v4.1.0 - Marshalled Mamba

General

• container configs: use correct key for conda configs (#4269)
• Coerce launch params_out to Path to fix AttributeError (#4299) (#4317)
• generate valid Markdown when piping schema docs to file (#4319)
• fix API docs bug in pydantic autodoc (#4320)
• Improve CLI startup speed (#4383)

Linting

• accept process_low_memory as a standard module label (#4264)
• improve linting for modules.json to add support for only installing subworkflows from a repository and provide more explicit error messages (#4287)
• improve singularity_tag linting check (add skip, handle exceptions correctly, check against oras) (#4358)
• make regex for meta keys more specific to avoid false positives (#4280)

Modules

• modules info: handle one element channels correctly (#4268)
• module lint for module name matching against nf-core module naming specifications (#4325)
• Clarify execution context of nf-core modules test command (#4346)
• Add nf-core modules containers create to build module containers via Seqera Wave and record them in the containers: section of meta.yml (#3954)
• Add a log hint in modules create for create containers and switch modules bump-versions to use Seqera containers (#4374)

Template

• New pre-commit hooks blocking large files and merge markers in pipeline template (#3935)
• add process_low_memory resource label to base.config (#4264)
• Simpler test data path in tests/nextflow.config (#4285)
• fix dead link (#4307)
• remove date placeholder from changelog title (#4333)
• correct always-true nf-core pipelines lint condition in the linting workflow and fix doc typos (broken #lint-tests anchor, duplicate word, stray code-span space) (#4324)
• Fix publishDir configuration in modules.config for multiqc (#4347)
• Switch to a more secure approach for PR comments by splitting the GitHub Actions workflow (#4342)

Download

• Included support for Apptainer in nf-core pipelines download --container-system apptainer (#4352)

Version updates

• Update pre-commit hook pre-commit/mirrors-mypy to v2 (#4270)
• Update pre-commit npm dependencies to v3.8.4 (#4335)