 Ok. Right, thank you everybody for coming together, we're going to do the day one wrap up now, so I'm not going to talk for very long. Thank you everyone for working hard, it's been fun walking around saying everyone their heads down buried in deep code, discussions, that's what we like to see. I'm going to get one person from each group to come up and just quickly summarise some of the things that they've been working on. Mae'n dda i'r ddweud, nid yw'r ddau, a ddim yn ddod i'r ddau. Iheithio, iawn? Dwi'n ddau'r ddau'r ddau'r grwp erioed wedi bod yn ymddangos, si'n fawr i ddweud o'i bod yn y dyfodol. Mae'n ddweud o'n ddweud o'r ddau o'n ddau i gyflymau a gwahanol o'r rhai ddau. A wedi gweld, roeddwn i ddweud o'r ddau o'r ymdwylltau, a'r ddweud o'r 20 ddweud o'r ddau o'r ddau. So, all of this work has already been merged, and I'm very happy with the productivity today, so please, if you could give a round of applause. So, the documentation group is kind of special in a way that we have many first time contributors, so it's very amazing to see people kind of push, understand things little by little, and start contributing. So, that's the quick summary. Who wants to go next? Pipelines? Sorry. So there we are. Okay so we are working on pipelines and the general idea was either DSL2 transition bug fixes and we also got a lot of new pipelines adjusted today and I think we still haven't reviewed them all so hopefully we get this done soon ac we try to implement the body system to rapidly review PRs, and I think it worked well because nobody complained about open PRs. Maybe just quickly go over the pipelines that we worked on. So eager was, James and Jack worked on it, started to work on the conversion to DSL2. Then on Zarec we try to do some bug fixes, make the AWS tests run smoother, and Susanna started working on a multi-QC fix. For the liver CT analysis, Lewis and Aaron worked on various things. Okay, sorry, it got cut off. We will have to format this better tomorrow. And then for Fung's scan, Anna, Lewis and Jasmin worked on the BGIS summary table for the SM RNA-seq Alex and Rob finished the FASP adapter detection PR and merged templates, template updates. And documented stuff. And then for tax profiler, it looks also like lots of new tools. And single cell RNA-seq issue cleanup. And yeah, iGenome's various other things. Tau typing is a new pipeline. I think that we still need to review. And then HGTSEC is, I think, working on the new module structure that recently got merged to get it fixed there. Protein fold, more bug fixes. And last but not least, airflow, I think, from Susanna and Tizella to have great condo versions and working on Docker profile for M1 chips. Oh, sorry, one more pipeline differential abundance for Bosch and Tizella. So they were, I think, getting started on how to structure this and move it to NFCore from the cubic pipelines. Infrastructure, or that one, you go. Thanks. So team modules, let me also refresh. So many people contributing to the modules team today where we focused on adding new modules, fixing module tests and improved modules. So all of these are the listed team members and maybe summarising with general updates. So Christian is currently working on simplifying the creation of ARM images to be able to run all the pipelines on the Apple M1 and M2 chips. And Alan made a modules and pull request to fix the URLs in the module template. And then we were also working on fixing all of the tests that are failing now after the NFCore modules were structuring, so several people were fixing some of those tests. And then adding a bunch of new modules. So just to mention some, the pretext map module, the cofam scan module, the OpenMS ID filter module, Fulcrum genomics FQGREP module, Chris Presso II, MAGEC, and DSEC differential wrapper that hopefully will then be added to the pipeline. And Louisa was also working on updating the module, the BGC download. Just do add some fixes there. So that's the sum up for today. Subwork flows. That did make some last minute changes afternoon, everyone. So in subwork flows, we're mostly focused on working, as you know, we all changed the module format on you, but that's been in preparation for subwork flows. So these are our team members here and on day one here. So the first thing that we were, we kind of talked for a while about different naming conventions and what we could do with that. And it didn't actually fit on one slide, so we came up with the idea of putting it on a Star Wars scroller here. All right, I guess we're going to get DMC'd on the sound there. So basically we needed to first come up with the input file format and that's the first one. And we need to also come up with a wider frequent input file formats, such as like BAM files and CRAM files, but we just called it BAM instead. We also need to keep up with the meta YAML tags there. The subwork flows should support all possible file types, support by that tool as well. And this was just kind of a whole list of various things that we wanted to cover with this to give you an idea of the scope. So there's also no ordering guidelines. The operation should describe as best possible the subwork flow task. We needed to come up with like, do you call it aligning or mapping? I believe HESH found something that starts with an E that's like a standard for how these are named. And so basically these are all things that we're trying to answer here with this too, if you get the point. And they all should also be lowercase. So anyways, so Seroch, first they've been working on converting all of their subwork flows, renaming them and then porting those into NFCOR modules. I kind of did, partial kind of got me started on a little side quest from December, 2020, where I'm trying to integrate PyTest into the actual template. Instead of just running them on GitHub actions, we'll be running them on PyTest workflow instead. And then I'll do some cool other things like only test on modules that change for example and not test on things that haven't changed based on those. So stay tuned for that. We also have been working with the FG Bio and their new pipeline that's coming out and trying to come back around and import those into NFCOR modules as well, which is a problem because they didn't follow the conventions. We did merge BCL demultiplexing as well with Matthias, who's online. That was from Demultiplex and then he started work on FastQ Align. And we started a few more. And then we also had a BAM mark duplicates as well and that's a work in progress. And then we've also started work on porting in all the RNA-seq sub workflows. And that's it, thank you. Nice to see the whites of your eyes as you tried to keep up with that list. Is it scrolled past? Yes, and now the infrastructure team. Yes, it was Niklas and Sofia, but also Pruno. And others always joined us and asked questions and fixed stuff, like Alan. And Niklas actually played around with the NF tests. He, we have now in this PR a simple prototype for a prototype for a simple process and a module, which then depends on other module input. Yeah, NF test is testing instead of like Python, a PyTest in Python, it is actually in Nextflow. So Nextflow code tests Nextflow code. Julia implemented the NFC sub workflows install command, including nested sub workflows. So we can not only test Nextflow with Nextflow, we can have sub workflows and sub workflows. She fixed the bug in NFC modules updates, which was due to change we made for the modules. And Sofia worked, looked into the website because it takes a bit to get familiar with the structure there. I moved the docs from some links to real files, which hopefully fixes the edit button errors there. And Pruno created the Nextflow context for source graph, which makes it a lot easier to query, to make code queries on all our GitHub repos. So because we, I think we discussed it actually on Slack that we have some that would be nice to have a better search of where is what code used and source graph makes it possible. And he also started working on a proof of concept Nextflow plugin for provenance. So to see the origin of each files and follow files there. So for now, it will be just a simple list of published files, but hopefully in the future, it will be actually a JSON manifest. Yes, that is it from the infrastructure. Brilliant, thank you everyone. That's very quick run through. It seems a little bit unfair almost to go through all of the summaries as far as we have. I was paranoid that you guys would be talking for like 45 minutes each. So there's a lot to cover there. And of course it doesn't really do it justice. So massive thank you to everyone so far. I've done a huge amount of work in not very many hours. And take a moment if you get any spare time to look at these HackMD notes because they've got, you saw there were lots of links and more detail in there. They should be pinned to over Slack channels I think. So you can go and kind of reread them yourself. And hopefully we'll keep adding to them over the next couple of days and see how much more progress we can make. A couple of things I forgot to say at lunchtime when the introduction talk. When you're working on pipelines or modules or anything else, if you spot anything which you think is inadequately documented, could you please add a label, an issue, and make sure that issue is labelled with the ingot hub as documentation. And then the documentation team will be able to find that easily and add it to the project board because we can search across the whole GitHub organisation for any issues labelled with documentation. So just as kind of a small note on how to do that to help them out. Otherwise, I think we're basically done for today. So the plan for the rest of this evening then is we're going to go and have a social and we're going to go down to the secure labs office which is about a 10-minute walk. We can go down in a few different groups because I think if we try and all go in one go we'll lose half the people. Of course, if you want to go back to your hotel and drop bags or anything, that's no problem at all, just look up on. If you type Secura into Google Maps you should be able to find it. But for those of us who are going to go straight down, people I spoke to earlier, do you mind just coming up to the front and waving so people can recognise you? We've got a few volunteers from Secura. Come on, Rob. Rob, Chris, am I asking all else? Harshal can always do it if necessary. So if you're going to walk straight down and just come over here and when someone has a big enough group they'll start walking down and then someone will actually let you into your office when we get there. So it will give everyone a chance to see Secura. There will be a few Secura staff hanging around there. I don't know if Paolo and Evan are going to be there but probably we're going to have some pizzas and some beer. And there will be other stuff. I don't actually know what else that will be there. Then tomorrow morning the rooms will be open from around 9 in the morning and we'll kind of kick off properly at 10. So turn up any time between those times. Anything else? Any questions, comments? Wave your hand. Great, people who are online feel free to keep hacking through our nights but maybe for you guys it's still your daytime and just keep updating Slack so everyone knows what you've been working on. Keep chatting. Meet yourselves as visible as possible and we'll catch up with everyone tomorrow and include all those in the daily wrap-ups tomorrow. Great, okay. Thank you very much. Everyone, we'll see you all tomorrow.