Fix typos

Author: mribeirodantas

CHANGELOG.md

@@ -32,7 +32,7 @@
 
 **Highlights**
 
-- Pipeline commands are renamed from `nf-core <comand>` to `nf-core pipelines <command>` to follow the same command structure as modules and subworkflows commands.
+- Pipeline commands are renamed from `nf-core <command>` to `nf-core pipelines <command>` to follow the same command structure as modules and subworkflows commands.
 - More customisation for pipeline templates. The template has been divided into features which can be skipped, e.g. you can create a new pipeline without any traces of FastQC in it.
 - A new Text User Interface app when running `nf-core pipelines create` to help us guide you through the process better (no worries, you can still use the cli if you give all values as parameters)
 - We replaced nf-validation with nf-schema in the pipeline template
@@ -185,7 +185,7 @@
 
 ### Download
 
-- Replace `--tower` with `--platform`. The former will remain for backwards compatability for now but will be removed in a future release. ([#2853](https://github.com/nf-core/tools/pull/2853))
+- Replace `--tower` with `--platform`. The former will remain for backwards compatibility for now but will be removed in a future release. ([#2853](https://github.com/nf-core/tools/pull/2853))
 - Better error message when GITHUB_TOKEN exists but is wrong/outdated
 - New `--tag` argument to add custom tags during a pipeline download ([#2938](https://github.com/nf-core/tools/pull/2938))
 
@@ -494,7 +494,7 @@
 - Refactored the CLI parameters related to container images. Although downloading other images than those of the Singularity/Apptainer container system is not supported for the time being, a generic name for the parameters seemed preferable. So the new parameter `--singularity-cache-index` introduced in [#2247](https://github.com/nf-core/tools/pull/2247) has been renamed to `--container-cache-index` prior to release ([#2336](https://github.com/nf-core/tools/pull/2336)).
 - To address issue [#2311](https://github.com/nf-core/tools/issues/2311), a new parameter `--container-library` was created allowing to specify the container library (registry) from which container images in OCI format (Docker) should be pulled ([#2336](https://github.com/nf-core/tools/pull/2336)).
 - Container detection in configs was improved. This allows for DSL2-like container definitions inside the container parameter value provided to process scopes [#2346](https://github.com/nf-core/tools/pull/2346).
-- Add apptainer to the list of false positve container strings ([#2353](https://github.com/nf-core/tools/pull/2353)).
+- Add apptainer to the list of false positive container strings ([#2353](https://github.com/nf-core/tools/pull/2353)).
 
 #### Updated CLI parameters
 
@@ -564,7 +564,7 @@ _In addition, `-r` / `--revision` has been changed to a parameter that can be pr
 
 - Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175) & [#2177](https://github.com/nf-core/tools/pull/2177))
 - Removed the `nf-core modules mulled` command and all its code dependencies ([2199](https://github.com/nf-core/tools/pull/2199)).
-- Take into accout the provided `--git_remote` URL when linting all modules ([2243](https://github.com/nf-core/tools/pull/2243)).
+- Take into account the provided `--git_remote` URL when linting all modules ([2243](https://github.com/nf-core/tools/pull/2243)).
 
 ### Subworkflows
 
@@ -973,7 +973,7 @@ Please note that there are many excellent integrations for Prettier available, f
   - `input:` / `output:` not being specified in module
   - Allow for containers from other biocontainers resource as defined [here](https://github.com/nf-core/modules/blob/cde237e7cec07798e5754b72aeca44efe89fc6db/modules/cat/fastq/main.nf#L7-L8)
 - Fixed traceback when using `stageAs` syntax as defined [here](https://github.com/nf-core/modules/blob/cde237e7cec07798e5754b72aeca44efe89fc6db/modules/cat/fastq/main.nf#L11)
-- Added `nf-core schema docs` command to output pipline parameter documentation in Markdown format for inclusion in GitHub and other documentation systems ([#741](https://github.com/nf-core/tools/issues/741))
+- Added `nf-core schema docs` command to output pipeline parameter documentation in Markdown format for inclusion in GitHub and other documentation systems ([#741](https://github.com/nf-core/tools/issues/741))
 - Allow conditional process execution from the configuration file ([#1393](https://github.com/nf-core/tools/pull/1393))
 - Add linting for when condition([#1397](https://github.com/nf-core/tools/pull/1397))
 - Added modules ignored table to `nf-core modules bump-versions`. ([#1234](https://github.com/nf-core/tools/issues/1234))
@@ -992,7 +992,7 @@ Please note that there are many excellent integrations for Prettier available, f
 
 - Update repo logos to utilize [GitHub's `#gh-light/dark-mode-only`](https://docs.github.com/en/github/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax#specifying-the-theme-an-image-is-shown-to), to switch between logos optimized for light or dark themes. The old repo logos have to be removed (in `docs/images` and `assets/`).
 - Deal with authentication with private repositories
-- Bump minimun Nextflow version to 21.10.3
+- Bump minimum Nextflow version to 21.10.3
 - Convert pipeline template to updated Nextflow DSL2 syntax
 - Solve circular import when importing `nf_core.modules.lint`
 - Disable cache in `nf_core.utils.fetch_wf_config` while performing `test_wf_use_local_configs`.
@@ -1014,15 +1014,15 @@ Please note that there are many excellent integrations for Prettier available, f
   - Defaults in `nextflow.config` must now match the variable _type_ specified in the schema
   - If you want the parameter to not have a default value, use `null`
   - Strings set to `false` or an empty string in `nextflow.config` will now fail linting
-- Bump minimun Nextflow version to 21.10.3
-- Changed `questionary` `ask()` to `unsafe_ask()` to not catch `KeyboardInterupts` ([#1237](https://github.com/nf-core/tools/issues/1237))
+- Bump minimum Nextflow version to 21.10.3
+- Changed `questionary` `ask()` to `unsafe_ask()` to not catch `KeyboardInterrupts` ([#1237](https://github.com/nf-core/tools/issues/1237))
 - Fixed bug in `nf-core launch` due to revisions specified with `-r` not being added to nextflow command. ([#1246](https://github.com/nf-core/tools/issues/1246))
 - Update regex in `readme` test of `nf-core lint` to agree with the pipeline template ([#1260](https://github.com/nf-core/tools/issues/1260))
 - Update 'fix' message in `nf-core lint` to conform to the current command line options. ([#1259](https://github.com/nf-core/tools/issues/1259))
 - Fixed bug in `nf-core list` when `NXF_HOME` is set
 - Run CI test used to create and lint/run the pipeline template with minimum and latest edge release of NF ([#1304](https://github.com/nf-core/tools/issues/1304))
 - New YAML issue templates for tools bug reports and feature requests, with a much richer interface ([#1165](https://github.com/nf-core/tools/pull/1165))
-- Handle synax errors in Nextflow config nicely when running `nf-core schema build` ([#1267](https://github.com/nf-core/tools/pull/1267))
+- Handle syntax errors in Nextflow config nicely when running `nf-core schema build` ([#1267](https://github.com/nf-core/tools/pull/1267))
 - Erase temporary files and folders while performing Python tests (pytest)
 - Remove base `Dockerfile` used for DSL1 pipeline container builds
 - Run tests with Python 3.10
@@ -1128,7 +1128,7 @@ This marks the first Nextflow DSL2-centric release of `tools` which means that s
 - Updated `nf-core modules install` and `modules.json` to work with new directory structure ([#1159](https://github.com/nf-core/tools/issues/1159))
 - Updated `nf-core modules remove` to work with new directory structure [[#1159](https://github.com/nf-core/tools/issues/1159)]
 - Restructured code and removed old table style in `nf-core modules list`
-- Fixed bug causing `modules.json` creation to loop indefinitly
+- Fixed bug causing `modules.json` creation to loop indefinitely
 - Added `--all` flag to `nf-core modules install`
 - Added `remote` and `local` subcommands to `nf-core modules list`
 - Fix bug due to restructuring in modules template
@@ -1449,7 +1449,7 @@ making a pull-request. See [`.github/CONTRIBUTING.md`](.github/CONTRIBUTING.md)
 ### Linting
 
 - Refactored PR branch tests to be a little clearer.
-- Linting error docs explain how to add an additional branch protecton rule to the `branch.yml` GitHub Actions workflow.
+- Linting error docs explain how to add an additional branch protection rule to the `branch.yml` GitHub Actions workflow.
 - Adapted linting docs to the new PR branch tests.
 - Failure for missing the readme bioconda badge is now a warn, in case this badge is not relevant
 - Added test for template `{{ cookiecutter.var }}` placeholders

CITATION.cff

@@ -24,7 +24,7 @@ version: 2.4.1
 doi: 10.1038/s41587-020-0439-x
 date-released: 2022-05-16
 url: https://github.com/nf-core/tools
-prefered-citation:
+preferred-citation:
   type: article
   authors:
     - family-names: Ewels

docs/api/_src/api/index.md

@@ -8,4 +8,4 @@ This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/t
 - [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/)
+  - [nf-core/tools pipeline commands API reference](./api/pipelines/)

nf_core/__main__.py

@@ -1590,7 +1590,7 @@ def command_subworkflows_remove(ctx, directory, subworkflow):
     "limit_output",
     is_flag=True,
     default=False,
-    help="Limit ouput to only the difference in main.nf",
+    help="Limit output to only the difference in main.nf",
 )
 @click.option(
     "-a",

nf_core/components/update.py

@@ -55,7 +55,7 @@ def __init__(
         self.branch = branch
 
     def _parameter_checks(self):
-        """Checks the compatibilty of the supplied parameters.
+        """Checks the compatibility of the supplied parameters.
 
         Raises:
             UserWarning: if any checks fail.

nf_core/pipeline-template/docs/usage.md

@@ -146,7 +146,7 @@ The pipeline also dynamically loads configurations from [https://github.com/nf-c
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
-If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment.
 
 {%- if test_config %}
 

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -258,7 +258,7 @@ def toolBibliographyText() {
 }
 
 def methodsDescriptionText(mqc_methods_yaml) {
-    // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+    // Convert  to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file
     def meta = [:]
     meta.workflow = workflow.toMap()
     meta["manifest_map"] = workflow.manifest.toMap()

nf_core/pipelines/create/basicdetails.py

@@ -69,7 +69,7 @@ def compose(self) -> ComposeResult:
     @on(Input.Submitted)
     def show_exists_warn(self):
         """Check if the pipeline exists on every input change or submitted.
-        If the pipeline exists, show warning message saying that it will be overriden."""
+        If the pipeline exists, show warning message saying that it will be overridden."""
         config = {}
         for text_input in self.query("TextInput"):
             this_input = text_input.query_one(Input)

nf_core/pipelines/create/finaldetails.py

@@ -85,7 +85,7 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
     @on(Input.Submitted)
     def show_exists_warn(self):
         """Check if the pipeline exists on every input change or submitted.
-        If the pipeline exists, show warning message saying that it will be overriden."""
+        If the pipeline exists, show warning message saying that it will be overridden."""
         outdir = ""
         for text_input in self.query("TextInput"):
             this_input = text_input.query_one(Input)

nf_core/pipelines/create/githubrepo.py

@@ -67,7 +67,7 @@ def compose(self) -> ComposeResult:
             yield TextInput(
                 "repo_org",
                 "Organisation name",
-                "The name of the organisation where the GitHub repo will be cretaed",
+                "The name of the organisation where the GitHub repo will be created",
                 default=self.parent.TEMPLATE_CONFIG.org,
                 classes="column",
             )

nf_core/pipelines/create/template_features.yml

@@ -101,7 +101,7 @@ github_badges:
 nf_core_configs:
   skippable_paths: False
   short_description: "Add configuration files"
-  description: "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions"
+  description: "The pipeline will include configuration profiles containing custom parameters required to run nf-core pipelines at different institutions"
   help_text: |
     Nf-core has a repository with a collection of configuration profiles.
 

nf_core/pipelines/download.py

@@ -1692,7 +1692,7 @@ def tidy_tags_and_branches(self):
                         self.repo.create_head("latest", "latest")  # create a new head for latest
                         self.checkout("latest")
                     else:
-                        # desired revisions may contain arbitrary branch names that do not correspond to valid sematic versioning patterns.
+                        # desired revisions may contain arbitrary branch names that do not correspond to valid semantic versioning patterns.
                         valid_versions = [
                             Version(v) for v in desired_revisions if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v)
                         ]

nf_core/pipelines/launch.py

@@ -276,7 +276,7 @@ def merge_nxf_flag_schema(self):
             self.schema_obj.schema["definitions"] = {}
             self.schema_obj.schema["definitions"].update(self.nxf_flag_schema)
             self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/definitions/coreNextflow"})
-        # Add the new defintion to the allOf key so that it's included in validation
+        # Add the new definition to the allOf key so that it's included in validation
         # Put it at the start of the list so that it comes first
 
     def prompt_web_gui(self):
@@ -434,7 +434,7 @@ def prompt_param(self, param_id, param_obj, is_required, answers):
         question = self.single_param_to_questionary(param_id, param_obj, answers)
         answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
 
-        # If required and got an empty reponse, ask again
+        # If required and got an empty response, ask again
         while isinstance(answer[param_id], str) and answer[param_id].strip() == "" and is_required:
             log.error(f"'--{param_id}' is required")
             answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
@@ -457,7 +457,7 @@ def prompt_group(self, group_id, group_obj):
         Prompt for edits to a group of parameters (subschema in 'definitions')
 
         Args:
-          group_id: Paramater ID (string)
+          group_id: Parameter ID (string)
           group_obj: JSON Schema keys (dict)
 
         Returns:

nf_core/pipelines/refgenie.py

@@ -151,7 +151,7 @@ def update_config(rgc):
     - the NXF_REFGENIE_PATH environment variable
     - otherwise defaults to: $NXF_HOME/nf-core/refgenie_genomes.config
 
-    Additionaly, an 'includeConfig' statement is added to the file $NXF_HOME/config
+    Additionally, an 'includeConfig' statement is added to the file $NXF_HOME/config
     """
 
     # Compile nextflow refgenie_genomes.config from refgenie config

nf_core/utils.py

@@ -414,7 +414,7 @@ def wait_cli_function(poll_func: Callable[[], bool], refresh_per_second: int = 2
        refresh_per_second (int): Refresh this many times per second. Default: 20.
 
     Returns:
-       None. Just sits in an infite loop until the function returns True.
+       None. Just sits in an infinite loop until the function returns True.
     """
     try:
         spinner = Spinner("dots2", "Use ctrl+c to stop waiting and force exit.")
@@ -433,7 +433,7 @@ def poll_nfcore_web_api(api_url: str, post_data: Optional[Dict] = None) -> Dict:
 
     Takes argument api_url for URL
 
-    Expects API reponse to be valid JSON and contain a top-level 'status' key.
+    Expects API response to be valid JSON and contain a top-level 'status' key.
     """
     # Run without requests_cache so that we get the updated statuses
     with requests_cache.disabled():
@@ -717,12 +717,12 @@ def parse_anaconda_licence(anaconda_response, version=None):
         license = re.sub(r"GNU GENERAL PUBLIC LICENSE", "GPL", license, flags=re.IGNORECASE)
         license = license.replace("GPL-", "GPLv")
         license = re.sub(r"GPL\s*([\d\.]+)", r"GPL v\1", license)  # Add v prefix to GPL version if none found
-        license = re.sub(r"GPL\s*v(\d).0", r"GPL v\1", license)  # Remove superflous .0 from GPL version
+        license = re.sub(r"GPL\s*v(\d).0", r"GPL v\1", license)  # Remove superfluous .0 from GPL version
         license = re.sub(r"GPL \(([^\)]+)\)", r"GPL \1", license)
         license = re.sub(r"GPL\s*v", "GPL v", license)  # Normalise whitespace to one space between GPL and v
         license = re.sub(r"\s*(>=?)\s*(\d)", r" \1\2", license)  # Normalise whitespace around >= GPL versions
         license = license.replace("Clause", "clause")  # BSD capitilisation
-        license = re.sub(r"-only$", "", license)  # Remove superflous GPL "only" version suffixes
+        license = re.sub(r"-only$", "", license)  # Remove superfluous GPL "only" version suffixes
         clean_licences.append(license)
     return clean_licences
 

tests/pipelines/test_launch.py

@@ -129,7 +129,7 @@ def test_launch_web_gui_missing_keys(self, mock_poll_nfcore_web_api):
 
     @mock.patch(
         "nf_core.utils.poll_nfcore_web_api",
-        side_effect=[{"api_url": "foo", "web_url": "bar", "status": "recieved"}],
+        side_effect=[{"api_url": "foo", "web_url": "bar", "status": "received"}],
     )
     @mock.patch("webbrowser.open")
     @mock.patch("nf_core.utils.wait_cli_function")
@@ -298,7 +298,7 @@ def test_strip_default_params(self):
         assert self.launcher.schema_obj.input_params == {"input": "custom_input"}
 
     def test_build_command_empty(self):
-        """Test the functionality to build a nextflow command - nothing customsied"""
+        """Test the functionality to build a nextflow command - nothing customised"""
         self.launcher.get_pipeline_schema()
         self.launcher.merge_nxf_flag_schema()
         self.launcher.build_command()

tests/pipelines/test_schema.py

@@ -49,7 +49,7 @@ def test_load_lint_schema(self):
         self.schema_obj.load_lint_schema()
 
     def test_load_lint_schema_nofile(self):
-        """Check that linting raises properly if a non-existant file is given"""
+        """Check that linting raises properly if a non-existent file is given"""
         with pytest.raises(RuntimeError):
             self.schema_obj.get_schema_path("fake_file")
 
@@ -384,7 +384,7 @@ def __init__(self, data, status_code):
             return MockResponse(response_data, 200)
 
         if kwargs["url"] == "valid_url_success":
-            response_data = {"status": "recieved", "api_url": "https://nf-co.re", "web_url": "https://nf-co.re"}
+            response_data = {"status": "received", "api_url": "https://nf-co.re", "web_url": "https://nf-co.re"}
             return MockResponse(response_data, 200)
 
     @mock.patch("requests.post", side_effect=mocked_requests_post)