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mashehumashehu
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Merge remote-tracking branch 'upstream/main' into npm-workspace
# Conflicts: # package-lock.json # package.json # public/_redirects # public/components.json # public/pipelines.json # sites/docs/src/content/api_reference/1.10.1/bump_version.md # sites/docs/src/content/api_reference/1.10.1/create.md # sites/docs/src/content/api_reference/1.10.1/download.md # sites/docs/src/content/api_reference/1.10.1/index.md # sites/docs/src/content/api_reference/1.10.1/licences.md # sites/docs/src/content/api_reference/1.10.1/lint.md # sites/docs/src/content/api_reference/1.10.1/list.md # sites/docs/src/content/api_reference/1.10.1/utils.md # sites/docs/src/content/api_reference/1.10.1/workflow.md # sites/docs/src/content/api_reference/1.10.2/bump_version.md # sites/docs/src/content/api_reference/1.10.2/create.md # sites/docs/src/content/api_reference/1.10.2/download.md # sites/docs/src/content/api_reference/1.10.2/index.md # sites/docs/src/content/api_reference/1.10.2/licences.md # sites/docs/src/content/api_reference/1.10.2/lint.md # sites/docs/src/content/api_reference/1.10.2/list.md # sites/docs/src/content/api_reference/1.10.2/utils.md # sites/docs/src/content/api_reference/1.10.2/workflow.md # sites/docs/src/content/api_reference/1.10/bump_version.md # sites/docs/src/content/api_reference/1.10/create.md # sites/docs/src/content/api_reference/1.10/download.md # sites/docs/src/content/api_reference/1.10/index.md # sites/docs/src/content/api_reference/1.10/licences.md # sites/docs/src/content/api_reference/1.10/lint.md # sites/docs/src/content/api_reference/1.10/list.md # sites/docs/src/content/api_reference/1.10/utils.md # sites/docs/src/content/api_reference/1.10/workflow.md # sites/docs/src/content/api_reference/1.11/bump_version.md # sites/docs/src/content/api_reference/1.11/create.md # sites/docs/src/content/api_reference/1.11/download.md # sites/docs/src/content/api_reference/1.11/index.md # sites/docs/src/content/api_reference/1.11/licences.md # sites/docs/src/content/api_reference/1.11/lint.md # sites/docs/src/content/api_reference/1.11/list.md # sites/docs/src/content/api_reference/1.11/utils.md # sites/docs/src/content/api_reference/1.11/workflow.md # sites/docs/src/content/api_reference/1.12.1/bump_version.md # sites/docs/src/content/api_reference/1.12.1/create.md # sites/docs/src/content/api_reference/1.12.1/download.md # sites/docs/src/content/api_reference/1.12.1/index.md # sites/docs/src/content/api_reference/1.12.1/launch.md # sites/docs/src/content/api_reference/1.12.1/licences.md # sites/docs/src/content/api_reference/1.12.1/lint.md # sites/docs/src/content/api_reference/1.12.1/list.md # sites/docs/src/content/api_reference/1.12.1/modules.md # sites/docs/src/content/api_reference/1.12.1/schema.md # sites/docs/src/content/api_reference/1.12.1/sync.md # sites/docs/src/content/api_reference/1.12.1/utils.md # sites/docs/src/content/api_reference/1.12/bump_version.md # sites/docs/src/content/api_reference/1.12/create.md # sites/docs/src/content/api_reference/1.12/download.md # sites/docs/src/content/api_reference/1.12/index.md # sites/docs/src/content/api_reference/1.12/launch.md # sites/docs/src/content/api_reference/1.12/licences.md # sites/docs/src/content/api_reference/1.12/lint.md # sites/docs/src/content/api_reference/1.12/list.md # sites/docs/src/content/api_reference/1.12/modules.md # sites/docs/src/content/api_reference/1.12/schema.md # sites/docs/src/content/api_reference/1.12/sync.md # sites/docs/src/content/api_reference/1.12/utils.md # sites/docs/src/content/api_reference/1.13.1/api/bump_version.md # sites/docs/src/content/api_reference/1.13.1/api/create.md # sites/docs/src/content/api_reference/1.13.1/api/download.md # sites/docs/src/content/api_reference/1.13.1/api/index.md # sites/docs/src/content/api_reference/1.13.1/api/launch.md # sites/docs/src/content/api_reference/1.13.1/api/licences.md # sites/docs/src/content/api_reference/1.13.1/api/lint.md # sites/docs/src/content/api_reference/1.13.1/api/list.md # sites/docs/src/content/api_reference/1.13.1/api/modules.md # sites/docs/src/content/api_reference/1.13.1/api/schema.md # sites/docs/src/content/api_reference/1.13.1/api/sync.md # sites/docs/src/content/api_reference/1.13.1/api/utils.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/actions_awsfulltest.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/actions_awstest.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/actions_ci.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/actions_schema_validation.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/conda_dockerfile.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/conda_env_yaml.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/files_exist.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/files_unchanged.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/index.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/merge_markers.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/nextflow_config.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/pipeline_name_conventions.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/pipeline_todos.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/readme.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/schema_lint.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/schema_params.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/template_strings.md # sites/docs/src/content/api_reference/1.13.1/lint_tests/version_consistency.md # sites/docs/src/content/api_reference/1.13.2/api/bump_version.md # sites/docs/src/content/api_reference/1.13.2/api/create.md # sites/docs/src/content/api_reference/1.13.2/api/download.md # sites/docs/src/content/api_reference/1.13.2/api/index.md # sites/docs/src/content/api_reference/1.13.2/api/launch.md # sites/docs/src/content/api_reference/1.13.2/api/licences.md # sites/docs/src/content/api_reference/1.13.2/api/lint.md # sites/docs/src/content/api_reference/1.13.2/api/list.md # sites/docs/src/content/api_reference/1.13.2/api/modules.md # sites/docs/src/content/api_reference/1.13.2/api/schema.md # sites/docs/src/content/api_reference/1.13.2/api/sync.md # sites/docs/src/content/api_reference/1.13.2/api/utils.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/actions_awsfulltest.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/actions_awstest.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/actions_ci.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/actions_schema_validation.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/conda_dockerfile.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/conda_env_yaml.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/files_exist.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/files_unchanged.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/index.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/merge_markers.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/nextflow_config.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/pipeline_name_conventions.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/pipeline_todos.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/readme.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/schema_lint.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/schema_params.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/template_strings.md # sites/docs/src/content/api_reference/1.13.2/lint_tests/version_consistency.md # sites/docs/src/content/api_reference/1.13.3/api/bump_version.md # sites/docs/src/content/api_reference/1.13.3/api/create.md # sites/docs/src/content/api_reference/1.13.3/api/download.md # sites/docs/src/content/api_reference/1.13.3/api/index.md # sites/docs/src/content/api_reference/1.13.3/api/launch.md # sites/docs/src/content/api_reference/1.13.3/api/licences.md # sites/docs/src/content/api_reference/1.13.3/api/lint.md # sites/docs/src/content/api_reference/1.13.3/api/list.md # sites/docs/src/content/api_reference/1.13.3/api/modules.md # sites/docs/src/content/api_reference/1.13.3/api/schema.md # sites/docs/src/content/api_reference/1.13.3/api/sync.md # 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sites/docs/src/content/api_reference/2.2/pipeline_lint_tests/schema_lint.md # sites/docs/src/content/api_reference/2.2/pipeline_lint_tests/schema_params.md # sites/docs/src/content/api_reference/2.2/pipeline_lint_tests/template_strings.md # sites/docs/src/content/api_reference/2.2/pipeline_lint_tests/version_consistency.md # sites/docs/src/content/api_reference/2.3.1/api/bump_version.md # sites/docs/src/content/api_reference/2.3.1/api/create.md # sites/docs/src/content/api_reference/2.3.1/api/download.md # sites/docs/src/content/api_reference/2.3.1/api/index.md # sites/docs/src/content/api_reference/2.3.1/api/launch.md # sites/docs/src/content/api_reference/2.3.1/api/licences.md # sites/docs/src/content/api_reference/2.3.1/api/lint.md # sites/docs/src/content/api_reference/2.3.1/api/list.md # sites/docs/src/content/api_reference/2.3.1/api/modules.md # sites/docs/src/content/api_reference/2.3.1/api/schema.md # sites/docs/src/content/api_reference/2.3.1/api/sync.md # sites/docs/src/content/api_reference/2.3.1/api/utils.md # sites/docs/src/content/api_reference/2.3.1/index.md # sites/docs/src/content/api_reference/2.3.1/module_lint_tests/index.md # sites/docs/src/content/api_reference/2.3.1/module_lint_tests/main_nf.md # sites/docs/src/content/api_reference/2.3.1/module_lint_tests/meta_yml.md # sites/docs/src/content/api_reference/2.3.1/module_lint_tests/module_deprecations.md # sites/docs/src/content/api_reference/2.3.1/module_lint_tests/module_todos.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/actions_awsfulltest.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/actions_awstest.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/actions_ci.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/actions_schema_validation.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/files_exist.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/files_unchanged.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/index.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/merge_markers.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/modules_json.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/multiqc_config.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/nextflow_config.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/pipeline_name_conventions.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/pipeline_todos.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/readme.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/schema_description.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/schema_lint.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/schema_params.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/template_strings.md # sites/docs/src/content/api_reference/2.3.1/pipeline_lint_tests/version_consistency.md # sites/docs/src/content/api_reference/2.3.2/api/bump_version.md # sites/docs/src/content/api_reference/2.3.2/api/create.md # sites/docs/src/content/api_reference/2.3.2/api/download.md # sites/docs/src/content/api_reference/2.3.2/api/index.md # sites/docs/src/content/api_reference/2.3.2/api/launch.md # sites/docs/src/content/api_reference/2.3.2/api/licences.md # sites/docs/src/content/api_reference/2.3.2/api/lint.md # sites/docs/src/content/api_reference/2.3.2/api/list.md # sites/docs/src/content/api_reference/2.3.2/api/modules.md # sites/docs/src/content/api_reference/2.3.2/api/schema.md # sites/docs/src/content/api_reference/2.3.2/api/sync.md # sites/docs/src/content/api_reference/2.3.2/api/utils.md # sites/docs/src/content/api_reference/2.3.2/index.md # sites/docs/src/content/api_reference/2.3.2/module_lint_tests/index.md # sites/docs/src/content/api_reference/2.3.2/module_lint_tests/main_nf.md # sites/docs/src/content/api_reference/2.3.2/module_lint_tests/meta_yml.md # sites/docs/src/content/api_reference/2.3.2/module_lint_tests/module_deprecations.md # sites/docs/src/content/api_reference/2.3.2/module_lint_tests/module_todos.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/actions_awsfulltest.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/actions_awstest.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/actions_ci.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/actions_schema_validation.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/files_exist.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/files_unchanged.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/index.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/merge_markers.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/modules_json.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/multiqc_config.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/nextflow_config.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/pipeline_name_conventions.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/pipeline_todos.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/readme.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/schema_description.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/schema_lint.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/schema_params.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/template_strings.md # sites/docs/src/content/api_reference/2.3.2/pipeline_lint_tests/version_consistency.md # sites/docs/src/content/api_reference/2.3/api/bump_version.md # sites/docs/src/content/api_reference/2.3/api/create.md # sites/docs/src/content/api_reference/2.3/api/download.md # sites/docs/src/content/api_reference/2.3/api/index.md # sites/docs/src/content/api_reference/2.3/api/launch.md # sites/docs/src/content/api_reference/2.3/api/licences.md # sites/docs/src/content/api_reference/2.3/api/lint.md # sites/docs/src/content/api_reference/2.3/api/list.md # sites/docs/src/content/api_reference/2.3/api/modules.md # sites/docs/src/content/api_reference/2.3/api/schema.md # sites/docs/src/content/api_reference/2.3/api/sync.md # sites/docs/src/content/api_reference/2.3/api/utils.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/actions_awsfulltest.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/actions_awstest.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/actions_ci.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/actions_schema_validation.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/files_exist.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/files_unchanged.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/index.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/merge_markers.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/modules_json.md # sites/docs/src/content/api_reference/2.3/pipeline_lint_tests/nextflow_config.md # sites/doc…
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‎.github/CODEOWNERS

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@@ -1 +1,2 @@
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src/content/docs @nf-core/docs
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src/content/tutorials @nf-core/training @nf-core/outreach

‎.github/renovate.json5

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@@ -1,12 +1,20 @@
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{
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$schema: "https://docs.renovatebot.com/renovate-schema.json",
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extends: ["github>nf-core/ops//.github/renovate/default.json5", "config:recommended", "schedule:monthly"],
4-
customManagers: [
2+
"$schema": "https://docs.renovatebot.com/renovate-schema.json",
3+
"extends": ["github>nf-core/ops//.github/renovate/default.json5", "config:recommended", "schedule:monthly"],
4+
"customManagers": [
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{
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customType: "regex",
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fileMatch: ["^linting\\.yml$"],
8-
matchStrings: ["https://github.com/(?<depName>.*)/releases/download/(?<currentValue>.*)/.*.tar.gz"],
9-
datasourceTemplate: "github-release-attachments"
6+
"customType": "regex",
7+
"fileMatch": ["^linting\\.yml$"],
8+
"matchStrings": ["https://github.com/(?<depName>.*)/releases/download/(?<currentValue>.*)/.*.tar.gz"],
9+
"datasourceTemplate": "github-release-attachments"
10+
}
11+
],
12+
"packageRules": [
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{
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"packageName": "*",
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"dependencyType": "direct",
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"manager": "npm",
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"enabled": false
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}
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]
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}

‎.github/rich-codex.yml

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@@ -2,47 +2,248 @@ timeout: 300
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outputs:
33
- command: nf-core --help
44
img_paths:
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- public_html/assets/markdown_assets/developers/creating_with_nf_core/nfcore_help.svg
5+
- public/images/contributing/creating_with_nf_core/nfcore_help.svg
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- command: nf-core list
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head: 19
88
img_paths:
9-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/nfcore_list.svg
9+
- public/images/contributing/creating_with_nf_core/nfcore_list.svg
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- command: nf-core create --name demo --description "Pipeline for training" --author "Phil" --plain
1111
fake_command: nf-core create
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img_paths:
13-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/nfcore_create.svg
13+
- public/images/contributing/creating_with_nf_core/nfcore_create.svg
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- command: cd nf-core-demo && git status
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fake_command: git status
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img_paths:
17-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/git_status.svg
17+
- public/images/contributing/creating_with_nf_core/git_status.svg
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- command: cd nf-core-demo && git branch
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fake_command: git branch
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img_paths:
21-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/git_branch.svg
21+
- public/images/contributing/creating_with_nf_core/git_branch.svg
2222
- command: cd nf-core-demo && git log --oneline
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fake_command: git log --oneline
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img_paths:
25-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/git_log.svg
25+
- public/images/contributing/creating_with_nf_core/git_log.svg
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- command: nextflow run nf-core-demo/ -profile test,docker --outdir test_results
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title: nextflow run
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img_paths:
29-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/nextflow_run_1.svg
29+
- public/images/contributing/creating_with_nf_core/nextflow_run_1.svg
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- command: cd nf-core-demo && nf-core lint && grep -rl TODO .
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fake_command: nf-core lint
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img_paths:
33-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/nfcore_lint_warnings.svg
33+
- public/images/contributing/creating_with_nf_core/nfcore_lint_warnings.svg
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- command: |
3535
cd nf-core-demo && \
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grep -rl TODO . | xargs sed -i 's/TODO//g' && \
3737
echo "ADDED" >> CODE_OF_CONDUCT.md && \
3838
nf-core lint
3939
fake_command: nf-core lint
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img_paths:
41-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/nfcore_lint_failure.svg
41+
- public/images/contributing/creating_with_nf_core/nfcore_lint_failure.svg
4242
- command: nextflow run nf-core-demo/ --help
4343
img_paths:
44-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/nextflow_run_help.svg
44+
- public/images/contributing/creating_with_nf_core/nextflow_run_help.svg
4545
- command: nextflow run nf-core-demo/ -profile test,docker
4646
title: nextflow run
4747
img_paths:
48-
- public_html/assets/markdown_assets/developers/creating_with_nf_core/nextflow_run_no_outdir.svg
48+
- public/images/contributing/creating_with_nf_core/nextflow_run_no_outdir.svg
49+
- command: git clone https://github.com/nf-core/modules.git --depth 1 && cd modules && nf-core modules create fastqc --author @janedoe --label process_low --meta --force
50+
fake_command: nf-core modules create fastqc --author @janedoe --label process_low --meta
51+
img_paths:
52+
- public/images/contributing/modules/nf-core-modules-create.svg
53+
- command: nf-core list
54+
head: 19
55+
img_paths:
56+
- public/images/tools/nf-core-list.svg
57+
- command: nf-core list rna rna-seq
58+
img_paths:
59+
- public/images/tools/nf-core-list-rna.svg
60+
- command: nf-core list -s stars
61+
head: 18
62+
img_paths:
63+
- public/images/tools/nf-core-list-stars.svg
64+
- command: nf-core launch rnaseq -r 3.8.1
65+
trim_after: 'Command line'
66+
img_paths:
67+
- public/images/tools/nf-core-launch-rnaseq.svg
68+
- command: mkdir tmp && cd tmp && nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d
69+
img_paths:
70+
- public/images/tools/nf-core-download.svg
71+
- command: cd tmp && tree -L 2 nf-core-rnaseq/
72+
img_paths:
73+
- public/images/tools/nf-core-download-tree.svg
74+
- command: nf-core licences deepvariant
75+
timeout: 10
76+
img_paths:
77+
- public/images/tools/nf-core-licences.svg
78+
- command: cd tmp && nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain
79+
fake_command: nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain
80+
img_paths:
81+
- public/images/tools/nf-core-create.svg
82+
- command: |
83+
cd tmp/nf-core-nextbigthing && \
84+
echo "lint: { pipeline_todos: false }" >> .nf-core.yml && \
85+
nf-core lint
86+
fake_command: nf-core lint
87+
img_paths:
88+
- public/images/tools/nf-core-lint.svg
89+
- command: |
90+
cd tmp && \
91+
echo "{input: myfiles.csv, outdir: results}" > nf-params.json
92+
nf-core schema validate nf-core-rnaseq/3_8 nf-params.json
93+
timeout: 10
94+
fake_command: nf-core schema validate nf-core-rnaseq/3_8 nf-params.json
95+
after_command: rm nf-params.json
96+
img_paths:
97+
- public/images/tools/nf-core-schema-validate.svg
98+
- command: |
99+
cd tmp/nf-core-nextbigthing && \
100+
sed '25,30d' nextflow_schema.json > nextflow_schema.json.tmp && \
101+
mv nextflow_schema.json.tmp nextflow_schema.json && \
102+
nf-core schema build --no-prompts
103+
timeout: 10
104+
fake_command: nf-core schema build --no-prompts
105+
img_paths:
106+
- public/images/tools/nf-core-schema-build.svg
107+
- command: cd tmp/nf-core-nextbigthing && nf-core schema lint
108+
fake_command: nf-core schema lint
109+
img_paths:
110+
- public/images/tools/nf-core-schema-lint.svg
111+
- command: |
112+
cd tmp/nf-core-nextbigthing && \
113+
git config --global user.email "[email protected]" && \
114+
git config --global user.name "nf-core_bot" && \
115+
git commit -am "Bump version" && \
116+
nf-core sync
117+
fake_command: nf-core sync
118+
img_paths:
119+
- public/images/tools/nf-core-sync.svg
120+
- command: cd tmp/nf-core-nextbigthing && nf-core bump-version 1.1
121+
fake_command: nf-core bump-version 1.1
122+
img_paths:
123+
- public/images/tools/nf-core-bump-version.svg
124+
- command: cd tmp && nf-core create-logo nextbigthing
125+
fake_command: nf-core create-logo nextbigthing
126+
img_paths:
127+
- public/images/tools/nf-core-create-logo.svg
128+
- command: cd tmp/nf-core-nextbigthing && nf-core modules list remote
129+
head: 25
130+
fake_command: nf-core modules list remote
131+
img_paths:
132+
- public/images/tools/nf-core-modules-list-remote.svg
133+
- command: cd tmp/nf-core-nextbigthing && nf-core modules list local
134+
head: 25
135+
fake_command: nf-core modules list local
136+
img_paths:
137+
- public/images/tools/nf-core-modules-list-local.svg
138+
- command: cd tmp/nf-core-nextbigthing && nf-core modules info abacas
139+
fake_command: nf-core modules info abacas
140+
img_paths:
141+
- public/images/tools/nf-core-modules-info.svg
142+
- command: cd tmp/nf-core-nextbigthing && nf-core modules install abacas
143+
fake_command: nf-core modules install abacas
144+
img_paths:
145+
- public/images/tools/nf-core-modules-install.svg
146+
- command: cd tmp/nf-core-nextbigthing && nf-core modules update --all --no-preview
147+
fake_command: nf-core modules update --all --no-preview
148+
img_paths:
149+
- public/images/tools/nf-core-modules-update.svg
150+
- command: cd tmp/nf-core-nextbigthing && nf-core modules remove abacas
151+
fake_command: nf-core modules remove abacas
152+
img_paths:
153+
- public/images/tools/nf-core-modules-remove.svg
154+
- command: |
155+
cd tmp/nf-core-nextbigthing && \
156+
sed "s/process_medium/process_low/g" modules/nf-core/fastqc/main.nf > modules/nf-core/fastqc/main.nf.patch && \
157+
mv modules/nf-core/fastqc/main.nf.patch modules/nf-core/fastqc/main.nf && \
158+
nf-core modules patch fastqc
159+
fake_command: nf-core modules patch fastqc
160+
img_paths:
161+
- public/images/tools/nf-core-modules-patch.svg
162+
- command: |
163+
cd tmp && \
164+
git clone https://github.com/nf-core/modules.git && cd modules && \
165+
nf-core modules create fastqc --author @nf-core-bot --label process_low --meta --force
166+
timeout: 10
167+
fake_command: nf-core modules create fastqc --author @nf-core-bot --label process_low --meta --force
168+
img_paths:
169+
- public/images/tools/nf-core-modules-create.svg
170+
- command: |
171+
cd tmp/modules && \
172+
sed -i 's/1.13a/1.10/g' modules/multiqc/main.nf && \
173+
nf-core modules lint multiqc
174+
fake_command: nf-core modules lint multiqc
175+
img_paths:
176+
- public/images/tools/nf-core-modules-lint.svg
177+
- command: cd tmp/modules && nf-core modules test fastqc --no-prompts
178+
timeout: 30
179+
extra_env:
180+
PROFILE: 'conda'
181+
fake_command: nf-core modules test fastqc --no-prompts
182+
img_paths:
183+
- public/images/tools/nf-core-modules-test.svg
184+
- command: cd tmp/modules && nf-core modules bump-versions fastqc
185+
fake_command: nf-core modules bump-versions fastqc
186+
img_paths:
187+
- public/images/tools/nf-core-modules-bump-version.svg
188+
- command: cd tmp/nf-core-nextbigthing && nf-core subworkflows list remote
189+
head: 25
190+
fake_command: nf-core subworkflows list remote
191+
img_paths:
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- public/images/tools/nf-core-subworkflows-list-remote.svg
193+
- command: |
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cd tmp/nf-core-nextbigthing && \
195+
echo "repository_type: pipeline" >> .nf-core.yml && \
196+
nf-core subworkflows list local
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head: 25
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fake_command: nf-core subworkflows list local
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img_paths:
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- public/images/tools/nf-core-subworkflows-list-local.svg
201+
- command: |
202+
cd tmp/nf-core-nextbigthing && \
203+
echo "repository_type: pipeline" >> .nf-core.yml && \
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nf-core subworkflows info bam_rseqc
205+
head: 15
206+
tail: 10
207+
fake_command: nf-core subworkflows info bam_rseqc
208+
img_paths:
209+
- public/images/tools/nf-core-subworkflows-info.svg
210+
- command: |
211+
cd tmp/nf-core-nextbigthing && \
212+
echo "repository_type: pipeline" >> .nf-core.yml && \
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nf-core subworkflows install bam_rseqc
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fake_command: nf-core subworkflows install bam_rseqc
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img_paths:
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- public/images/tools/nf-core-subworkflows-install.svg
217+
- command: |
218+
cd tmp/nf-core-nextbigthing && \
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echo "repository_type: pipeline" >> .nf-core.yml && \
220+
nf-core subworkflows update --all --no-preview
221+
timeout: 30
222+
fake_command: nf-core subworkflows update --all --no-preview
223+
img_paths:
224+
- public/images/tools/nf-core-subworkflows-update.svg
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- command: |
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cd tmp/nf-core-nextbigthing && \
227+
echo "repository_type: pipeline" >> .nf-core.yml && \
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nf-core subworkflows remove bam_rseqc
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fake_command: nf-core subworkflows remove bam_rseqc
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img_paths:
231+
- public/images/tools/nf-core-subworkflows-remove.svg
232+
- command: |
233+
cd tmp/modules && \
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nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force
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img_paths:
236+
- public/images/tools/nf-core-subworkflows-create.svg
237+
- command: cd tmp/modules && nf-core subworkflows test bam_rseqc --no-prompts
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timeout: 30
239+
extra_env:
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PROFILE: 'conda'
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fake_command: nf-core subworkflows test bam_rseqc --no-prompts
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img_paths:
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- public/images/tools/nf-core-subworkflows-test.svg
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- command: cd tmp/modules && nf-core subworkflows lint bam_stats_samtools
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extra_env:
246+
PROFILE: 'conda'
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fake_command: nf-core subworkflows lint bam_stats_samtools
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img_paths:
249+
- public/images/tools/nf-core-subworkflows-lint.svg

‎.github/workflows/add-netlify-link.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ jobs:
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steps:
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- name: Check for changed files
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id: changed-files
15-
uses: tj-actions/changed-files@0874344d6ebbaa00a27da73276ae7162fadcaf69 # v44
15+
uses: tj-actions/changed-files@d6babd6899969df1a11d14c368283ea4436bca78 # v44
1616

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- name: Add Netlify link to PR
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if: steps.changed-files.outputs.all_changed_files != ''

‎.github/workflows/add-tools-api-docs.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@ jobs:
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- name: Run pre-commit
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id: pre-commit
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run: pre-commit run --all-files
59+
run: git add . && pre-commit run --all-files
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continue-on-error: true
6161

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- name: Commit & push changes

‎.github/workflows/broken-link-checker.yml

+21
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,21 @@
1+
name: Check Broken Links
2+
3+
on:
4+
schedule:
5+
- cron: '0 0 * * *' # This will run daily at 00:00
6+
7+
jobs:
8+
linkChecker:
9+
runs-on: ubuntu-latest
10+
steps:
11+
- name: Waiting for 200 from the Netlify Preview
12+
uses: jakepartusch/wait-for-netlify-action@f1e137043864b9ab9034ae3a5adc1c108e3f1a48 # v1.4
13+
id: waitFor200
14+
with:
15+
site_name: 'nf-core'
16+
max_timeout: 600 # 10 Minutes
17+
- name: Check for broken links
18+
uses: JustinBeckwith/linkinator-action@v1
19+
with:
20+
paths: 'https://deploy-preview-${{github.event.pull_request.number}}--nf-core.netlify.app'
21+
recurse: true

‎.github/workflows/build-json-files-and-md-cache.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ jobs:
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id: date
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run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
2020
# Set up the main website repo
21-
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
21+
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
2222
with:
2323
fetch-depth: 0 # Don't do a shallow clone
2424
token: ${{secrets.NF_CORE_BOT_AUTH_TOKEN}} # Needed for pushing back to the repo

‎.github/workflows/fix-linting.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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# Use the @nf-core-bot token to check out so we can push later
16-
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
16+
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
1717
with:
1818
token: ${{ secrets.nf_core_bot_auth_token }}
1919

‎.github/workflows/linting.yml

+2-2
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ jobs:
99
pre-commit:
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runs-on: ubuntu-latest
1111
steps:
12-
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
12+
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
1313
- uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
1414
with:
1515
node-version: 20
@@ -18,7 +18,7 @@ jobs:
1818
vale:
1919
runs-on: ubuntu-latest
2020
steps:
21-
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
21+
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
2222
- name: Install Vale
2323
run: |
2424
wget https://github.com/errata-ai/vale/releases/download/v3.0.5/vale_3.0.5_Linux_64-bit.tar.gz -O vale.tar.gz

‎.github/workflows/playwright.yml

+1-1
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ jobs:
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timeout-minutes: 30
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runs-on: ubuntu-latest
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steps:
17-
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
17+
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
1818
- uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
1919
with:
2020
node-version: 18

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