github-actions[bot]
commented
1 year ago nf-core lint overall result: Passed :white_check_mark: :warning:
Posted for pipeline commit 82a124d
+| ✅ 130 tests passed |+
#| ❔ 20 tests were ignored |#
!| ❗ 1 tests had warnings |!
### :heavy_exclamation_mark: Test warnings:
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'1.1.0'``
### :grey_question: Tests ignored:
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-genomenote_logo_light.png`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomenote_logo_light.png`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomenote_logo_dark.png`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/config.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awstest.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awsfulltest.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `conf/igenomes.config`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ignored: `manifest.name`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ignored: `manifest.homePage`
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md`
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/CONTRIBUTING.md`
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/ISSUE_TEMPLATE/bug_report.yml`
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/ISSUE_TEMPLATE/config.yml`
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/workflows/linting.yml`
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `assets/nf-core-genomenote_logo_light.png`
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/images/nf-core-genomenote_logo_light.png`
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/images/nf-core-genomenote_logo_dark.png`
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `lib/NfcoreTemplate.groovy`
* [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - actions_ci
* [actions_awstest](https://nf-co.re/tools-docs/lint_tests/actions_awstest.html) - 'awstest.yml' workflow not found: `/home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml`
### :white_check_mark: Tests passed:
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitignore`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.nf-core.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.editorconfig`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierignore`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierrc.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CHANGELOG.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CITATIONS.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow_schema.json`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow.config`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `README.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/.dockstore.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/CONTRIBUTING.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/PULL_REQUEST_TEMPLATE.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/branch.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/ci.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting_comment.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.html`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.txt`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/sendmail_template.txt`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/modules.config`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/test.config`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/test_full.config`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/output.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/usage.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/nfcore_external_java_deps.jar`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreSchema.groovy`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreTemplate.groovy`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/Utils.groovy`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/WorkflowMain.groovy`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `main.nf`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/multiqc_config.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/base.config`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/WorkflowGenomenote.groovy`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `modules.json`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `pyproject.toml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `Singularity`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `parameters.settings.json`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.nf-core.yaml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `bin/markdown_to_html.r`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `conf/aws.config`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/workflows/push_dockerhub.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `docs/images/nf-core-genomenote_logo.png`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.markdownlint.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.yamllint.yml`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Checks.groovy`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Completion.groovy`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Workflow.groovy`
* [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.travis.yml`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.nextflowVersion`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.description`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.version`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.enabled`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.enabled`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.enabled`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.enabled`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.cpus`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.memory`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.time`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.outdir`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.input`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.show_hidden_params`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.schema_ignore_params`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.mainScript`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.file`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.file`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.file`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.file`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.name`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.enable_conda`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``timeline.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``report.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``trace.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.file`` ended with ``.html``
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ``manifest.nextflowVersion`` started with >= or !>=
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_version` is set to `master`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master`
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Lines for loading custom profiles found
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitattributes` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.prettierrc.yml` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/.dockstore.yml` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/branch.yml` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/linting_comment.yml` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.txt` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/sendmail_template.txt` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/README.md` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/nfcore_external_java_deps.jar` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreSchema.groovy` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitignore` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.prettierignore` matches the template
* [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `pyproject.toml` matches the template
* [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Nextflow minimum version badge matched config. Badge: `23.04.1`, Config: `23.04.1`
* [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Zenodo placeholder was replaced with DOI.
* [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - No TODO strings found
* [pipeline_name_conventions](https://nf-co.re/tools-docs/lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention
* [template_strings](https://nf-co.re/tools-docs/lint_tests/template_strings.html) - Did not find any Jinja template strings (127 files)
* [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema lint passed
* [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema title + description lint passed
* [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Input mimetype lint passed: 'text/csv'
* [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Schema matched params returned from nextflow config
* [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - No `System.exit` calls found
* [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml
* [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml
* [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: clean-up.yml
* [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: fix-linting.yml
* [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml
* [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml
* [merge_markers](https://nf-co.re/tools-docs/lint_tests/merge_markers.html) - No merge markers found in pipeline files
* [modules_json](https://nf-co.re/tools-docs/lint_tests/modules_json.html) - Only installed modules found in `modules.json`
* [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
* [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'.
* [modules_structure](https://nf-co.re/tools-docs/lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
### Run details
* nf-core/tools version 2.8
* Run at `2023-08-22 14:43:07`
I had a bunch of code suggestions in the #78 reviews, but it wasn't practical to link changes across multiple files / multiple parts of the same file together. I also wanted to experiment things re. the copy to
data_to_load- and found a solution ! So in the end, I decide to put everything in commits.I've tried to separate all the commits and give them clear messages. Let me know if you have any question.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).