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update api docs to new structure #3054

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update API docs with new pipeline command structure
  • Loading branch information
mashehu committed Jul 9, 2024
commit 0eaa72002e9c11679fcbbd43ea5c39b1679e2424
15 changes: 9 additions & 6 deletions docs/api/_src/api/index.md
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# API Reference
# nf-core/tools documentation

```{toctree}
:glob: true
:maxdepth: 1
This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/tools) package.

*
```
## Contents

- [Pipeline commands](./pipeline_lint_tests/) (run by `nf-core pipelines lint`)
- [Module commands](./module_lint_tests/) (run by `nf-core modules lint`)
- [Subworkflow commands](./subworkflow_lint_tests/) (run by `nf-core subworkflows lint`)
- [nf-core/tools Python package API reference](./api/)
- [nf-core/tools pipeline commands API referece](./api/pipelines/)
9 changes: 0 additions & 9 deletions docs/api/_src/api/licences.md

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9 changes: 0 additions & 9 deletions docs/api/_src/api/modules.md

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# nf_core.bump_version

```{eval-rst}
.. automodule:: nf_core.bump_version
.. automodule:: nf_core.pipelines.bump_version
:members:
:undoc-members:
:show-inheritance:
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# nf_core.create

```{eval-rst}
.. automodule:: nf_core.create
.. automodule:: nf_core.pipelines.create
:members:
:undoc-members:
:show-inheritance:
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# nf_core.download

```{eval-rst}
.. automodule:: nf_core.download
.. automodule:: nf_core.pipelines.download
:members:
:undoc-members:
:show-inheritance:
8 changes: 8 additions & 0 deletions docs/api/_src/api/pipelines/index.md
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# API Reference
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```{toctree}
:glob: true
:maxdepth: 1

*
```
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# nf_core.launch

```{eval-rst}
.. automodule:: nf_core.launch
.. automodule:: nf_core.pipelines.launch
:members:
:undoc-members:
:show-inheritance:
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# nf_core.lint

:::{seealso}
See the [Lint Tests](../pipeline_lint_tests/index.md) docs for information about specific linting functions.
See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests) docs for information about specific linting functions.
:::

```{eval-rst}
.. automodule:: nf_core.lint
.. automodule:: nf_core.pipelines.lint
:members: run_linting
:undoc-members:
:show-inheritance:
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# nf_core.list

```{eval-rst}
.. automodule:: nf_core.list
.. automodule:: nf_core.pipelines.list
:members:
:undoc-members:
:show-inheritance:
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# nf_core.params_file

```{eval-rst}
.. automodule:: nf_core.params_file
.. automodule:: nf_core.pipelines.params_file
:members:
:undoc-members:
:show-inheritance:
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# nf_core.schema

```{eval-rst}
.. automodule:: nf_core.schema
.. automodule:: nf_core.pipelines.schema
:members:
:undoc-members:
:show-inheritance:
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# nf_core.sync

```{eval-rst}
.. automodule:: nf_core.sync
.. automodule:: nf_core.pipelines.sync
:members:
:undoc-members:
:show-inheritance:
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# nf_core.utils

```{eval-rst}
.. automodule:: nf_core.utils
.. automodule:: nf_core.pipelines.utils
:members:
:undoc-members:
:show-inheritance:
9 changes: 0 additions & 9 deletions docs/api/_src/api/subworkflows.md

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22 changes: 5 additions & 17 deletions docs/api/_src/index.md
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# nf-core/tools documentation

```{toctree}
:caption: 'Contents:'
:glob: true
:hidden: true
:maxdepth: 2

pipeline_lint_tests/index.rst
module_lint_tests/index.rst
subworkflow_lint_tests/index.rst
api/index.rst
```

This documentation is for the `nf-core/tools` package.
This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/tools) package.

## Contents

- [Pipeline code lint tests](pipeline_lint_tests/index.md) (run by `nf-core pipelines lint`)
- [Module code lint tests](module_lint_tests/index.md) (run by `nf-core modules lint`)
- [Subworkflow code lint tests](subworkflow_lint_tests/index.md) (run by `nf-core subworkflows lint`)
- [nf-core/tools Python package API reference](api/index.md)
- [Pipeline code lint tests](./pipeline_lint_tests/) (run by `nf-core pipelines lint`)
- [Module code lint tests](./module_lint_tests/) (run by `nf-core modules lint`)
- [Subworkflow code lint tests](./subworkflow_lint_tests/) (run by `nf-core subworkflows lint`)
- [nf-core/tools Python package API reference](./api/)
17 changes: 10 additions & 7 deletions docs/api/_src/module_lint_tests/index.md
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# Module lint tests
# Module Lint Tests

```{toctree}
:glob: true
:maxdepth: 1

*
```
- [environment_yml](./environment_yml/)
- [main_nf](./main_nf/)
- [meta_yml](./meta_yml/)
- [module_changes](./module_changes/)
- [module_deprecations](./module_deprecations/)
- [module_patch](./module_patch/)
- [module_tests](./module_tests/)
- [module_todos](./module_todos/)
- [module_version](./module_version/)
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md
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# actions_awsfulltest

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.actions_awsfulltest
.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_awsfulltest
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/actions_awstest.md
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# actions_awstest

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.actions_awstest
.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_awstest
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/actions_ci.md
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# actions_ci

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.actions_ci
.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_ci
```
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# actions_schema_validation

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.actions_schema_validation
.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_schema_validation
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/base_config.md
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# base_config

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.base_config
.. automethod:: nf_core.pipelines.lint.PipelineLint.base_config
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/files_exist.md
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# files_exist

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.files_exist
.. automethod:: nf_core.pipelines.lint.PipelineLint.files_exist
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/files_unchanged.md
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# files_unchanged

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.files_unchanged
.. automethod:: nf_core.pipelines.lint.PipelineLint.files_unchanged
```
31 changes: 24 additions & 7 deletions docs/api/_src/pipeline_lint_tests/index.md
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# Pipeline lint tests
# Pipeline Lint Tests

```{toctree}
:glob: true
:maxdepth: 1

*
```
- [actions_awsfulltest](./actions_awsfulltest/)
- [actions_awstest](./actions_awstest/)
- [actions_ci](./actions_ci/)
- [actions_schema_validation](./actions_schema_validation/)
- [base_config](./base_config/)
- [files_exist](./files_exist/)
- [files_unchanged](./files_unchanged/)
- [merge_markers](./merge_markers/)
- [modules_config](./modules_config/)
- [modules_json](./modules_json/)
- [modules_structure](./modules_structure/)
- [multiqc_config](./multiqc_config/)
- [nextflow_config](./nextflow_config/)
- [nfcore_yml](./nfcore_yml/)
- [pipeline_name_conventions](./pipeline_name_conventions/)
- [pipeline_todos](./pipeline_todos/)
- [readme](./readme/)
- [schema_description](./schema_description/)
- [schema_lint](./schema_lint/)
- [schema_params](./schema_params/)
- [system_exit](./system_exit/)
- [template_strings](./template_strings/)
- [version_consistency](./version_consistency/)
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/merge_markers.md
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# merge_markers

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.merge_markers
.. automethod:: nf_core.pipelines.lint.PipelineLint.merge_markers
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/modules_config.md
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# modules_config

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.modules_config
.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_config
```
4 changes: 2 additions & 2 deletions docs/api/_src/pipeline_lint_tests/modules_json.md
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# nextflow_config
# modules_json

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.modules_json
.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_json
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/modules_structure.md
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# modules_structure

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.modules_structure
.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_structure
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/multiqc_config.md
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# multiqc_config

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.multiqc_config
.. automethod:: nf_core.pipelines.lint.PipelineLint.multiqc_config
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/nextflow_config.md
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# nextflow_config

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.nextflow_config
.. automethod:: nf_core.pipelines.lint.PipelineLint.nextflow_config
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/nfcore_yml.md
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# nfcore_yml

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.nfcore_yml
.. automethod:: nf_core.pipelines.lint.PipelineLint.nfcore_yml
```
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# pipeline_name_conventions

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.pipeline_name_conventions
.. automethod:: nf_core.pipelines.lint.PipelineLint.pipeline_name_conventions
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/pipeline_todos.md
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# pipeline_todos

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.pipeline_todos
.. automethod:: nf_core.pipelines.lint.PipelineLint.pipeline_todos
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/readme.md
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@@ -1,5 +1,5 @@
# readme

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.readme
.. automethod:: nf_core.pipelines.lint.PipelineLint.readme
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/schema_description.md
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# schema_description

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.schema_description
.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_description
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/schema_lint.md
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# schema_lint

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.schema_lint
.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_lint
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/schema_params.md
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# schema_params

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.schema_params
.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_params
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/system_exit.md
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# system_exit

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.system_exit
.. automethod:: nf_core.pipelines.lint.PipelineLint.system_exit
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/template_strings.md
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# template_strings

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.template_strings
.. automethod:: nf_core.pipelines.lint.PipelineLint.template_strings
```
2 changes: 1 addition & 1 deletion docs/api/_src/pipeline_lint_tests/version_consistency.md
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# version_consistency

```{eval-rst}
.. automethod:: nf_core.lint.PipelineLint.version_consistency
.. automethod:: nf_core.pipelines.lint.PipelineLint.version_consistency
```
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