Hi folks! Next week, Seqera / @Evan Floden is joining ZS to discuss Regulatory-grade bioinformatics for precision medicine 💊🔓 linkedin https://www.linkedin.com/feed/update/urn:li:activity:7322644550093561856 I thought it might be of interest to people in this channel! 🙂

Hey folks, Wanted to share a cool potential feature for the nf-core website called Advisories that is currently going through the new RFC process for approval by the core team. I think it has the potential to solve the concerns around bugs and version incompatibility tracking. PR implementing Advisories RFC proposal (comments/feedback from anyone welcome and encouraged)

Hi all 👋 On behalf of the nf-core/maintainers team and #C07B5FK9GKA, we are running a very short (2-question) anonymous survey about nf-core/test-datasets. In particular, we want to gather your input of what sort of meta-information you would like recorded about each test-data file, that would help facilitate your development of nf-core modules, subworkflows, and pipelines for your particular context. You can access the survey here: https://tally.so/r/mRNrvK Thank you in advance for your feedback!

Hi NF-Core team and developers! My name is Dylan Renard a current MS in Bioinformatics student at JHU working with the Iowa State Hygienic Laboratory. I wanted to ask general advice about NF-CORE pipeline validation. Specifically if there are any recommended guidelines or papers on how to get a Nextflow pipeline clinically validated or ensure consistent sequencing analysis results. The pipeline interacts with illumina and Oxford Nanopore sequencing files and right now I've just been developing on toy datasets. Any feedback or point in the right direction is appreciated! This is my first production level Nextflow pipeline so I hope it is a showstopper! 🙂

bjorn.langer from Nextflow was added to this channel by alexander.peltzer. You can review their permissions in Channel details. Happy collaborating!

Ok folks, we're making issues for this ticket and split things up a little. https://github.com/nf-core/stats/issues/73

Ok group discussion agreed upon the following: • Creating meta issues for services we use to query specific metrics • Cross-ref individual metrics to these tickets, e.g. "Github stars" would cross-ref the "Github API Queries" ticket https://github.com/nf-core/stats/issues/76 • Repeat until we have at least a decent list of metrics of highest importance / agreement 🙂 • Milestone planning can then be done via the Github Milestones with the individual issues to put up for future implementation more effectively. Pinging @Edmund / @Gregor Sturm FYI 🙂

I just added one table of the database as a test dataset to the

regulatory

branch: https://github.com/nf-core/stats/tree/regulatory/regulatory/data

For the online folks, we're working on several aspects here at the hackathon: • Updating the regulatory guidelines docs and strategy https://github.com/nf-core/website/pull/3610 • Implementing missing metrics into nf-core/stats to be able to have a proof of concept pipeline report for regulatory readiness • Figuring out API calls required to get metrics done that are not covered by Github API (e.g. citations, some other things - see a list of these at https://github.com/nf-core/stats/issues?q=state%3Aopen%20label%3Aregulatory • Preparing a proof of concept report to be filled with the points brought up by the team Not so easy to coordinate this efficiently as things are moving quickly, but i fyou feel like you can contribute to any of the above, please try posting issues / labeling them accordingly and review stuff if you can / want to 👍🏻

This is the command to extract the workflow graph from nextflow pipelines I mentionen in the hackathon: nextflow run your_pipeline.nf -with-dag workflow_dag.dot

- Licensing
  - All nf-core pipelines utilize the MIT licence, which allows for public as well as commercial usage of said pipelines
  - Pipelines that do not adhere to this, have extra documentation that highlights which parts require specific software licences

Regarding this bit - probably outside of the scope of this hackathon but i thought it worth noting that just because a pipeline is MIT licensed doesnt mean its dependencies are

What is 'weight' here

I think thats a website thing how certain sections are shown on the website - @mashehu might know more exactly 🙂

What would be your feeling how the following components of a "pipeline trust score" should be weighted?

1. Maintenance Activity: Based on last release time
    2. Issue Resolution: Based on closed issue ratio and median resolution time
    3. PR Management: Based on closed PR ratio and median PR closure time
    4. Community Engagement: Based on stars and forks

1+4 lower, 2+3 higher? So maybe 20+30+30+20% ?

Ok folks, we made quite some progress here today

• Massive documentation overhaul (overview with more details and general context, checklist for everyone wanting to do regulatory related work on a pipeline) • Added more metrics to nf-core/stats - allowing users to also improve their pipelines to improve pipeline quality even further • Draft template up for creation of regulatory readiness pipeline report --> this is to be auto populated using data from point 2 😉

We'll push these things across the finish line now and will continue on them to get some MVP up soon - hopefully we can then improve gradually even further

Great work guys 🙂

New guidelines for regulatory topics + checklist is up on the webpage -> see here: https://nf-co.re/docs/guidelines/regulatory/overview

Please open tickets / PRs. Intention is to keep it relatively clean, so maybe first bring up topics before we add every use case to it 👍🏻

Also keep in mind that we can only provide guidance, help and some generalizable things for everyone who wants to use nf-core pipelines under regulated conditions - there won't be a one shoe fits all solution for this 👍🏻

Super nice, great work 👏🏻 🎉

What do you think about breaking the new docs into multiple pages to make it easier to navigate?

Hi all. A group of us on the µbioinfo slack (microbial genomics/bioinformatics) are putting together an informal group to share/create templates, policies, docs for accrediting bioinformatics tools/pipelines. If anyone is interested in participating please take a look at the accreditation channel here: join.slack.com/t/microbial-bioinfo/shared_invite/…

For those that might be interested we have recently successfully obtained IVDR accreditation for our cancer WGS analytics 'diagnostic product'. Under the hood the software is 90% #C04CQ1LK7U1 with additional safe guards, orchestration and verifications on top. If this work group is interested in what we encountered and the choices we made happy to connect you with the people that did the actual work. hartwigmedicalfoundation.nl/…/hartwig-receives-ce-certification-for-hartwig-medical-oncoact-the-first-complete-ivdr-certified-whole-genome-cancer-diagnostics-solution important note, this is work 3 years in the making!

So a confession first, I spent two months building a tool and only now thought to ask whether anyone needs it in bioinformatics. Classic engineer right? Measure never, cut twice. Background. I come from regulated software industry, where traceability is not a hobby, it is a compliance requirement. Every change points to a requirement, every requirement points to a test, and when a bug is found you must say exactly which product type it reached. Auditors visit. They do not laugh istg! So I assumed bioinformatics was the same, and built github.com/QuietFlare/clew. It reads the Nextflow lineage store and answers for ex: these two samples were swapped at intake, what did they touch, and what do I do with each output, and can seal that answer as a report. Now the stupid question. Is that a real need? When a reference input or container turns out faulty after a run, does anyone in clinical or regulated settings have to produce an impact record an auditor would ask and accept? Or does everyone just type -resume, say a small prayer, and move on? I would honestly like to know which world I built this for. Thread in Slack conversation

Hey folks, I thought it might be of interest to this group that we added lineage for all full size tests for all pipelines. They should be queryable using the seqera platform API. During the hackathon @Adam Talbot also worked on a plugin that can compare snapshots on the full size tests to validate if outputs changed since we cannot use nf-test for this. It still needs to be rolled out to the template to be available in all pipelines. sarek example: github.com/nf-core/sarek/pull/2327/changes Last, @Rayan Hassaïne added reporting to the website to track which pipelines have full size test and have it running successfully (waiting to be merged PR)

The pipeline health page is https://nf-co.re/pipeline_health