nf-core lint fails on newly created pipeline #2329
Description
Description of the bug
Using the latest version of dev when I create a new pipeline with a custom Pipeline prefix and Skip template areas and then run nf-core lint in the pipeline folder the linting fails which shouldn't be the case because it's a fresh pipeline.
Also seeing a number of linting tests that are ignored which don't make any sense. Need to track this down and fix it.
$ nf-core create
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.9.dev0 - https://nf-co.re
? Workflow name test
? Description test
? Author test
? Do you want to customize which parts of the template are used? Yes
? Pipeline prefix bug
? Skip template areas? [iGenomes config]
INFO Creating new nf-core pipeline: 'bug/test'
INFO Initialising pipeline git repository
INFO Done. Remember to add a remote and push to GitHub:
cd /home/harshil/webinar/bug-test
git remote add origin [email protected]:USERNAME/REPO_NAME.git
git push --all origin
INFO This will also push your newly created dev branch and the TEMPLATE branch for syncing.
$ cd bug-test
$ nf-core lint
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.9.dev0 - https://nf-co.re
INFO Testing pipeline: .
╭─ [?] 15 Pipeline Tests Ignored ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_exist: File is ignored: CODE_OF_CONDUCT.md │
│ files_exist: File is ignored: assets/nf-core-test_logo_light.png │
│ files_exist: File is ignored: docs/images/nf-core-test_logo_light.png │
│ files_exist: File is ignored: docs/images/nf-core-test_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 does not exist: CODE_OF_CONDUCT.md │
│ files_unchanged: File does not exist: .github/ISSUE_TEMPLATE/config.yml │
│ files_unchanged: File does not exist: assets/nf-core-test_logo_light.png │
│ files_unchanged: File does not exist: docs/images/nf-core-test_logo_light.png │
│ files_unchanged: File does not exist: docs/images/nf-core-test_logo_dark.png │
│ actions_awstest: 'awstest.yml' workflow not found: ./.github/workflows/awstest.yml │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [!] 22 Pipeline Test Warnings ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_exist: File not found: conf/igenomes.config │
│ 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: 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 nextflow.config: Specify your pipeline's command line flags │
│ 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 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 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 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release │
│ pipeline_todos: TODO string in ci.yml: You can customise CI pipeline run tests as required │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 1 Pipeline Test Failed ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_unchanged: .github/ISSUE_TEMPLATE/bug_report.yml does not match the template │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [!] 3 Module Test Warnings ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Module name │ File path │ Test message │
│╶──────────────────────────────────────────┼─────────────────────────────────────────────┼───────────────────────────────────────────────────────────────────────────╴│
│ custom/dumpsoftwareversions │ modules/nf-core/custom/dumpsoftwareversions │ New version available │
│ fastqc │ modules/nf-core/fastqc │ New version available │
│ multiqc │ modules/nf-core/multiqc │ New version available │
│ ╵ ╵ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY │
├───────────────────────┤
│ [✔] 156 Tests Passed │
│ [?] 15 Tests Ignored │
│ [!] 25 Test Warnings │
│ [✗] 1 Test Failed │
╰───────────────────────╯
Tip: Some of these linting errors can automatically be resolved with the following command:
nf-core lint --fix files_unchanged