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Published April 28, 2023 | Version 2.8
Software Open

The nf-core framework for community-curated bioinformatics pipelines.

Authors/Creators

Description

v2.8 - Ruthenium Monkey - [2023-04-27] Template
  • Explicitly disable conda when a container profile (#2140)
  • Turn on automatic clean up of intermediate files in work/ on successful pipeline completion in full-test config (#2163) [Contributed by @jfy133]
  • Add documentation to usage.md on how to use params.yml files, based on nf-core/ampliseq text (#2173) [Contributed by @jfy133, @d4straub]
  • Make jobs automatically resubmit for a much wider range of exit codes (now 104 and 130..145) (#2170)
  • Add a clean-up GHA which closes issues and PRs with specific labels (#2183)
  • Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([https://github.com/nf-core/tools/pull/2194]) [Contributed by @Midnighter, @jfy133]
  • Consistent syntax for branch checks in PRs (#2202)
  • Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
  • Updated AWS tests to use newly moved seqeralabs/action-tower-launch instead of nf-core/tower-action
  • Remove .cff files from .editorconfig [(#2145)[https://github.com/nf-core/tools/pull/2145]]
  • Simplify pipeline README (#2186)
  • Added support for the apptainer container engine via -profile apptainer. (#2244) [Contributed by @jfy133]
  • Added config docker.registry to pipeline template for a configurable default container registry when using Docker containers. Defaults to quay.io (#2133)
  • Add tower.yml file to the pipeline template (#2251)
  • Add mastodon badge to README (#2253)
  • Removed quay.io from all module Docker container references as this is now supplied at pipeline level. (#2249)
  • Remove CITATION.cff file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline (#2059).
Linting
  • Update modules lint test to fail if enable_conda is found (#2213)
  • Read module lint configuration from .nf-core.yml, not .nf-core-lint.yml (#2221)
  • nf-core schema lint now defaults to linting nextflow_schema.json if no filename is provided (#2225)
  • Warn if /zenodo.XXXXXX is present in the Readme (#2254)
  • Lint all labels in a module (#2227)
Modules
  • Add an --empty-template option to create a module without TODO statements or examples (#2175 & #2177)
  • Removed the nf-core modules mulled command and all its code dependencies (2199).
  • Take into accout the provided --git_remote URL when linting all modules (2243).
Subworkflows
  • Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL (#2177)
  • Fix nf-core subworkflows test not running subworkflow tests (#2181)
  • Add tests for nf-core subworkflows create-test-yml (#2219)
General
  • Deprecate Python 3.7 support because it reaches EOL (#2210)
  • nf-core modules/subworkflows info now prints the include statement for the module/subworkflow (#2182).
  • Add a clean-up GHA which closes issues and PRs with specific labels (#2183)
  • update minimum version of rich to 13.3.1 (#2185)
  • Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to nextflow.config) (#2196)
  • Use nfcore/gitpod:dev container in the dev branch (#2196)
  • Replace requests_mock with responses in test mocks (#2165).
  • Add warning when installing a module from an org_path that exists in multiple remotes in modules.json (#2228 #2239).
  • Add the possibility to translate refgenie asset aliases to the ones used in a pipeline with an alias_translations.yaml file (#2242).
  • Add initial CHM13 support (1988)

Notes

If you use `nf-core tools` in your work, please cite the `nf-core` publication

Files

nf-core/tools-2.8.zip

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Additional details

Related works

Is supplement to
https://github.com/nf-core/tools/tree/2.8 (URL)