diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 09c5b01c3..782a08ac9 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -71,10 +71,6 @@ jobs: mkdir create-test-wf && cd create-test-wf export NXF_WORK=$(pwd) nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" - # echo current directory - pwd - # echo content of current directory - ls -la nextflow run nf-core-testpipeline -profile self_hosted_runner,test --outdir ./results - name: Upload log file artifact diff --git a/CHANGELOG.md b/CHANGELOG.md index 7473015f5..201665682 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # nf-core/tools: Changelog -## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-07] +## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08] **Highlights** diff --git a/README.md b/README.md index 58fb708a0..3597f1ea1 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ For documentation of the internal Python functions, please refer to the [Tools P ## Installation -For full installation instructions, please see the [nf-core documentation](https://nf-co.re/docs/usage/tools). +For full installation instructions, please see the [nf-core documentation](https://nf-co.re/docs/nf-core-tools/installation). Below is a quick-start for those who know what they're doing: ### Bioconda diff --git a/nf_core/components/list.py b/nf_core/components/list.py index 05a8f7112..4c20e6086 100644 --- a/nf_core/components/list.py +++ b/nf_core/components/list.py @@ -25,7 +25,7 @@ def __init__( self.remote = remote super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) - def _configure_repo_and_paths(self, nf_dir_req=True) -> None: + def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: """ Override the default with nf_dir_req set to False to allow info to be run from anywhere and still return remote info diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 9cce94acb..37e43a536 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -5,7 +5,7 @@ import logging import re from pathlib import Path -from typing import Any, List, Optional, Tuple, Union +from typing import Any, Dict, List, Optional, Tuple, Union log = logging.getLogger(__name__) @@ -50,7 +50,7 @@ def __init__( self.passed: List[Tuple[str, str, Path]] = [] self.warned: List[Tuple[str, str, Path]] = [] self.failed: List[Tuple[str, str, Path]] = [] - self.inputs: List[list[dict[str, dict[str, str]]]] = [] + self.inputs: List[List[Dict[str, Dict[str, str]]]] = [] self.outputs: List[str] = [] self.has_meta: bool = False self.git_sha: Optional[str] = None diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index b6d7f0d0f..f9ba9d30c 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -391,8 +391,8 @@ def get_new_and_old_lines(patch): def try_apply_single_patch(file_lines, patch, reverse=False): """ Tries to apply a patch to a modified file. Since the line numbers in - the patch does not agree if the file is modified, the old and new - lines inpatch are reconstructed and then we look for the old lines + the patch do not agree if the file is modified, the old and new + lines in the patch are reconstructed and then we look for the old lines in the modified file. If all hunk in the patch are found in the new file it is updated with the new lines from the patch file.