<!-- .slide: data-background="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg" --> <a href="https://www.nf-co.re"><img src="https://i.imgur.com/hEDjpCs.png" width="65%"><img></a> ### 🚀 Infrastructure Team 🚀 _10th-12th October 2022 - BCN_ This file: [https://hackmd.io/@nf-core/r1xktIpfo/edit](https://hackmd.io/@nf-core/r1xktIpfo/edit) The Hackathon Oct 2022 [Project Board](https://github.com/orgs/nf-core/projects/38/views/11) <img src="https://openmoji.org/data/color/svg/E040.svg" width=50> @nf-core / <img src="https://openmoji.org/data/color/svg/E045.svg" width=50> @nf-core --- # Infrastructure Team - Leads - @mirpedrol - @mashehu --- # General development work :hammer_and_wrench: nf-core/tools subworkflow functionality :heavy_check_mark: improve nf-core/tools test coverage :dark_sunglasses: Prototype nf-test in nf-core/modules repository :bug: Bug fixes for nf-co.re --- # Remember - Add yourself to Team Members slide - Assign yourself on issues on the [project board](https://github.com/orgs/nf-core/projects/38/views/11) - Post your progress here **daily**! - Sign up for a reviewing buddy (see slide)! --- # Team Members - [Nicolas Vannieuwkerke](https://github.com/nvnieuwk) - [Sofia Haglund](https://github.com/sofiahag) - [Adrien Coulier](https://github.com/Aratz) - [Arthur Gymer](https://github.com/awgymer) - [Bruno Grande](https://github.com/brunograndephd) --- # Day Three - [Sofia] Continue working on landing pages for nf-co.re/docs/usage + nf-co.re/docs/contributing [#317](https://github.com/nf-core/nf-co.re/issues/317). - [Adrien] Finished code coverage of `tools/nf-core/sync.py`  --- - [Adrien] Improve code coverage of `tools/nf-core/__main__` (cli interface) [#1937](https://github.com/nf-core/tools/issues/1937) - [Björn] `nf-core subworkflows info` command ([#1889](https://github.com/nf-core/tools/pull/1889)) - [Bruno] Annotate each published file with associated task in `nf-prov` plugin ([#4](https://github.com/Sage-Bionetworks-Workflows/nf-prov/pull/4)) - [Alex/Robert/Edmund/Phil] - Adding Custom Runners for nf-core CI for future events [#1940](https://github.com/nf-core/tools/issues/1940) --- - [Júlia,Arthur,Matthias] continue working on reduce code redundancy for `nf-core modules/subworkflows` - [Matthias] Won the hackathon quiz :trophy: - [Matthias] Working on stats :chart_with_upwards_trend: - [Pol] Autocanceling previous tests when pushing changes in pipelines - [Matthias] add :point_up: also in modules repo CI --- ## `nf-test` (Nicolas) [nf-core/modules #2199](https://github.com/nf-core/modules/pull/2199) - Updated the prototypes to changes made in `nf-test` v0.6.2 - Added a prototype that has a separate config file - Devs will add `tags` and `snapshot testing` based on our suggestions yesterday - `snapshot testing` could be an alternative to the `yaml` implementation now (needs to be discussed) --- # Day Two - [Sofia] Working on adding new pages for /usage and /contributing ([#317](https://github.com/nf-core/nf-co.re/issues/317)) - [Adrien] Improve code coverage of `tools/nf-core/sync.py` ([#1936](https://github.com/nf-core/tools/pull/1936)) - [Arthur] Small changes to test yml template to fix case when using `contains` ([#1924](https://github.com/nf-core/tools/pull/1924)) - [Björn] nf-core subworkflows list command ([#1888](https://github.com/nf-core/tools/pull/1888)) --- ## nf-test (Nicolas) - Added a prototype for tests that use more workflows - Added a subworkflow prototype - Opened several issues to fit `nf-test` to add requirements for the modules repo - https://github.com/askimed/nf-test/issues/28 => additional config file support - https://github.com/askimed/nf-test/issues/29 => yaml test file + tags --- ## nf-prov plugin (Bruno) - Small contribution to Nextflow core ([#3284](https://github.com/nextflow-io/nextflow/pull/3284)) - Polished PR for generating a simple list of published files ([#2](https://github.com/Sage-Bionetworks-Workflows/nf-prov/pull/2)) - Opened follow-up PR for JSON output and `prov` config scope ([#3](https://github.com/Sage-Bionetworks-Workflows/nf-prov/pull/3)) - Drafted PR for aggregating task information and run config ([#4](https://github.com/Sage-Bionetworks-Workflows/nf-prov/pull/4)) --- - [Björn] almost done with `nf-core subworkflows list` command ([#1919](https://github.com/nf-core/modules/pull/1919)) - [Júlia,Arthur,Matthias] reduce code redundancy for `nf-core modules/subworkflows` - [Júlia] Bug fixes in install command (it updates modules.json for all moduels included in a subworkflow, it allows installing subworkflows from a new remote repo) - [Matthias] fixed broken linting in `dev` branch (twice!) --- # Day One - [Nicolas] `nf-test` [#2199](https://github.com/nf-core/modules/pull/2199): - added a prototype for simple processes - added a prototype for modules that depend on other modules for their input data - [Julia] Implement `nf-core subworkflows install` installing all modules imported in the subworkflow --- - [Julia] Fix bug in `nf-core modules update` - [Sofia] Getting familiar with the website structure. Looking into making listing pages for /usage and /developers, and why many markdown links seem to be broken. - [Matthias] Replace symlinks for docs with actual files. --- - [Bruno] Create a Nextflow Sourcegraph context - Useful for searching across multiple GitHub organizations + More powerful and useful than GitHub's native code search - [Example query](https://sourcegraph.com/search?q=context:%40BrunoGrandePhD/nextflow+onFlowComplete&patternType=standard) - [Bruno] Start working on a proof of concept Nextflow plugin for provenance ([nf-prov](https://github.com/Sage-Bionetworks-Workflows/nf-prov)) - Initial version will generate a simple list of published files - Long-term plan will hopefully generate a richer JSON manifest ---