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Updating the usage documentation #365 #366

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Updating the usage documentation #365 #366

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Simplified and explained the processes a bit more. Paths and examples where out of data, this has now been fixed.

Closes #365

@DLBPointon DLBPointon added the documentation Improvements or additions to documentation label Feb 25, 2025
@DLBPointon DLBPointon self-assigned this Feb 25, 2025
@DLBPointon DLBPointon linked an issue Feb 25, 2025 that may be closed by this pull request
Setup documentation needs updating #365
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@DLBPointon DLBPointon added this to the Release 1 milestone Feb 25, 2025
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github-actions bot commented Feb 25, 2025 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8aceaca

+| ✅ 126 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.2.2'
  • 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
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • files_exist - File is ignored: conf/igenomes.config
  • 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: LICENSE or LICENSE.md or LICENCE or LICENCE.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: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2025-03-05 10:26:27

@DLBPointon DLBPointon linked an issue Mar 4, 2025 that may be closed by this pull request
The local test dataset does not contain a file at the given location. #364
Open
@DLBPointon DLBPointon changed the base branch from dp24_specified_reads to dev March 5, 2025 10:19
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Successfully merging this pull request may close these issues.

Setup documentation needs updating The local test dataset does not contain a file at the given location.
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