-Disposition: inline; filename="seqeralabs-nf-dragen_logo_light.png"
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no logo to display

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Shall we delete all the email/slack/teams stuff anyway, it's not relevant.

Can we do that in the template?

maxulysse
maxulysse approved these changes May 3, 2024
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minor comments, but looking good

@adamrtalbot adamrtalbot merged commit 0ba9671 into dev May 8, 2024
@adamrtalbot adamrtalbot deleted the TEMPLATE branch May 8, 2024 12:12
@adamrtalbot adamrtalbot restored the TEMPLATE branch May 8, 2024 12:12
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@maxulysse maxulysse maxulysse approved these changes

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@adamrtalbot @maxulysse