Nextflow camp 2019: nf-core community updates
nf-core (http://nf-co.re) is a community effort to collect, curate and collaborate on high quality nextflow bioinformatics workflows. Shared pipelines give increased reproducibility between groups and greater collective development power. To help users and developers we have written an nf-core companion tool with a workflow template, code linting and helper functions for downloading pipelines for offline use and staying up to date. All nf-core pipelines make the best use of Nextflow features possible, with support for Conda, Docker and Singularity, with reference genomes available from the cloud. Consistency between pipelines means that all work in a similar manner with comparable requirements. Now in its second year, the nf-core community continues to develop at a rapid pace. More and more pipelines are being added to the list of stable releases, and the suite of framework tools continues to grow. In this talk I will describe recent updates from the nextflow nf-core community - what's new with pipelines, best-practices, tips & tricks and the nf-core companion tools.
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Nextflow camp 2019: nf-core community updates
- 2. core A community effort to collect a curated set of analysis pipelines built using Nextflow.
- 3. Best practice guidelines Development tools Ready to use pipelines
- 4. What's new?
- 5. Community Institutes Slack GitHub Twitter 0 200 400 600 800 0 3 0 3 2017
- 6. Community Institutes Slack GitHub Twitter 0 200 400 600 800 322 127 50 12 2018
- 7. Community Institutes Slack GitHub Twitter 0 200 400 600 800 730 223 214 27 2019
- 8. Community
- 9. Community
- 11. Community
- 12. Community
- 13. Community
- 14. Community
- 15. Community
- 16. Community
- 28. Tools
- 29. Parameters params.foo = bar println(params.foo) $ nextflow run pipeline --foo baz params.foo
- 32. Parameters parameters.settings.json { "parameters": [ { "name": "foo", "label": "Example params variable", "usage": "Set this variable at your peril", "type": "string", "render": "radio-button", "choices": ["bar", "baz"], "default_value": "bar", } ] }
- 34. Parameters parameters.settings.json Auto-generate Pipeline CLI help Markdown documentation User interfaces
- 35. Parameters
- 36. Centralised Configs PREVIOUSLY Add config to nf-core template Wait for nf-core/tools release Wait for sync PRs to be merged Wait for pipeline release Wait for pipeline release
- 38. Centralised Configs Add config to nf-core/configs NEW! Immediately available in all pipelines
- 39. Centralised Configs Institutional configuration profiles for all pipelines for all users single point to update NEW!
- 40. Centralised Configs Automatic hostname detection Bonus! ========================================================== WARNING! You are running with `-profile singularity` but your machine hostname is 'rackham.uppmax.uu.se' It's highly recommended that you use `-profile uppmax` ========================================================== NEW!
- 42. Website
- 43. Website
- 44. Website
- 45. Website
- 46. Website
- 47. Website
- 48. What's next?
- 50. GitHub Actions GitHub Package Registry
- 51. GitHub Actions
- 52. GitHub Actions
- 53. GitHub Package Registry $ docker pull docker.pkg.github.com/nf-core/rnaseq/rnaseq:dev
- 54. Full-size tests
- 55. Full-size tests
- 56. Full-size tests
- 57. Manuscript
- 58. Citation nf-core: Community curated bioinformatics pipelines PA Ewels, A Peltzer, S Fillinger, J Alneberg, H Patel, A Wilm, MU Garcia, P Di Tommaso, S Nahnsen bioRxiv 610741; doi: https://doi.org/10.1101/610741
- 61. nf_corehttps://nf-co.re nf-core hackathon 4th - 6th March 2020 The Francis Crick Institute, London
- 62. Phil Ewels phil.ewels@scilifelab.se tallphil ewels https://nf-co.re nf_core @apeltzer @sven1103 @drpatelh @MaxUlysse @alneberg Alexander Peltzer Sven F. Harshil Patel Maxime Garcia Johannes Alneberg @nf-core/core