What a difference a day makes The amount of water flowing into Lake Oroville dropped from a hundred ninety thousand cubic feet per second to a hundred thirty thousand in less than fifteen hours a Beautiful sunny day without rain allowed that to happen and California Department of Water Resources officials say they expect that to drop another Fifty percent by tomorrow Saturday. So we're looking okay. We fully expect that we won't have to use the emergency spillway If the rain had continued today There was a strong possibility that the water would have come over the top of the emergency spillway That slope of land next to the controlled spillway and that's the way this dam was designed as part of that contingency plan DWR cleared much of the trees and brush from the emergency spillway That will reduce the amount of debris that would end up in the lake below and float into the Feather River Also, they were able to reduce water releases overnight from sixty five thousand cubic feet per second to fifty five We've released more than double this amount in 1997 and only as recently as 2006 released more water than this and there wasn't any any impacts to the community in 2006 So we don't expect to see any flood event the controlled spillway suffered massive erosion a hole nearly the size of a football field That sent water off its man-made path taking land and trees with it The downstream effects of that turn the Feather River into a mud bath in downtown Oroville The Department of Fish and Wildlife moved about four million small salmon and steelhead from the Feather River fish hatchery to keep them alive Meanwhile officials reassured the public at a news conference that neither the dam nor communities downstream are in any danger This problem is with the spillway is not with Orville Dam There's no erosion going on with Orville Dam Orville Dam is completely intact and is not in jeopardy in any way from this event


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It's still my video, maybe. All right, great stuff. Hopefully, everyone can hear me and see me. Welcome wherever you're listening, and then on YouTube or in Gather. Or maybe you're listening to this long after this has passed, in which case. Good to see you here as well. Thank you, firstly, for everyone coming to the End of Core Hackathon. This is the final meeting that we'll do. This is the wrap up. So we're going to go through the different groups like we have the last couple of days talking about what everyone has achieved in the last three days focusing on today. And then we'll come back to me at the end and I'll do a little wrap up summary of some of the fun bits. And most importantly, I'll tell everyone who the winners are for the different competitions and who's going to get NF Core Ducks in the post. So with that, I'm going to pass over to Fran, who's going to tell us all about the documentation team. Thank you. Fran, you're muted. OK, OK. Hi. So this time, hopefully, no other technical issues. So thank you, everyone who was in the documentation team. I'm very impressed. I told everyone to add their progress to the progress slides, but that is the only thing that didn't really work.  We have 36 issues or PRs that got labeled with Done in this time. And I managed to put them into different groups. One group was created for this hackathon, which got the most, actually. The other one was created during the hackathon, which was still quite a few. But surprisingly, a large amount actually got created for the hackathon a year ago. So great on actually finally getting these issues too close. So these are the ones that are done. But actually, there's a few more that are pretty much done that are currently in review and we're waiting either for the final lint checks to be done or just like a person pressing a button basically saying that this is done. So this is 12 more issues that can be solved very, very quickly. And then we only have eight issues that are still officially in progress. So super good for everyone. We basically worked on pretty much everything we wanted to. And one of those is mine. So I'm at fault here. For me, the highlights were basically that we have a lot of documentation that will help people to work on pipelines. Like we have now documentation on how to contribute on existing pipelines, how to use and install prettier, how to use the pipeline schema properly, these kind of things. I was really glad to see that for beginners like myself, there's more documentation available now. So that is it from my side. And now I will hand over to Matthias. I'm just going to say this, but by the number of GitHub tabs you have open in your browser window there, we can see how much reviewing you've been doing as well. So that was awesome work from the documentation team. Yes, hello from me, from the infrastructure team. Website part, Sophia worked on parameters like the link icon next to parameter, which is finally merged, looked into some other issues where we still need to figure stuff out. Nicola was working on adding the module usage examples to have a modules page on F core, actually already for the new website rewrite. And Adran got his PR merged. So we have now tests for creation of tests for sub workflows. Then I actually got to do a bit of work on the schema, the YAML schema validation for the meta YAMLs and the tools command and the modules linting command. So we are almost there now. I just need to fix one more test then it should be good. So Coutic was still working on the schema converting nulls to none. Fabian was adding stuff to the Pytest fixtures to make the tests faster, which is really needed and will be really nice and had them added profiles for Google. And James tried to sneak in documentation for something very important, the partial alignment format, which we all know and love is that you need to add enough widespread spaces that everything is very nicely aligned. So thank you, James, for that documentation. But now over to London and Google. Do you want to, shall we share your screen or will you- I can keep sharing screen, you just say next slide. Hello everyone. Right, so we've kind of been in stealth mode the past couple of days mostly because we didn't know whether we could achieve this. So for a long time, next slide please. For a long time, what we've been doing on NFCore is actually doing full size tests on AWS. And that's been awesome because we've had to test these pipelines in the cloud which typically you can't do otherwise. And so as a result of Isha and Adam starting the team, it's a crazy sort of welcome into the team starting at the hackathon but they've absolutely just smashed everything. So Isha was working on GCP, her team gave us tons of credits whilst we were here to start using these accounts and testing on NFCore. And so we've created a compute environment in NFCore for now, which is just a placeholder in the future we'll have a more permanent option hopefully. But then Isha started testing on GCP by the NFCore and various test profiles just to see that we could get it working. Next slide please. Adam done the same thing on Azure. He's got tons of experience with Azure and so it's just been awesome having it. As you know, we've got credits from Azure in September about $20, $25,000 in credits from them which we haven't really put through Paces because we've not known what time of day it is really with Azure but Adam knows his way around that stuff and so he's set it up in half a day basically and done all of the same stuff and tested it out. Next slide please. And then Rob and I were working on the bane of our existence which is GitHub Actions and rewriting all of the existing AWS CI tests to make them more generic to run on any cloud vendor. And so this turned into a bit of a crazy rabbit hole where things were breaking for unobvious reasons. But we've spent pretty much the best part of today fixing all of that up, adding secrets to the NFCore account adding workflow dispatch logic that allows you to either run all of the tests full size tests on all the cloud providers or for you to be able to select which cloud provider you'd like to run the tests on a bit like what we've got already but in this way allowing you to select where you'd like to run them. We even added a custom runner. So we used Adams as your magic to add custom runners because the CI tests weren't running and we needed to get this done before having this conversation right now. So we managed to get that done and we're in a state now where RNAseq is ready to go with the CI tests. We just need to test once we've merged into master because we can't test a couple of things until we've done that. And then once we've done that, it's great. So next slide, please. This is what it looks like. This is the testing. So I'm not sure how clearly you can see this but there's this. So RNAseq runs two tests for salmon and for ASEM. And we can now see in tower via the integration and the get up actions that the full size tests are being triggered on all three cloud providers for both of those different options. So yeah, this is a massive step forward for us to test NFCore pipelines on all of these different clouds. When this is stabilized, we'll push it to the template and hopefully make it available for everyone. That's it from us. Thank you. Back to Tübingen with the infrastructure team. We just a quick summary. We were total 17 team members with fluctuation with like documentation and stuff like that and other groups. And main thing is a lot happened in tools with 37 PRs merged and 27 issues closed and more closed and merged than open. So we go out with the miners, which is good in this case. And on the website, there were eight PRs merged and three issues closed. There we, it's more of a equilibrium between opened and merged issues. And I guess that was it almost from us because we also had some smaller achievements. We have the team win of the quiz. We broke Github, we broke Kahoot and we broke the tests, so we're not running. So success from the infrastructure team, everything was not working. That wish you a good evening and on to who's next. Is it you? I think Maxime, but I can't. Maxime, let's see. I cannot share the screen while you're still sharing the screen. Thank you. Stop and we have the module. So I let Adam present the module. Great. Very pleased to talk to you today about the progress that's been made on modules and thank you to all of you who've contributed on this. I want to just start with a wrap up around those of us that have been working on imaging and really a very thank you from us from welcoming us with microscopists and image analysis into the CNF core community. It's really exciting to be joining you and to bringing imaging to NF core. In imaging, the team largely over in the teaming insight have started at least 11 modules now and several of these are either merged or lined up for merge once we can get through tests and get our way through the merge queue. And this gives us a place we've almost got the pieces we would need for a draft workflow for multiplex imaging processing using key NF core or using all NF core modules. And this sets us on a sort of longer term roadmap of bringing our MC micro pipeline into NF core. So a huge shout out to everyone who's worked on that. And thank you for all of us who've held our hands, reviewed and advised us on that. And thank you to everyone here. And if you want to learn more about bringing imaging to NF core, you can join us now on the new microscopy channel. It's got folks from the MC micro pipeline from Janelia from the EBI. And we look forward to talking more about this. You know, a number of modules. I went away with the statuses on here but we've made really good progress particularly on getting test data set up and getting modules merged and getting test pass and all sorts of things like this. And these do key processes in multiplex imaging like core subtraction, background subtraction, registration and cell segmentation. We've also on the sequencing side got continued growth here. There are nine new modules that started work on just today. So I think there's huge progress going to be going on after the hackathon. Thank you to all who've worked on these and progress still going on on 15 more modules. Some of these merged, some of these tests complete and really getting very close to merging. So congratulations to all who've worked on these as well. We've really expanded the suite of modules that are going to be available here. And that's me from me just to say thank you to all who have worked on modules during the hackathon. It's been an absolutely great time. Thanks. And I can stop the share and pass back. No, that's still because it's still us. So let's share again. Sorry about that. And now about like the sub workflow. So sub workflow, thank you everyone like again to work on sub workflow. What we like, what we, what Edmond did was like to add like some more CI so that we can finally facilitate like the usage of NF tests. So at some point I will be like super happy when we like manage to do that. That would be nice. There's not something that we will be able to do right now but that's like a good first step like to be able to switch completely to that and ditch by test. So I think that's a good thing for everyone. And then the situation I guess was a bit like slower for the sub workflow like today. So I have like two sub workflow for Selvanger and one sub workflow like fixing like the index and being in BAM sub workflow. And I think that's all for the sub workflow team but thank you very much like to all of the different contributors because that's been like a huge stuff. And as usual, like people have been like shifting in between teams. So yes, thank you everyone.  No, it's me. Oh, sorry, it's a pipeline. Yes, of course. It's the most important one, no. Hmm. All right. So we are working on pipelines of course and James has made up the shocking like of gifts in this presentation. In total, we had eight new pipelines worked on today. So I counted everything as a new pipeline that doesn't have a first release but some of them have been around for a little bit now. Then we also had three pipelines that are non-end of core pipelines but I think they either converted to follow the end of core or next flow standard or completely converted to next flow. So that's pretty awesome. And then we attend existing pipelines and two of them are converted to DSL too. So for the new pipelines, we have Panjinom and looks like Simon made bunches of progress today by updating tests and adding new local modules. Variant catalog is actually ready for the first release review which is needs a little bit more documentation and we can then hopefully release it pretty soon. Viral integration is also getting ready for its first release. So we have a bunch of the new pipelines will soon be migrated to the old pipelines in the next second on. Metapep as well has made bunches of progress it looks like been moved to the end of core repository, bunch of issues solved. So great work there. And same for spinning Jenny, which was proposed I think on Monday and then looks like it was immediately worked on and so much stuff was done already. And we now know it's a pipeline it's actually a non-biinformatics pipeline probably one of the first ones and it's for models and economics. Then we have Lightsheet, the Lightsheet-Greekon pipeline which is also part of the imaging pipelines and as I think it was mentioned already there's a new microscopy channel to discuss everything microscopy related and also Conrad managed to fix the next flow bug. So congratulations to that. Yeah, we have another new pipeline the BAM to PASQ pipeline that is also almost ready for the pseudo PR for the release. Nice work, Susanna. And something happened here on the slides but MacMap and Semi-Sag both had a lot of stuff done in the last few days. I think the MacMap was especially worked on a tubing and everybody was making many, we're able to solve many issues here. Yeah, then we come to the non and of core pipelines. So we have the ensemble sequence pipelines pipeline I'm not so sure what the pipeline is about but we're modifying the dependencies and then also starting to work on next processes. So nice work. We have the aquatics symbiosis co-bion check pipeline. Yeah, I don't actually know what the pipeline is about but really nice work. And we have a cosmic CMC pipeline. I think it's one of the cancer genomics pipelines but yeah, maybe we need to check out the repository here. Then we have bunches of old pipelines that need bug fixes and feature requests and template mergers and all these things. Oh, and of course the SL2 conversion. So dual RNA-seq it's been on a really good way to be ready for the SL2 release. Same for EGAR, I think yesterday on a Monday there were many more successes but we still need to get a few reviews in and finish some of these issues here. As I like, we've made a little progress on a little progress on some small issues but also Alison wrote some really nice documentation for us cut. So thank you a lot for that. Viorecon is getting a new SAP workflow for Freyja for wastewater variant analysis. That's really cool. Tax Profiler has been working on fixing issues with Sophia, Lillian, James and also a bunch of things are ready for review. So it looks like we need to do a few more reviews in the next few days to get everything merged. Protein fold has made progress for the GelView visualization. Ampli-SEQ is also able to merge some of their things from I think that we're still on a review like yesterday or Monday, similar for FuncScan and then the last two pipelines I think are TuxEq and RNA-SEQ. So Viorecon worked on supporting some optional data and RNA-SEQ had a release, I'm guessing Harshal. So yay, congrats to that. As a summary, we had I think at least 42 team members but I have the feeling there was probably quite a few more that just didn't end up in the slides. There were about 25 pipelines worked on or at least those were the pipelines that ended up in the HECMD slides. Two new pipelines started. We had for the first time three non-NF core line and of core pipelines being worked on. QuantumS and RNA-SEQ had releases, QuantumS directly on Monday morning and we in total completed 31 issues. Six are ready for review on 33 are in progress and I would think there are probably many more issues that just didn't end up on the project board which we used for counting here. So James made these slides. Yeah, good job everyone. I'm looking forward to the next hackathon and I hope everyone had as much fun as we did in tubing either online or in one of the other hubs. Amazing and thank you James for making the slides. Awesome, right. Is everyone finished or have I forgotten anyone? Speak up now, otherwise I'm gonna go into the final stretch. Okay, firstly, yeah, so to reiterate, thank you very much for all of your hard work. Everyone has a huge amount of work. This final wrap up is always one of the most difficult to do because everyone's like fantastically putting in their things at last minute and everyone's doing our slides with like two minutes before the deadline. I'm no exception. Also wanted to point out that due to the nature of this hackathon, both it's the biggest we've ever done by a large margin. Also the fact that we've got all the different distributed sites. I know that some of the sites you've had slightly different focus. So some sites have been working on getting set up in the local infrastructures, more introductory work for Nexflown and of course other sites have been working on more like local specific projects like some of the projects being worked on in Cambridge. And I think probably quite a lot of work has not ended up in these wrap ups. So if you're watching these talks just now and thinking everything I did in the last three days has not been mentioned. We want to know and it's not too late. So please do tell us in the Slack channels because we will write up a blog post about this event in the next week or two. So it's still time to like get everything together and usually a lot of stuff comes out of the woodwork as the dust settles. So we want to hear about what you've worked on, what you've done in your contributions. So please, please do tell us. Right, I'm going to share my screen. Hopefully everyone can see this, no problem. So my talk is just a little bit fun really and a bit of a retrospective on the past three days from my point of view. So I kicked off the introduction with some statistics about who's joining the hackathon. Some of these stats have changed a little bit. This is the one that's had the most drastic change. So everyone here, you are now officially part of the NFCORE community. So welcome, thank you for being part of our hackathon. And I hope that you come back for future events and boost up that section of this pie chart saying people have been before, it's been a lot of fun. We hit quite a lot of milestones. One of the ones that flagged up was the number of people that are part of our GitHub organization. This number is always pretty low because you don't actually have to be part of the GitHub organization and of course to do most things.  But we've hit 700 people now, which is massive. So these are 700 highly engaged people working on this and actually developing code for NFCORE. So that's really significant, I think. If you're not part of the GitHub organization and you've never really thought about it, there's a Slack channel called GitHub Invites where you can go and ask and post your GitHub username and we can add you and then you can start assigning yourself to issues and pull requests and all that kind of stuff. So really cool and I think we're about five and a half thousand on Slack now and I was wondering if we were gonna hit six during this event and we got pretty close. So I reckon another two or three weeks and we'll be probably 6,000 people on the NFCORE Slack, which is crazy. Right, the important stuff onto the socials and highlights and also of course who won. So I'm gonna start off with the winners because I don't wanna keep you waiting too long. So I'm gonna start off with the bingo actually. So the bingo was these bingo boards where everyone got a different board with different cards and you had to tick off as silly things happened and the winners were, these people, I'm not gonna read out everyone's names every time because it's gonna take ages and I'm gonna just embarrass myself. So these are the times of day yesterday that the bingos were won. So no one won it on day one and all the winners came in on day two out of three and we could just pips the winner at 10, 19 in the morning. But she's told me she's already got 20 NFCORE ducks. So I'm not sure we're gonna send her another one. So I thought we'd add in a fourth place here. So Nicholas is just snuck in at the end there. So congratulations to all of you with your excellent bingo skills. Send us me or someone in the core team or your details in the Slack message or we'll follow up with you and we'll get something in the post. So congratulations to everyone who did the bingo and also congratulations to everyone who managed to get a bingo, but not onto the leaderboard. The socks. So I know some people had some doubts about Maxime's performance at hiding socks this time round, but I think that they did all end up hidden in the end and not all of them quite as easy as the one in this screen grab but with all the scooters, all the racing cars stuck on it. But yeah, thank you Maxime for putting loads of time into hiding always and sorting out the gather town. Much appreciated. I think in the end, there are 10 pairs of socks to be found if I'm not mistaken. And the winners to find those 10 were these people. So Matthias is the winner number one, but also if you will get duck in the post. So congratulations. And is it, is it this or someone in Germany was very sad to not get there in time I'm sorry, but I think you, you work with James, right? So maybe, maybe he can give you a duck if you plead hard enough. So awesome work. Right, the Kahoot quiz. Most of you were, well, a lot of you were there. So you'll, you'll see in the results already, but for anyone who missed it, the results are, oh yeah, I had 143 people joining the quiz simultaneously. I know that some sites did this async but unfortunately we couldn't really include you in the results here. So 143 people all at once answering the same questions. And these are our winners. Congratulations everybody. We'll follow up with you for a duck. Right, onto the photos. When I started putting these slides together, I thought I'd just do kind of highlights through the three days. And I started trying to group them and stuff, but it got more and more random as we went on. So in the end, we've just got a bunch of photos, which I really picked, it's my apologies. But amazing work. Everyone who contributed a photo on this Slack channel for all the different challenges. I think there's only like two or three challenges out of all of them, which had no answers, which is amazing because we put in a lot. I wasn't sure quite what the response would be. And yeah, I think it's been one of my highlights of this hackathon is looking for all the photos of everyone doing crazy stuff. So here we have a London site being an NFCore Apple, I believe, on a logo on the left hand side and Arshall doing a signature selfie face. We should trademark that phrase as well. What have we done here? Oh yeah, we've got the very difficult hackathon hangman. Everyone on the left in Stockholm and I don't know what was going on. Apparently this is a social activity, a planking contest or something in Germany. What did I put next? Oh yeah, this was the funniest jokes challenge. This was my favorite. I've now told this to most of the people I know. Yeah, I thought that was a very good job. I don't think we did that one. Excellent job. Suitably nerdy. We had, here we've got the team in Brazil on the left or pulling a cheesiest grins, but then that dirtiest monitor, that made me sad that did. That was impressive. But it was one of the challenges, photo of your dirtiest computer screen you could find. But then I thought there was another challenge about who had the most stickers and that sort of made up for it for me. Hopefully Marcel will lend you a screen wipe. Great work. What did I do next? Yeah, we've got some pictures from Galatown. We've got some fluffy dogs. Got people really acing it on their avatars there. Like for like, got Maxime on a beach and I think Rika's coffee cup. Don't know why I put that there. Favorite coffee cups. Got some apples. Got fans, Apple logo Matisse's pixel art work, we've got some Apple cores up, hosted on laptops and things. Great job everyone. Oh, I've got some nice sunsets and some fluffy animals. Always see all the animals joining in the activities. Yeah, I think it started getting a bit more random at this point. Got some temporary tattoos from the, these were from a summit last year in Barcelona. We were one of the freebies we gave away in the gift packs with some little temporary tattoos. So that's what the Brazilian crew are rocking up in the top right there. Lots of photos of people enjoying their pizzas. Which is very good to see. I'm glad that's worked out for everyone who's done that already. More pizzas, more stickers. Hopefully everyone has sorted on the pizzas or will be sorted soon. Teamed down in South Africa there. Okay, set up with stickers. That's the most important thing. An Edinburgh top right, Barcelona. Yes, Jimmy. And I'll put in a quick, a few of the group photos at the end for those of them who, for the people who managed to get outside and take a photo of their local sites. I don't have everyone here by any means and some were coming in with mere seconds to go before I started presenting. So apologies if I missed anyone. I think these guys are from Francesco, so it's Italy, I guess. I've got some Poland here. Also top works on the whiteboard drawings, guys. I'm seriously impressed there. Oh, that was a bit low res, sorry. My bad, I think that's people in Germany and tubing in. Who have we got here? Oh, I should have looked up where everyone was from first. Sorry, I'm not sure which site this is. Anyone gonna help me in Stockholm? No. You can tell me in Slack, sorry. This is the French crew. How long must this have taken? These, those are all race cars and we're quite zoomed out here. So a serious effort on the Cather town space there. I'm really impressed. That must have taken a long time and a lot of accurate driving. Yeah, good work. Oh yeah, special mention to the crew in Cambridge, the Wacom Trust Sango Institute and the EBI and all the folks on the genome campus down there. Amazing turnout. So big thanks especially to Bianca who organized that site. I hope you all had a brilliant time and thoroughly hooked now on NextLow and NF Core. And yeah, I hope you got a lot done. That's amazing. And final one, I thought my personal favorite photo of a whole scavenger hunt, I think it's got to be these guys in tubing and rocking out with the air guitar. Oh, it's very, maybe chuckle when I saw this. Not just doing air guitar, but doing it in such a picturesque location. Excellent work. Loads of photos I haven't done. Go and take a look on the scavenger channel if you haven't. Yeah, really happy things. Right, and just to finish up a few little reminders, we've got the survey for the NextLow and NF Core survey which we do every year. I posted the link in Slack as well. It's a long one. Please do go and fill it in if you haven't. It really, really helps. We've got the dates for the next events. So it will be in Barcelona and Boston. We're going to have both an NF Core hackathon and summit. I haven't actually confirmed this, but I assume that it's definitely going to be in person at those sites. And I assume that we'll have at least some online component for some of them, but please do pick off those dates in your diary. And for things like that, those kinds of questions where I'm not quite sure, please head over to this website and tap in your email address and we'll send you any updates when we have them. We did the quick, very badly organized tower demo for Harshal, just for anyone who is interested. If you missed it, or if you didn't know what's happening or anything, we've got another one coming up in April where you can go and sign up and join. Yeah, and that's it for all the notices, I think. Big thank you to all of our sponsors. Chan Zuckerberg Initiative funded us through their central open source for science grants. Sakira Labs helped out with funding for the pizza along with CETI grants and big supporters of our community. And as Harshal mentioned, all of the three cloud providers helping us out with credits for a cloud computer so that we can automate all of our testing for all of this pipelines, which makes a huge difference. So thank you. And thank you to the amazing core team and also thank you to the amazing local site organizers. We could not have done this without you, obviously. I'm really, really happy to see so many people getting involved in helping us organize these events. It's been really, really nice to see. Okay, with that, I'd like to say thank you one last time. Hope to see you in October or before and come back and merge your poor questions if you haven't done before then. Thanks for all of your efforts. And yeah, yeah, just great stuff. Cheers everyone.


I know this steak isn't real, I know that when I put it in my mouth, the matrix is telling my brain that it is juicy and delicious. After nine years, you know what I realize? Ignorance is bliss.