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Dev #78

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Test to run the download GHA

mirpedrol and others added 14 commits September 1, 2022 14:59
@mirpedrol
Template update for nf-core/tools version 2.5.1
ce5468b
@mirpedrol
Merge branch 'TEMPLATE' of https://github.com/nf-core/testpipeline in…
bd2c3f8 
…to template-updates-2.12
@mirpedrol
fix pre-commit version
8659825
@mirpedrol
Merge pull request #75 from nf-core/template-updates-2.12
c834600 
Template updates 2.12
@nf-core-bot
Template update for nf-core/tools version 2.14.1
54a3cb8
@mashehu
Merge branch 'dev' of github.com:nf-core/testpipeline into nf-core-te…
fb376e5 
…mplate-merge-2.14.1

# Conflicts:
#	.devcontainer/devcontainer.json
#	.editorconfig
#	.github/CONTRIBUTING.md
#	.github/workflows/awsfulltest.yml
#	.github/workflows/awstest.yml
#	.github/workflows/branch.yml
#	.github/workflows/ci.yml
#	.github/workflows/clean-up.yml
#	.github/workflows/download_pipeline.yml
#	.github/workflows/fix-linting.yml
#	.github/workflows/linting.yml
#	.github/workflows/linting_comment.yml
#	.github/workflows/release-announcements.yml
#	.pre-commit-config.yaml
#	CITATIONS.md
#	README.md
#	assets/nf-core-testpipeline_logo_light.png
#	bin/check_samplesheet.py
#	conf/modules.config
#	docs/images/nf-core-testpipeline_logo_dark.png
#	docs/images/nf-core-testpipeline_logo_light.png
#	docs/usage.md
#	lib/NfcoreTemplate.groovy
#	lib/Utils.groovy
#	lib/WorkflowMain.groovy
#	lib/WorkflowTestpipeline.groovy
#	main.nf
#	modules.json
#	modules/local/samplesheet_check.nf
#	modules/nf-core/custom/dumpsoftwareversions/main.nf
#	modules/nf-core/custom/dumpsoftwareversions/meta.yml
#	modules/nf-core/fastqc/main.nf
#	modules/nf-core/fastqc/tests/main.nf.test
#	modules/nf-core/fastqc/tests/main.nf.test.snap
#	modules/nf-core/multiqc/environment.yml
#	modules/nf-core/multiqc/main.nf
#	modules/nf-core/multiqc/tests/main.nf.test
#	modules/nf-core/multiqc/tests/main.nf.test.snap
#	nextflow.config
#	nextflow_schema.json
#	workflows/testpipeline.nf
@mashehu
fix linting
d4aaa9b
@mirpedrol
fix linting
1129af2
@mirpedrol
Merge pull request #81 from nf-core/nf-core-template-merge-2.14.1
164617e 
Important! Template update for nf-core/tools v2.14.1
@mirpedrol
run lint --release on PRs to master
a5890a3
@mirpedrol
remove 'pipelines' from command
7d5d5a3
@mirpedrol
fix linting
7b2d08a
@mirpedrol
Merge pull request #89 from mirpedrol/lint-release
745c668 
run lint --release on PRs to master
@mirpedrol
Merge branch 'master' into dev
ff9e535
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github-actions bot commented Aug 30, 2024 •
edited
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit fcffe1a

+| ✅ 186 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  26 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

  • nextflow_config - Config manifest.version should not contain dev for a release: 1.0dev
  • files_unchanged - assets/nf-core-testpipeline_logo_light.png does not match the template
  • version_consistency - manifest.version was not numeric: 1.0dev!
  • included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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 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 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 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.1
  • Run at 2024-10-11 12:22:43

mashehu and others added 2 commits October 11, 2024 12:16
@mashehu
one down
2b7b79e
@mashehu
Merge pull request #95 from nf-core/nf-core-template-merge-2.14.2.dev0
fcffe1a 
Important! Template update for nf-core/tools v2.14.2.dev0
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3 participants
@mirpedrol @nf-core-bot @mashehu