From 6ddd824fd0fcbae83579075eaf72393c8d3d71e5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 16 Oct 2024 11:13:19 +0200 Subject: [PATCH 01/28] write only relevant fields in `.nf-core.yml` --- nf_core/utils.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/nf_core/utils.py b/nf_core/utils.py index 87dd307e7..bad733cd4 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1115,6 +1115,23 @@ def __getitem__(self, item: str) -> Any: def get(self, item: str, default: Any = None) -> Any: return getattr(self, item, default) + def model_dump(self, **kwargs) -> Dict[str, Any]: + # Get the initial data + data = super().model_dump(**kwargs) + + if self.repository_type == "modules": + # Fields to exclude for modules + fields_to_exclude = ["template", "update"] + else: # pipeline + # Fields to exclude for pipeline + fields_to_exclude = ["bump_version"] + + # Remove the fields based on repository_type + for field in fields_to_exclude: + data.pop(field, None) + + return data + def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path], Optional[NFCoreYamlConfig]]: """ From 313a4d1b20f4bab6c19a78b4d6fe2028348b9a2c Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 16 Oct 2024 13:59:08 +0200 Subject: [PATCH 02/28] switch from docstrings to Field descsriptions --- nf_core/utils.py | 46 +++++++++++++++++++++++++++------------------- 1 file changed, 27 insertions(+), 19 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index bad733cd4..6ba1c8c5c 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -19,7 +19,7 @@ import time from contextlib import contextmanager from pathlib import Path -from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union +from typing import Any, Callable, Dict, Generator, List, Literal, Optional, Tuple, Union import git import prompt_toolkit.styles @@ -30,7 +30,7 @@ import rich.markup import yaml from packaging.version import Version -from pydantic import BaseModel, ValidationError, field_validator +from pydantic import BaseModel, Field, ValidationError, field_validator from rich.live import Live from rich.spinner import Spinner @@ -1094,20 +1094,28 @@ def get(self, item: str, default: Any = None) -> Any: class NFCoreYamlConfig(BaseModel): """.nf-core.yml configuration file schema""" - repository_type: str - """ Type of repository: pipeline or modules """ - nf_core_version: Optional[str] = None - """ Version of nf-core/tools used to create/update the pipeline""" - org_path: Optional[str] = None - """ Path to the organisation's modules repository (used for modules repo_type only) """ - lint: Optional[LintConfigType] = None - """ Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation """ - template: Optional[NFCoreTemplateConfig] = None - """ Pipeline template configuration """ - bump_version: Optional[Dict[str, bool]] = None - """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information.""" - update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = None - """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information.""" + repository_type: Literal["pipeline", "modules"] = Field(..., description="Type of repository") + nf_core_version: Optional[str] = Field( + None, description="Version of nf-core/tools used to create/update the pipeline" + ) + org_path: Optional[str] = Field( + None, description="Path to the organisation's modules repository (used for modules repo_type only)" + ) + lint: Optional[LintConfigType] = Field( + None, + description="Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation", + ) + template: Optional[NFCoreTemplateConfig] = Field( + None, description="Pipeline template configuration", exclude=repository_type == "modules" + ) + bump_version: Optional[Dict[str, bool]] = Field( + None, + description="Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information.", + ) + update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = Field( + None, + description="Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information.", + ) def __getitem__(self, item: str) -> Any: return getattr(self, item) @@ -1117,7 +1125,7 @@ def get(self, item: str, default: Any = None) -> Any: def model_dump(self, **kwargs) -> Dict[str, Any]: # Get the initial data - data = super().model_dump(**kwargs) + config = super().model_dump(**kwargs) if self.repository_type == "modules": # Fields to exclude for modules @@ -1128,9 +1136,9 @@ def model_dump(self, **kwargs) -> Dict[str, Any]: # Remove the fields based on repository_type for field in fields_to_exclude: - data.pop(field, None) + config.pop(field, None) - return data + return config def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path], Optional[NFCoreYamlConfig]]: From 16e6ff29e376aa5b0e08818862cc403db66508cb Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 16 Oct 2024 12:00:53 +0000 Subject: [PATCH 03/28] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9c19a34ee..337321732 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220)) - create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226)) +- Fix pydantic dump ([#3227](https://github.com/nf-core/tools/pull/3227)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] From 87ab7eefc3fbb3d4fd0f4b206675f3f37e18a36a Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 16 Oct 2024 15:51:30 +0200 Subject: [PATCH 04/28] update test to new error --- tests/pipelines/lint/test_nfcore_yml.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/pipelines/lint/test_nfcore_yml.py b/tests/pipelines/lint/test_nfcore_yml.py index 955c00da8..b49b60436 100644 --- a/tests/pipelines/lint/test_nfcore_yml.py +++ b/tests/pipelines/lint/test_nfcore_yml.py @@ -33,7 +33,9 @@ def test_nfcore_yml_fail_repo_type(self): with open(self.nf_core_yml, "w") as fh: fh.write(new_content) lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) - lint_obj._load() + # assert that it raises assertion error + with self.assertRaises(AssertionError): + lint_obj._load() results = lint_obj.nfcore_yml() assert "Repository type in `.nf-core.yml` is not valid." in str(results["failed"]) assert len(results.get("warned", [])) == 0 From ff32ff114895e5858c1d825c30840b392db76518 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 18 Oct 2024 07:31:41 +0000 Subject: [PATCH 05/28] chore(deps): update dependency prompt_toolkit to <=3.0.48 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index f167a5580..b7f1c39ca 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ packaging pillow pdiff pre-commit -prompt_toolkit<=3.0.36 +prompt_toolkit<=3.0.48 pydantic>=2.2.1 pyyaml questionary>=2.0.1 From 5d56b43976a145b5a24f2a3a2572c3f638872e8c Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 18 Oct 2024 07:31:47 +0000 Subject: [PATCH 06/28] chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 67aa3204c..f8b13439e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.9 + rev: v0.7.0 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 09181a7dd789341802fc1fa3876429c6de79af9f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 18 Oct 2024 07:31:52 +0000 Subject: [PATCH 07/28] chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 67aa3204c..252439656 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,7 +19,7 @@ repos: alias: ec - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.11.2" + rev: "v1.12.0" hooks: - id: mypy additional_dependencies: From 09a47327466533f4cd87dce25116e0a82cd14927 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 18 Oct 2024 07:32:43 +0000 Subject: [PATCH 08/28] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 364a079a7..3683b8f50 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220)) - create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226)) +- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] From f62edb00f1264e74cc62eb6cc75d8d9f9e2a021d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 18 Oct 2024 07:32:50 +0000 Subject: [PATCH 09/28] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 364a079a7..df9494197 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220)) - create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226)) +- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 ([#3230](https://github.com/nf-core/tools/pull/3230)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] From 250e63bf3beda137261a3ba291604916c2c70c52 Mon Sep 17 00:00:00 2001 From: Marcel Ribeiro-Dantas Date: Sat, 19 Oct 2024 10:36:26 -0300 Subject: [PATCH 10/28] Fix typos --- CHANGELOG.md | 22 +++++++++---------- CITATION.cff | 2 +- docs/api/_src/api/index.md | 2 +- nf_core/__main__.py | 2 +- nf_core/components/update.py | 2 +- nf_core/pipeline-template/docs/usage.md | 2 +- .../utils_nfcore_pipeline_pipeline/main.nf | 2 +- nf_core/pipelines/create/basicdetails.py | 2 +- nf_core/pipelines/create/finaldetails.py | 2 +- nf_core/pipelines/create/githubrepo.py | 2 +- .../pipelines/create/template_features.yml | 2 +- nf_core/pipelines/download.py | 2 +- nf_core/pipelines/launch.py | 6 ++--- nf_core/pipelines/refgenie.py | 2 +- nf_core/utils.py | 8 +++---- tests/pipelines/test_launch.py | 4 ++-- tests/pipelines/test_schema.py | 4 ++-- tests/test_utils.py | 2 +- 18 files changed, 35 insertions(+), 35 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5ad584d68..8491b9366 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,7 +32,7 @@ **Highlights** -- Pipeline commands are renamed from `nf-core ` to `nf-core pipelines ` to follow the same command structure as modules and subworkflows commands. +- Pipeline commands are renamed from `nf-core ` to `nf-core pipelines ` 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 diff --git a/CITATION.cff b/CITATION.cff index 017666c01..d1246b69d 100644 --- a/CITATION.cff +++ b/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 diff --git a/docs/api/_src/api/index.md b/docs/api/_src/api/index.md index 035a89688..f25e166a9 100644 --- a/docs/api/_src/api/index.md +++ b/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/) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 08589fc24..94c15521c 100644 --- a/nf_core/__main__.py +++ b/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", diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 3e4694adc..bf176fb6d 100644 --- a/nf_core/components/update.py +++ b/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. diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md index ae2761797..7034bb8d6 100644 --- a/nf_core/pipeline-template/docs/usage.md +++ b/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 %} diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index 78fed1fcf..263eca55d 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/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() diff --git a/nf_core/pipelines/create/basicdetails.py b/nf_core/pipelines/create/basicdetails.py index 09484fa2e..2bd2ea1c7 100644 --- a/nf_core/pipelines/create/basicdetails.py +++ b/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) diff --git a/nf_core/pipelines/create/finaldetails.py b/nf_core/pipelines/create/finaldetails.py index bd15cf9dd..dad81689a 100644 --- a/nf_core/pipelines/create/finaldetails.py +++ b/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) diff --git a/nf_core/pipelines/create/githubrepo.py b/nf_core/pipelines/create/githubrepo.py index 99e7b09ab..b37dfb617 100644 --- a/nf_core/pipelines/create/githubrepo.py +++ b/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", ) diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index 3eb654726..0a3180286 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/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. diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index b9028d4b3..917665ff3 100644 --- a/nf_core/pipelines/download.py +++ b/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) ] diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py index a80639ea9..c527e8a7a 100644 --- a/nf_core/pipelines/launch.py +++ b/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: diff --git a/nf_core/pipelines/refgenie.py b/nf_core/pipelines/refgenie.py index 426ca5eb7..1b3e93606 100644 --- a/nf_core/pipelines/refgenie.py +++ b/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 diff --git a/nf_core/utils.py b/nf_core/utils.py index 068da22de..c11a3c629 100644 --- a/nf_core/utils.py +++ b/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 diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py index 5e230528a..3eafc3423 100644 --- a/tests/pipelines/test_launch.py +++ b/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() diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py index 2abaf07bd..fdbef76ef 100644 --- a/tests/pipelines/test_schema.py +++ b/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) diff --git a/tests/test_utils.py b/tests/test_utils.py index bde561d95..b13c8eb37 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -113,7 +113,7 @@ def test_pip_package_pass(self): @mock.patch("requests.get") def test_pip_package_timeout(self, mock_get): """Tests the PyPi connection and simulates a request timeout, which should - return in an addiional warning in the linting""" + return in an additional warning in the linting""" # Define the behaviour of the request get mock mock_get.side_effect = requests.exceptions.Timeout() # Now do the test From 9b078db3e746970f32ef2cd8084150ddeb8063f9 Mon Sep 17 00:00:00 2001 From: Marcel Ribeiro-Dantas Date: Sat, 19 Oct 2024 10:46:39 -0300 Subject: [PATCH 11/28] Fix typos (second round) --- CHANGELOG.md | 4 ++-- nf_core/pipeline-template/conf/base.config | 2 +- nf_core/pipeline-template/docs/usage.md | 2 +- nf_core/pipelines/refgenie.py | 2 +- nf_core/utils.py | 2 +- tests/pipelines/test_download.py | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8491b9366..4f23989f7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -528,7 +528,7 @@ _In addition, `-r` / `--revision` has been changed to a parameter that can be pr - GitPod base image: Always self-update to the latest version of Nextflow. Add [pre-commit](https://pre-commit.com/) dependency. - GitPod configs: Update Nextflow as an init task, init pre-commit in pipeline config. - Refgenie: Create `nxf_home/nf-core/refgenie_genomes.config` path if it doesn't exist ([#2312](https://github.com/nf-core/tools/pull/2312)) -- Add CI tests to test running a pipeline whe it's created from a template skipping different areas +- Add CI tests to test running a pipeline when it's created from a template skipping different areas ## [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27] @@ -1209,7 +1209,7 @@ This marks the first Nextflow DSL2-centric release of `tools` which means that s ## [v1.13.2 - Copper Crocodile CPR :crocodile: :face_with_head_bandage:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-23] - Make module template pass the EC linter [[#953](https://github.com/nf-core/tools/pull/953)] -- Added better logging message if a user doesn't specificy the directory correctly with `nf-core modules` commands [[#942](https://github.com/nf-core/tools/pull/942)] +- Added better logging message if a user doesn't specify the directory correctly with `nf-core modules` commands [[#942](https://github.com/nf-core/tools/pull/942)] - Fixed parameter validation bug caused by JSONObject [[#937](https://github.com/nf-core/tools/issues/937)] - Fixed template creation error regarding file permissions [[#932](https://github.com/nf-core/tools/issues/932)] - Split the `create-lint-wf` tests up into separate steps in GitHub Actions to make the CI results easier to read diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config index fa292339e..16a4fe6cd 100644 --- a/nf_core/pipeline-template/conf/base.config +++ b/nf_core/pipeline-template/conf/base.config @@ -20,7 +20,7 @@ process { maxErrors = '-1' // Process-specific resource requirements - // NOTE - Please try and re-use the labels below as much as possible. + // NOTE - Please try and reuse the labels below as much as possible. // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md index 7034bb8d6..67fda7865 100644 --- a/nf_core/pipeline-template/docs/usage.md +++ b/nf_core/pipeline-template/docs/usage.md @@ -116,7 +116,7 @@ First, go to the [{{ name }} releases page](https://github.com/{{ name }}/releas This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. {% if multiqc %}For example, at the bottom of the MultiQC reports.{% endif %} -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. +To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. :::tip If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. diff --git a/nf_core/pipelines/refgenie.py b/nf_core/pipelines/refgenie.py index 1b3e93606..46197e9cc 100644 --- a/nf_core/pipelines/refgenie.py +++ b/nf_core/pipelines/refgenie.py @@ -144,7 +144,7 @@ def update_config(rgc): This function is executed after running 'refgenie pull /' The refgenie config file is transformed into a nextflow.config file, which is used to - overwrited the 'refgenie_genomes.config' file. + overwrite the 'refgenie_genomes.config' file. The path to the target config file is inferred from the following options, in order: - the 'nextflow_config' attribute in the refgenie config file diff --git a/nf_core/utils.py b/nf_core/utils.py index c11a3c629..da8f69d5a 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -721,7 +721,7 @@ def parse_anaconda_licence(anaconda_response, version=None): 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 = license.replace("Clause", "clause") # BSD capitalisation license = re.sub(r"-only$", "", license) # Remove superfluous GPL "only" version suffixes clean_licences.append(license) return clean_licences diff --git a/tests/pipelines/test_download.py b/tests/pipelines/test_download.py index a898d37b7..e55258252 100644 --- a/tests/pipelines/test_download.py +++ b/tests/pipelines/test_download.py @@ -516,7 +516,7 @@ def test_singularity_image_filenames(self, tmp_path): result = download_obj.singularity_image_filenames("nf-core/ubuntu:20.04") assert result[0].endswith("/cachedir/nf-core-ubuntu-20.04.img") - ## Test phase III: Container wil lbe cached but also copied to out_path + ## Test phase III: Container will be cached but also copied to out_path # out_path: str, Path to cache # cache_path: str, Path to cache download_obj.container_cache_utilisation = "copy" From 5fea053f0e6b3d4bc3f63dff4ef0a91bbcb817c2 Mon Sep 17 00:00:00 2001 From: Marcel Ribeiro-Dantas Date: Sat, 19 Oct 2024 10:50:42 -0300 Subject: [PATCH 12/28] Undo accidental typos fixes --- tests/pipelines/test_launch.py | 2 +- tests/pipelines/test_schema.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py index 3eafc3423..ed23872f6 100644 --- a/tests/pipelines/test_launch.py +++ b/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": "received"}], + side_effect=[{"api_url": "foo", "web_url": "bar", "status": "recieved"}], ) @mock.patch("webbrowser.open") @mock.patch("nf_core.utils.wait_cli_function") diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py index fdbef76ef..ab543d8b9 100644 --- a/tests/pipelines/test_schema.py +++ b/tests/pipelines/test_schema.py @@ -384,7 +384,7 @@ def __init__(self, data, status_code): return MockResponse(response_data, 200) if kwargs["url"] == "valid_url_success": - response_data = {"status": "received", "api_url": "https://nf-co.re", "web_url": "https://nf-co.re"} + response_data = {"status": "recieved", "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) From 08c43f5667db812708a5f01f1ea6ad491309732d Mon Sep 17 00:00:00 2001 From: Marcel Ribeiro-Dantas Date: Sat, 19 Oct 2024 10:58:46 -0300 Subject: [PATCH 13/28] Fix typos (third round) --- nf_core/modules/lint/main_nf.py | 2 +- nf_core/pipelines/launch.py | 2 +- nf_core/pipelines/schema.py | 4 ++-- nf_core/utils.py | 4 ++-- .../__snapshots__/test_create_app/test_github_details.svg | 2 +- .../__snapshots__/test_create_app/test_type_custom.svg | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index 54a69b113..df5a48d5b 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -269,7 +269,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar): url = None line = raw_line.strip(" \n'\"}:") - # Catch preceeding "container " + # Catch preceding "container " if line.startswith("container"): line = line.replace("container", "").strip(" \n'\"}:") diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py index c527e8a7a..aab0ec428 100644 --- a/nf_core/pipelines/launch.py +++ b/nf_core/pipelines/launch.py @@ -316,7 +316,7 @@ def launch_web_gui(self): raise AssertionError('"api_url" not in web_response') if "web_url" not in web_response: raise AssertionError('"web_url" not in web_response') - # DO NOT FIX THIS TYPO. Needs to stay in sync with the website. Maintaining for backwards compatability. + # DO NOT FIX THIS TYPO. Needs to stay in sync with the website. Maintaining for backwards compatibility. if web_response["status"] != "recieved": raise AssertionError( f'web_response["status"] should be "recieved", but it is "{web_response["status"]}"' diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 127aa123d..2c1eb397f 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -51,7 +51,7 @@ def __init__(self): self.defs_notation = None self.ignored_params = [] - # Update the validation plugin code everytime the schema gets changed + # Update the validation plugin code every time the schema gets changed def set_schema_filename(self, schema: str) -> None: self._schema_filename = schema self._update_validation_plugin_from_config() @@ -969,7 +969,7 @@ def launch_web_builder(self): raise AssertionError('"api_url" not in web_response') if "web_url" not in web_response: raise AssertionError('"web_url" not in web_response') - # DO NOT FIX THIS TYPO. Needs to stay in sync with the website. Maintaining for backwards compatability. + # DO NOT FIX THIS TYPO. Needs to stay in sync with the website. Maintaining for backwards compatibility. if web_response["status"] != "recieved": raise AssertionError( f'web_response["status"] should be "recieved", but it is "{web_response["status"]}"' diff --git a/nf_core/utils.py b/nf_core/utils.py index 1e662b4c8..0b3c53f3a 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -607,11 +607,11 @@ def request_retry(self, url, post_data=None): while True: # GET request if post_data is None: - log.debug(f"Seding GET request to {url}") + log.debug(f"Sending GET request to {url}") r = self.get(url=url) # POST request else: - log.debug(f"Seding POST request to {url}") + log.debug(f"Sending POST request to {url}") r = self.post(url=url, json=post_data) # Failed but expected - try again diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg index 77a293fb7..708e95b1d 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -241,7 +241,7 @@ The name of the organisation where the The name of the new GitHub repository -GitHub repo will be cretaed +GitHub repo will be created ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ ▊nf-core                               ▎▊mypipeline                            ▎ ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index cff030915..f2607746d 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -258,7 +258,7 @@ ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ profiles containing  custom parameters  -requried to run  +required to run  nf-core pipelines at  different institutions From d5fb5f82c55114bedf297bf07bd4ff11bf4b8caa Mon Sep 17 00:00:00 2001 From: Marcel Ribeiro-Dantas Date: Sat, 19 Oct 2024 12:14:03 -0300 Subject: [PATCH 14/28] Update textual snapshots --- .../test_create_app/test_github_details.svg | 258 +++++++++--------- .../test_create_app/test_type_custom.svg | 254 ++++++++--------- 2 files changed, 256 insertions(+), 256 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg index 708e95b1d..03eeaab0d 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -19,258 +19,258 @@ font-weight: 700; } - .terminal-661775892-matrix { + .terminal-660530708-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-661775892-title { + .terminal-660530708-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-661775892-r1 { fill: #c5c8c6 } -.terminal-661775892-r2 { fill: #e3e3e3 } -.terminal-661775892-r3 { fill: #989898 } -.terminal-661775892-r4 { fill: #e1e1e1 } -.terminal-661775892-r5 { fill: #4ebf71;font-weight: bold } -.terminal-661775892-r6 { fill: #a5a5a5;font-style: italic; } -.terminal-661775892-r7 { fill: #454a50 } -.terminal-661775892-r8 { fill: #e2e3e3;font-weight: bold } -.terminal-661775892-r9 { fill: #1e1e1e } -.terminal-661775892-r10 { fill: #008139 } -.terminal-661775892-r11 { fill: #000000 } -.terminal-661775892-r12 { fill: #e2e2e2 } -.terminal-661775892-r13 { fill: #18954b } -.terminal-661775892-r14 { fill: #e2e2e2;font-weight: bold } -.terminal-661775892-r15 { fill: #969696;font-weight: bold } -.terminal-661775892-r16 { fill: #808080 } -.terminal-661775892-r17 { fill: #7ae998 } -.terminal-661775892-r18 { fill: #507bb3 } -.terminal-661775892-r19 { fill: #0a180e;font-weight: bold } -.terminal-661775892-r20 { fill: #dde6ed;font-weight: bold } -.terminal-661775892-r21 { fill: #001541 } -.terminal-661775892-r22 { fill: #fea62b;font-weight: bold } -.terminal-661775892-r23 { fill: #a7a9ab } -.terminal-661775892-r24 { fill: #e2e3e3 } + .terminal-660530708-r1 { fill: #c5c8c6 } +.terminal-660530708-r2 { fill: #e3e3e3 } +.terminal-660530708-r3 { fill: #989898 } +.terminal-660530708-r4 { fill: #e1e1e1 } +.terminal-660530708-r5 { fill: #4ebf71;font-weight: bold } +.terminal-660530708-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-660530708-r7 { fill: #454a50 } +.terminal-660530708-r8 { fill: #e2e3e3;font-weight: bold } +.terminal-660530708-r9 { fill: #1e1e1e } +.terminal-660530708-r10 { fill: #008139 } +.terminal-660530708-r11 { fill: #000000 } +.terminal-660530708-r12 { fill: #e2e2e2 } +.terminal-660530708-r13 { fill: #18954b } +.terminal-660530708-r14 { fill: #e2e2e2;font-weight: bold } +.terminal-660530708-r15 { fill: #969696;font-weight: bold } +.terminal-660530708-r16 { fill: #808080 } +.terminal-660530708-r17 { fill: #7ae998 } +.terminal-660530708-r18 { fill: #507bb3 } +.terminal-660530708-r19 { fill: #0a180e;font-weight: bold } +.terminal-660530708-r20 { fill: #dde6ed;font-weight: bold } +.terminal-660530708-r21 { fill: #001541 } +.terminal-660530708-r22 { fill: #fea62b;font-weight: bold } +.terminal-660530708-r23 { fill: #a7a9ab } +.terminal-660530708-r24 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Create GitHub repository - -  Now that we have created a new pipeline locally, we can create a new GitHub repository and push    -  the code to it. - - - - -Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -for login. Show  -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊GitHub username▎▊••••••••••••                  ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -The name of the organisation where the The name of the new GitHub repository -GitHub repo will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                               ▎▊mypipeline                            ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▌⚠️ You can't create a repository directly in the nf-core organisation. -▌Please create the pipeline repo to an organisation where you have access or use your user  -▌account. A core-team member will be able to transfer the repo to nf-core once the development -▌has started. - -▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - -▊▔▔▔▔▔▔▔▔▎Private -▊▎Select to make the new GitHub repo private. -▊▁▁▁▁▁▁▁▁▎ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all  + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Create GitHub repository + +  Now that we have created a new pipeline locally, we can create a new GitHub repository and push    +  the code to it. + + + + +Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +for login. Show  +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊GitHub username▎▊••••••••••••                  ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +The name of the organisation where the The name of the new GitHub repository +GitHub repo will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                               ▎▊mypipeline                            ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▌⚠️ You can't create a repository directly in the nf-core organisation. +▌Please create the pipeline repo to an organisation where you have access or use your user  +▌account. A core-team member will be able to transfer the repo to nf-core once the development +▌has started. + +▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + +▊▔▔▔▔▔▔▔▔▎Private +▊▎Select to make the new GitHub repo private. +▊▁▁▁▁▁▁▁▁▎ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index f2607746d..cc34c9253 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,256 +19,256 @@ font-weight: 700; } - .terminal-829842075-matrix { + .terminal-829252251-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-829842075-title { + .terminal-829252251-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-829842075-r1 { fill: #c5c8c6 } -.terminal-829842075-r2 { fill: #e3e3e3 } -.terminal-829842075-r3 { fill: #989898 } -.terminal-829842075-r4 { fill: #e1e1e1 } -.terminal-829842075-r5 { fill: #4ebf71;font-weight: bold } -.terminal-829842075-r6 { fill: #1e1e1e } -.terminal-829842075-r7 { fill: #0178d4 } -.terminal-829842075-r8 { fill: #e2e2e2 } -.terminal-829842075-r9 { fill: #507bb3 } -.terminal-829842075-r10 { fill: #808080 } -.terminal-829842075-r11 { fill: #dde6ed;font-weight: bold } -.terminal-829842075-r12 { fill: #001541 } -.terminal-829842075-r13 { fill: #14191f } -.terminal-829842075-r14 { fill: #454a50 } -.terminal-829842075-r15 { fill: #7ae998 } -.terminal-829842075-r16 { fill: #e2e3e3;font-weight: bold } -.terminal-829842075-r17 { fill: #0a180e;font-weight: bold } -.terminal-829842075-r18 { fill: #000000 } -.terminal-829842075-r19 { fill: #008139 } -.terminal-829842075-r20 { fill: #fea62b;font-weight: bold } -.terminal-829842075-r21 { fill: #a7a9ab } -.terminal-829842075-r22 { fill: #e2e3e3 } + .terminal-829252251-r1 { fill: #c5c8c6 } +.terminal-829252251-r2 { fill: #e3e3e3 } +.terminal-829252251-r3 { fill: #989898 } +.terminal-829252251-r4 { fill: #e1e1e1 } +.terminal-829252251-r5 { fill: #4ebf71;font-weight: bold } +.terminal-829252251-r6 { fill: #1e1e1e } +.terminal-829252251-r7 { fill: #0178d4 } +.terminal-829252251-r8 { fill: #e2e2e2 } +.terminal-829252251-r9 { fill: #507bb3 } +.terminal-829252251-r10 { fill: #808080 } +.terminal-829252251-r11 { fill: #dde6ed;font-weight: bold } +.terminal-829252251-r12 { fill: #001541 } +.terminal-829252251-r13 { fill: #14191f } +.terminal-829252251-r14 { fill: #454a50 } +.terminal-829252251-r15 { fill: #7ae998 } +.terminal-829252251-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-829252251-r17 { fill: #0a180e;font-weight: bold } +.terminal-829252251-r18 { fill: #000000 } +.terminal-829252251-r19 { fill: #008139 } +.terminal-829252251-r20 { fill: #fea62b;font-weight: bold } +.terminal-829252251-r21 { fill: #a7a9ab } +.terminal-829252251-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎        Toggle all features -▊▁▁▁▁▁▁▁▁▎ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use a GitHub Create a GitHub  Show help  -▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add Github CI testsThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI) ▁▁ -testing - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use reference genomesThe pipeline will be  Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most  -common reference  -genome files from  -iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add Github badgesThe README.md file of  Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add configuration The pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -profiles containing  -custom parameters  -required to run  -nf-core pipelines at  -different institutions - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use code lintersThe pipeline will  Show help  -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all  + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎        Toggle all features +▊▁▁▁▁▁▁▁▁▎ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use a GitHub Create a GitHub  Show help  +▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github CI testsThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI) ▁▁ +testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most  +common reference  +genome files from  +iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github badgesThe README.md file of  Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add configuration The pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +profiles containing  +custom parameters  +required to run  +nf-core pipelines at  +different institutions + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use code lintersThe pipeline will  Show help  +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  From e8dff3fc494e1775a90ef0569af93bc2735c24a1 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sat, 19 Oct 2024 15:56:48 +0000 Subject: [PATCH 15/28] chore(deps): update python:3.12-slim docker digest to 032c526 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 8269e9570..cc230cc07 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:af4e85f1cac90dd3771e47292ea7c8a9830abfabbe4faa5c53f158854c2e819d +FROM python:3.12-slim@sha256:032c52613401895aa3d418a4c563d2d05f993bc3ecc065c8f4e2280978acd249 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From 9ba36f3977361d197b1400c12831b2fbb299dd58 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Sun, 20 Oct 2024 18:10:01 +0000 Subject: [PATCH 16/28] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 318d31234..3f3650fb5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220)) - create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226)) - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229)) +- Update python:3.12-slim Docker digest to 032c526 ([#3232](https://github.com/nf-core/tools/pull/3232)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] From 00db9c700aeeeeeacb0f23f95591dfed0c021652 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 21 Oct 2024 17:08:45 +0200 Subject: [PATCH 17/28] use correct profile options for sfw test command --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 94c15521c..356b16f7f 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1371,7 +1371,7 @@ def command_subworkflows_create(ctx, subworkflow, directory, author, force, migr ) @click.option( "--profile", - type=click.Choice(["none", "singularity"]), + type=click.Choice(["docker", "singularity", "conda"]), default=None, help="Run tests with a specific profile", ) From ea03ff2d88e5d332d6e65fbc842614d374205f31 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 21 Oct 2024 15:11:38 +0000 Subject: [PATCH 18/28] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 45772a490..34b20ab13 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ - chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 ([#3230](https://github.com/nf-core/tools/pull/3230)) - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229)) - Update python:3.12-slim Docker digest to 032c526 ([#3232](https://github.com/nf-core/tools/pull/3232)) +- use correct profile options for sfw test command ([#3233](https://github.com/nf-core/tools/pull/3233)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] From 2ba0d30efb741b692aeaa39946d323c558d0a0a9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Tue, 22 Oct 2024 10:20:31 +0200 Subject: [PATCH 19/28] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 34b20ab13..95b7757c0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,7 @@ - chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 ([#3230](https://github.com/nf-core/tools/pull/3230)) - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229)) - Update python:3.12-slim Docker digest to 032c526 ([#3232](https://github.com/nf-core/tools/pull/3232)) -- use correct profile options for sfw test command ([#3233](https://github.com/nf-core/tools/pull/3233)) +- use correct `--profile` options for `nf-core subworkflows test` ([#3233](https://github.com/nf-core/tools/pull/3233)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] From 4abbc4a141d096b357010443c8d20363206f7491 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Tue, 22 Oct 2024 15:31:39 +0200 Subject: [PATCH 20/28] Update nf_core/utils.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- nf_core/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 6ba1c8c5c..b5129a368 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1132,7 +1132,7 @@ def model_dump(self, **kwargs) -> Dict[str, Any]: fields_to_exclude = ["template", "update"] else: # pipeline # Fields to exclude for pipeline - fields_to_exclude = ["bump_version"] + fields_to_exclude = ["bump_version", "org_path"] # Remove the fields based on repository_type for field in fields_to_exclude: From ff27b29a84fabdf9f69a35ddf51595e55ac39880 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Tue, 22 Oct 2024 15:32:29 +0200 Subject: [PATCH 21/28] Update nf_core/utils.py --- nf_core/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index b5129a368..9ef3cff2e 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1106,7 +1106,7 @@ class NFCoreYamlConfig(BaseModel): description="Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation", ) template: Optional[NFCoreTemplateConfig] = Field( - None, description="Pipeline template configuration", exclude=repository_type == "modules" + None, description="Pipeline template configuration" ) bump_version: Optional[Dict[str, bool]] = Field( None, From fdef700925a783e4fa2410704f9d7364e61d1d69 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 22 Oct 2024 14:01:04 +0000 Subject: [PATCH 22/28] [automated] Fix code linting --- nf_core/utils.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 6ba329cbb..8a6bc0841 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1105,9 +1105,7 @@ class NFCoreYamlConfig(BaseModel): None, description="Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation", ) - template: Optional[NFCoreTemplateConfig] = Field( - None, description="Pipeline template configuration" - ) + template: Optional[NFCoreTemplateConfig] = Field(None, description="Pipeline template configuration") bump_version: Optional[Dict[str, bool]] = Field( None, description="Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information.", From bc37fb0716b78d2a7802a1737aa25522fb41e4f5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 22 Oct 2024 16:05:12 +0200 Subject: [PATCH 23/28] no need for Field value --- nf_core/utils.py | 38 +++++++++++++++----------------------- 1 file changed, 15 insertions(+), 23 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 9ef3cff2e..bbbf7f178 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -30,7 +30,7 @@ import rich.markup import yaml from packaging.version import Version -from pydantic import BaseModel, Field, ValidationError, field_validator +from pydantic import BaseModel, ValidationError, field_validator from rich.live import Live from rich.spinner import Spinner @@ -1094,28 +1094,20 @@ def get(self, item: str, default: Any = None) -> Any: class NFCoreYamlConfig(BaseModel): """.nf-core.yml configuration file schema""" - repository_type: Literal["pipeline", "modules"] = Field(..., description="Type of repository") - nf_core_version: Optional[str] = Field( - None, description="Version of nf-core/tools used to create/update the pipeline" - ) - org_path: Optional[str] = Field( - None, description="Path to the organisation's modules repository (used for modules repo_type only)" - ) - lint: Optional[LintConfigType] = Field( - None, - description="Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation", - ) - template: Optional[NFCoreTemplateConfig] = Field( - None, description="Pipeline template configuration" - ) - bump_version: Optional[Dict[str, bool]] = Field( - None, - description="Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information.", - ) - update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = Field( - None, - description="Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information.", - ) + repository_type: Optional[Literal["pipeline", "modules"]] = None + """ Type of repository """ + nf_core_version: Optional[str] = None + """ Version of nf-core/tools used to create/update the pipeline """ + org_path: Optional[str] = None + """ Path to the organisation's modules repository (used for modules repo_type only) """ + lint: Optional[LintConfigType] = None + """ Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation """ + template: Optional[NFCoreTemplateConfig] = None + """ Pipeline template configuration """ + bump_version: Optional[Dict[str, bool]] = None + """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information. """ + update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = None + """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information. """ def __getitem__(self, item: str) -> Any: return getattr(self, item) From e7e21f28c2a646bb7a991c426b923764d92b1d6e Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 23 Oct 2024 10:59:51 +0200 Subject: [PATCH 24/28] fix worklfow_dispatch trigger and parse more review comments --- nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index d8987330d..1ca2ac2c7 100644 --- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml +++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml @@ -19,9 +19,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: octokit/request-action@v2.x + if: github.event_name != 'workflow_dispatch' id: check_approvals with: - route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews + route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - id: test_variables From 4c744e587eb4a9893621c77dc88d76b5f37b7f06 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 23 Oct 2024 09:02:22 +0000 Subject: [PATCH 25/28] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 45772a490..deaf6672b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ - Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223)) - Fix Manifest DOI text ([#3224](https://github.com/nf-core/tools/pull/3224)) - Do not assume pipeline name is url ([#3225](https://github.com/nf-core/tools/pull/3225)) +- fix worklfow_dispatch trigger and parse more review comments in awsfulltest ([#3235](https://github.com/nf-core/tools/pull/3235)) ### Download From 2674f5fe0fca6fc314b08e3cbcbfeb99294b8359 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 23 Oct 2024 09:24:16 +0000 Subject: [PATCH 26/28] Update pre-commit hook pre-commit/mirrors-mypy to v1.13.0 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9c5184b35..7eca8468e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,7 +19,7 @@ repos: alias: ec - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.12.0" + rev: "v1.13.0" hooks: - id: mypy additional_dependencies: From ad3773522e80a4f606c1c8f9fa03a06bd0bae14e Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 23 Oct 2024 09:49:07 +0000 Subject: [PATCH 27/28] chore(deps): update github actions --- .github/actions/create-lint-wf/action.yml | 2 +- .github/workflows/changelog.yml | 6 +++--- .github/workflows/create-lint-wf.yml | 4 ++-- .../workflows/create-test-lint-wf-template.yml | 8 ++++---- .github/workflows/create-test-wf.yml | 6 +++--- .github/workflows/deploy-pypi.yml | 4 ++-- .github/workflows/fix-linting.yml | 4 ++-- .github/workflows/lint-code.yml | 4 ++-- .github/workflows/push_dockerhub_dev.yml | 2 +- .github/workflows/push_dockerhub_release.yml | 2 +- .github/workflows/pytest.yml | 18 +++++++++--------- .github/workflows/sync.yml | 8 ++++---- .github/workflows/update-textual-snapshots.yml | 4 ++-- .../workflows/update_components_template.yml | 4 ++-- .../pipeline-template/.github/workflows/ci.yml | 2 +- .../.github/workflows/download_pipeline.yml | 2 +- .../.github/workflows/fix-linting.yml | 4 ++-- .../.github/workflows/linting.yml | 10 +++++----- .../workflows/release-announcements.yml | 2 +- .../workflows/template_version_comment.yml | 2 +- 20 files changed, 49 insertions(+), 49 deletions(-) diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml index ecd0eef87..6ad6b7b15 100644 --- a/.github/actions/create-lint-wf/action.yml +++ b/.github/actions/create-lint-wf/action.yml @@ -83,7 +83,7 @@ runs: - name: Upload log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: nf-core-log-file-${{ matrix.NXF_VER }} path: create-lint-wf/log.txt diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml index cebcc854b..e89f6ff87 100644 --- a/.github/workflows/changelog.yml +++ b/.github/workflows/changelog.yml @@ -19,7 +19,7 @@ jobs: ) steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 with: token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} @@ -36,7 +36,7 @@ jobs: fi gh pr checkout $PR_NUMBER - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" @@ -65,7 +65,7 @@ jobs: echo "File changed: ${{ env.changed }}" - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" cache: "pip" diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index e0b4c67cf..5e32c4280 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -48,12 +48,12 @@ jobs: export NXF_WORK=$(pwd) # Get the repo code - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 name: Check out source-code repository # Set up nf-core/tools - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" cache: pip diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index d8df2f690..627b73fb6 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -40,7 +40,7 @@ jobs: - name: 🏗 Set up yq uses: frenck/action-setup-yq@v1 - name: checkout - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Create Matrix id: create_matrix run: | @@ -77,11 +77,11 @@ jobs: cd create-lint-wf-template export NXF_WORK=$(pwd) - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 name: Check out source-code repository - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" @@ -168,7 +168,7 @@ jobs: - name: Upload log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: nf-core-log-file-${{ matrix.TEMPLATE }} path: create-test-lint-wf/artifact_files.tar diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 782a08ac9..a6f3b5ac6 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -48,11 +48,11 @@ jobs: cd create-test-wf export NXF_WORK=$(pwd) - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 name: Check out source-code repository - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" @@ -75,7 +75,7 @@ jobs: - name: Upload log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: nf-core-log-file-${{ matrix.NXF_VER }} path: create-test-wf/log.txt diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml index 1202891e4..0e7ddf675 100644 --- a/.github/workflows/deploy-pypi.yml +++ b/.github/workflows/deploy-pypi.yml @@ -13,11 +13,11 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 name: Check out source-code repository - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 4334871c4..9feff8d51 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,7 +32,7 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml index 3bddd42d4..9581fa18b 100644 --- a/.github/workflows/lint-code.yml +++ b/.github/workflows/lint-code.yml @@ -18,10 +18,10 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" cache: "pip" diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml index c613e13a2..3d676eabd 100644 --- a/.github/workflows/push_dockerhub_dev.yml +++ b/.github/workflows/push_dockerhub_dev.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Build nfcore/tools:dev docker image run: docker build --no-cache . -t nfcore/tools:dev diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml index 5a076f6d3..4b7e8aacb 100644 --- a/.github/workflows/push_dockerhub_release.yml +++ b/.github/workflows/push_dockerhub_release.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Build nfcore/tools:latest docker image run: docker build --no-cache . -t nfcore/tools:latest diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index ae2df47e6..a29a6970e 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -61,7 +61,7 @@ jobs: name: Get test file matrix runs-on: "ubuntu-latest" steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 name: Check out source-code repository - name: List tests @@ -87,11 +87,11 @@ jobs: cd pytest export NXF_WORK=$(pwd) - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 name: Check out source-code repository - name: Set up Python ${{ needs.setup.outputs.python-version }} - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: ${{ needs.setup.outputs.python-version }} cache: "pip" @@ -148,14 +148,14 @@ jobs: echo "test=${test}" >> $GITHUB_ENV - name: Store snapshot report - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 if: always() with: name: Snapshot Report ${{ env.test }} path: ./snapshot_report.html - name: Upload coverage - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: coverage_${{ env.test }} path: .coverage @@ -170,9 +170,9 @@ jobs: mkdir -p pytest cd pytest - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 env: AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/ with: @@ -189,14 +189,14 @@ jobs: mv .github/.coveragerc . - name: Download all artifacts - uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 + uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4 - name: Run coverage run: | coverage combine --keep coverage*/.coverage* coverage report coverage xml - - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be # v4 + - uses: codecov/codecov-action@b9fd7d16f6d7d1b5d2bec1a2887e65ceed900238 # v4 with: files: coverage.xml env: diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index ea815a219..42d0f5c09 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -60,10 +60,10 @@ jobs: matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} fail-fast: false steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 name: Check out nf-core/tools - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 name: Check out nf-core/${{ matrix.pipeline }} with: repository: nf-core/${{ matrix.pipeline }} @@ -73,7 +73,7 @@ jobs: fetch-depth: "0" - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" @@ -102,7 +102,7 @@ jobs: - name: Upload sync log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: sync_log_${{ matrix.pipeline }} path: sync_log_${{ matrix.pipeline }}.txt diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml index 2adb1b8d8..32983d38c 100644 --- a/.github/workflows/update-textual-snapshots.yml +++ b/.github/workflows/update-textual-snapshots.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -33,7 +33,7 @@ jobs: # Install dependencies and run pytest - name: Set up Python - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" cache: "pip" diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml index e2ecebfcb..86e6ba7b8 100644 --- a/.github/workflows/update_components_template.yml +++ b/.github/workflows/update_components_template.yml @@ -11,10 +11,10 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Set up Python - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.x" diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml index 61738a414..33631fdc5 100644 --- a/nf_core/pipeline-template/.github/workflows/ci.yml +++ b/nf_core/pipeline-template/.github/workflows/ci.yml @@ -45,7 +45,7 @@ jobs: profile: "singularity" steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index fdd5492ca..6ba251e52 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -35,7 +35,7 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" architecture: "x64" diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml index 18e6f9e15..13992f5c5 100644 --- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml +++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,7 +32,7 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index 0eee862f9..878998ad9 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" @@ -31,12 +31,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.12" architecture: "x64" @@ -74,7 +74,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: linting-logs path: | diff --git a/nf_core/pipeline-template/.github/workflows/release-announcements.yml b/nf_core/pipeline-template/.github/workflows/release-announcements.yml index 035ed63bb..a200d141e 100644 --- a/nf_core/pipeline-template/.github/workflows/release-announcements.yml +++ b/nf_core/pipeline-template/.github/workflows/release-announcements.yml @@ -31,7 +31,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.10" - name: Install dependencies diff --git a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml index 87a218446..51f2f7f94 100644 --- a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml +++ b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 with: ref: ${{ github.event.pull_request.head.sha }} From 1ef913406762f5bf5e86cfe0b334d9d8daf39b5a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 23 Oct 2024 09:52:56 +0000 Subject: [PATCH 28/28] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 49201ac76..eac5adcdd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,7 @@ - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229)) - Update python:3.12-slim Docker digest to 032c526 ([#3232](https://github.com/nf-core/tools/pull/3232)) - use correct `--profile` options for `nf-core subworkflows test` ([#3233](https://github.com/nf-core/tools/pull/3233)) +- Update GitHub Actions ([#3237](https://github.com/nf-core/tools/pull/3237)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]