Add new command nf-core rocrate to create a Research Object (RO) crate for a pipeline
#2680
Commits on Sep 27, 2024
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Merge pull request nf-core#3180 from mirpedrol/check-max
Remove check_max() [skip changelog]
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Merge pull request nf-core#3168 from mirpedrol/genomes-map
Remove if/else block to include `igenomes.config` and add `igenomes_ignored.config`
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Commits on Sep 30, 2024
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Merge pull request nf-core#3154 from nf-core/renovate/pytest-textual-…
…snapshot-1.x Update dependency pytest-textual-snapshot to v1
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Merge pull request nf-core#3167 from mirpedrol/try-catch
Template: remove try-catch blocks from nextflow.config
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Merge pull request nf-core#3151 from nf-core/renovate/pre-commit-mirr…
…ors-mypy-1.x Update pre-commit hook pre-commit/mirrors-mypy to v1.11.2
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Merge pull request nf-core#3155 from nf-core/renovate/editorconfig-ch…
…ecker-editorconfig-checker.python-3.x Update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3
Commits on Oct 1, 2024
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Merge pull request nf-core#3149 from mirpedrol/pipeline-test-conda-sy…
…ngularity Template: test pipeline with conda and singularity on PRs to master
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Merge pull request nf-core#3169 from mirpedrol/citationsmd
exclude CITATIONS.md file when excluding citations from pipeline template
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Merge pull request nf-core#3166 from mirpedrol/import-statements
Template: Update modules and and local subworkflow syntax
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Merge pull request nf-core#3178 from MatthiasZepper/download_cli_refa…
…ctor Changes to nf-core pipelines download CLI
Commits on Oct 2, 2024
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Co-authored-by: Matthias Hörtenhuber <[email protected]>
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Co-authored-by: Matthias Hörtenhuber <[email protected]>
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Merge pull request nf-core#3185 from mirpedrol/sync-fixes
Fix nf-core pipelines sync
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Commits on Oct 3, 2024
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Merge pull request nf-core#3188 from mashehu/fix-run-prettier
Fix run_prettier on rendered template
Commits on Oct 4, 2024
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include review comments and links to docs
Co-authored-by: Júlia Mir Pedrol <[email protected]>
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Merge pull request nf-core#3189 from mashehu/sync-modules
add API docs for .nf-core.yml
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Merge pull request nf-core#3190 from mirpedrol/template-newlines
fix template new lines
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Merge pull request nf-core#3182 from MatthiasZepper/seqera_community_…
…containers Pipeline template: Modify download test action to capture the number of containers
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Merge pull request nf-core#3150 from nf-core/renovate/astral-sh-ruff-…
…pre-commit-0.x
Commits on Oct 6, 2024
Commits on Oct 7, 2024
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Merge pull request nf-core#3194 from mashehu/add-input-to-sync-gha
add pipeline name as an optional sync input
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Merge pull request nf-core#3195 from mashehu/fix-whitespaces
fix whitespaces in rendered template
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Merge pull request nf-core#3153 from nf-core/renovate/textual-dev-1.x
chore(deps): update dependency textual-dev to v1.6.1
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Merge pull request nf-core#3196 from mirpedrol/bump-to-3-0-0
bump version to 3.0.0
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Co-authored-by: Phil Ewels <[email protected]>
Commits on Oct 8, 2024
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Merge pull request nf-core#2989 from mirpedrol/release-checklist
Update release checklist
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Merge pull request nf-core#3199 from mirpedrol/release-review
Release review [skip changelog]
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Merge pull request nf-core#3198 from mashehu/migrate-to-main
`master` -> `main`
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Co-authored-by: Matthias Hörtenhuber <[email protected]>
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Merge pull request nf-core#3202 from nf-core/nvnieuwk-patch-1
Fix a typo in the linting action
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Commits on Oct 9, 2024
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Merge pull request nf-core#3203 from mashehu/fix-aws-ci
Template: run awsfulltest only when target branch is `master`
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Merge pull request nf-core#3204 from mirpedrol/editorconfig-lines
fix too many empty lines added to .editorconfig file
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Merge pull request nf-core#3205 from mashehu/fix-ignore-params
Use correct key for parsing `defaultIgnoreParams`
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Merge pull request nf-core#3201 from nf-core/fix-large-comment-header…
…-formatting Fix comment section headers so they don't give phantom merge conflict warnings
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Merge pull request nf-core#3206 from mirpedrol/jinja-newlines
fix more jinja newlines
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Merge pull request nf-core#3209 from mashehu/fix-snapshot-artifact-up…
…load CI: fix artifact upload of snapshot report
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Merge pull request nf-core#3208 from mirpedrol/update-subworkflows
update nf-core subworkflows [skip changelog]
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Merge pull request nf-core#3207 from mashehu/update-modules
Bump version to 3.0.1
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Merge pull request nf-core#3211 from mashehu/bump-to-3_0_2dev
bump version to 3.0.2dev
Commits on Oct 10, 2024
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Merge pull request nf-core#3213 from mirpedrol/fix-params-validation
Linting: Fix bug when linting schema params
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Apply suggestions from code review
Co-authored-by: Matthias Hörtenhuber <[email protected]>
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Update nf_core/pipeline-template/.github/workflows/ci.yml
Co-authored-by: Matthias Hörtenhuber <[email protected]>
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Merge pull request nf-core#3191 from nf-core/maxulysse-patch-5
TEMPLATE: Add null/ to .gitignore
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Commits on Oct 11, 2024
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Update nf_core/pipeline-template/.github/workflows/ci.yml
Co-authored-by: Matthias Hörtenhuber <[email protected]>
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Merge pull request nf-core#3214 from nf-core/maxulysse-patch-6
TEMPLATE: Parallelize pipeline GHA tests over docker/conda/singularity
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Merge pull request nf-core#3212 from mashehu/fix-template-version-com…
…ment-action TEMPLATE: Fix version comment action
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Merge branch 'fix-pipeline-commands-in-docstrings' of github.com:mash…
…ehu/tools into fix-pipeline-commands-in-docstrings
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Co-authored-by: Maxime U Garcia <[email protected]>
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Merge pull request nf-core#3215 from mashehu/fix-pipeline-commands-in…
…-docstrings Use updated pipeline commands in docstrings
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Co-authored-by: Matthias Hörtenhuber <[email protected]>
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Merge pull request nf-core#3217 from mashehu/fix-sync-action
disable automatic sync on release, fix handling empty pipeline input
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Merge pull request nf-core#3216 from mirpedrol/bump-to-3.0.2
bump version to 3.0.2 [skip changelog]
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Merge pull request nf-core#3218 from mirpedrol/fix-editorconfig
Template: fix pre-commit lining failing on pipelines template
Commits on Oct 14, 2024
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Co-authored-by: Júlia Mir Pedrol <[email protected]>
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Merge pull request nf-core#3221 from nf-core/bump-to-3_0_3dev
bump version to 3.0.3dev
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keep pipeline name in version.yml file
Why going for pipeline when we have shortname?
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Commits on Oct 15, 2024
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Update nf_core/pipeline-template/workflows/pipeline.nf
Co-authored-by: Júlia Mir Pedrol <[email protected]>
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Template: Do not assume pipeline name is url
I'd rather we use {{ name }} that way we see in the script what we have. If we have manifest.name we assume that people are using a name that org/pipeline, which should work for nf-core pipeline, but might not work for all. -
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Merge pull request nf-core#3223 from nf-core/maxulysse-patch-5
TEMPLATE: Keep pipeline name in version.yml file
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Merge pull request nf-core#3224 from nf-core/maxulysse-patch-6
Template: Fix Manifest DOI text
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Merge pull request nf-core#3220 from mashehu/fix-bump-version
Include .nf-core.yml in `nf-core pipelines bump-version`
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Merge branch 'add-toggle-all-shortcut' of github.com:mashehu/tools in…
…to add-toggle-all-shortcut
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Merge pull request nf-core#3226 from mashehu/add-toggle-all-shortcut
create: add shortcut to toggle all switches
Commits on Oct 16, 2024
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Merge pull request nf-core#3225 from nf-core/maxulysse-patch-7
Template: Do not assume pipeline name is url
Commits on Oct 17, 2024
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switch to add_workflow method to add main entity and add components a…
…s datasets with descriptions
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Merge branch 'add-rocreate' of github.com:mashehu/tools into add-rocr…
…eate # Conflicts: # CHANGELOG.md # nf_core/commands_pipelines.py # nf_core/pipelines/lint_utils.py # nf_core/pipelines/rocrate.py # nf_core/utils.py