feat(modules): add containers create subcommand#2
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…-subworkflow-linting
# Conflicts: # .github/RELEASE_CHECKLIST.md # .github/workflows/pytest.yml # requirements-dev.txt # requirements.txt # setup.py # Conflicts: # .devcontainer/build-devcontainer/Dockerfile # .github/workflows/fix-linting.yml # requirements-dev.txt
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update python:3.14-slim Docker digest to 6a27522 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Always prettify modules.json
…es via full path When a subworkflow includes another subworkflow using the full path (e.g., `../../../subworkflows/nf-core/vcf_gather_bcftools`), the linter incorrectly converted underscores to slashes, producing `vcf/gather/bcftools` instead of `vcf_gather_bcftools`. This happened because the `../../../` prefix check assumed all full-path includes were modules (where underscore-to-slash conversion is correct). Subworkflow includes via full paths also start with `../../../` but should preserve underscores since subworkflow directory names use them. The fix checks whether the include path contains `subworkflows/` before deciding how to derive the component name. Fixes nf-core#4073 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
feat(pipeline_template): add .lineage/ to .gitignore
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Cover full-path subworkflow includes (underscore preservation), full-path module includes (underscore-to-slash conversion), relative subworkflow includes, and mixed include scenarios. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…b.com:nf-core/tools into fix/subworkflow-include-underscore-conversion
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…underscore-conversion Fix lint: preserve underscores for subworkflow includes via full path
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Use branch-deploy action
Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: nf-core-bot <core@nf-co.re>
Adds nf-core modules containers create command to build docker and singularity containers for linux/amd64 and linux/arm64 using Wave. Includes create(), _extract_yaml_from_wave_output(), request_container(), request_image_inspect(), update_main_nf_container(), update_containers_in_meta(), and conda lock file methods, plus shared infrastructure changes (lint/__init__.py refactoring of sort_meta_yml to a class method is included as it is required by create). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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PR checklist
CHANGELOG.mdis updateddocsis updated