 Good morning everybody. Thank you for joining. Fantastic to have so many of you with us today. And welcome to the March 2021 NF Core hackathon. I've lost track of how many hackathons we've done for NF Core analysis, maybe the fourth or fifth, but this is by far the biggest and it's really exciting to get started. So this morning we're just going to have a couple of short talks. We're just going to quickly basically go through how the hackathon will run what there is free to expect. We're going to talk a little bit just in brief about what the different projects we have set up and then we'll split up for group distribution and hacking after that and we can all get started. So let me jump straight on and start talking through some of what we're going to do. So you can find all of this on the NF Core website. So that's where you should go if in any doubt whatsoever. There's a lovely schedule there which should display all the times in your own time zone wherever you are and even highlights the different table rows as we go through so you can easily see what's on it right now. And we're working over three days. So not everyone's going to be around all the time but hopefully you can join as much as possible. So the rough schedule looks like this today Monday with 20 seconds we are starting off with welcome, group assignment and then basically each day we have a morning of hacking. We have a quick informal group catch up around lunchtime if you're in Europe and then we kind of do a bit more hacking in the afternoon and then we have a kind of a wrap-up for Europeans in the time zone handover as we've caught it which is basically a summary of what we've done during the day in Europe and also that's a good time to check in with other people in other time zones so that they can have that as their start to the day if you like. All those days are pretty much the same apart from on the 24th and we will also have a social event after we finish more information on that soon. So the ones highlighted in green here will be on Zoom as we are right now and live streaming to YouTube. Those live streams will be on YouTube after the event as well so I expect quite a few people still on bed depending on your time zone if it's like 4am in the States or whatever and so we expect that and so all of these events are on YouTube so you can catch up whenever it makes most sense for you and then these ones in blue are more informal they're not going to be streamed they're not going to be saved and we're going to use a tool called Gypsy for that which is like Zoom and runs in your web browser and that's very informal and each project has their own Gypsy link which you can find in the Slack and you're basically free to use that link whenever you like just to kind of chat if it's useful and we'll have these times for when we actually do a little catch up and try and get everybody online. So who's here? A little bit of stats on who signed up to the Hackathon. This is by far the biggest hackathon we've had with NF Core by a long way. So far all the hackathons have pretty much grown exponentially and this is no exception. We have 127 people who filled in the registration form which is fantastic. I think the record we had until now was probably the hackathon we had last year which was about 60 people off the top of our hand so this is just really exciting to see so many people here today. A few of you about a third of you have been to some kind of NF Core event before and then we have lots of newcomers so welcome if this is your first event with NF Core and hopefully won't be your last and so it's really good to see lots of lots of new faces and we're pretty well spread actually. As normal we have a bit of a European bias due to the historical origins of NF Core but it was great to see a lot of people or a lot of dots appearing in other countries around the world which is really exciting. It's always been a big aim of mine with NF Core is to try and kind of make it as widespread and accessible as possible so it's really nice to see and welcome if you're joining from one of these areas especially. We've got a good mixture of people joining so we have a fair number of you filled in you have no experience writing NF Core pipelines which is kind of what we expect but quite a few people I've just noticed that these categories are not sorted okay but quite a few of you have said that you're either some experience or very experienced which is really good. This is also a bit of a departure from previous events where nearly everyone has been new to NF Core so it's great but we've got a good mixture today so welcome if you're new and hopefully there's going to be a lot of help around and a lot of you'll be able to mix and spend time with people who are a bit more experienced and pick up a lot and learn a lot during this event. Also part of the registration we asked you which of these kind of project themes you are most interested in we actually asked you to rank them but just to make it simple here I've just taken your top picks and pretty much reflect what we expected that a lot of people are interested in contributing to DSL2 which is this new language for next loan the next direction the next wave of the NF Core project and a lot of people are interested in writing pipelines and contributing to pipelines. This pretty much follows previous hackathons and what we expect and it's great and we have a corresponding kind of setup with a number of mentors and leaders we have in those groups so hopefully there will be plenty of support and lots of things to do and then there's you kind souls who are eager to help out with some documentation and framework tools which is always essential part of every NF Core hackathon and the NF Core community. Okay so how's this hackathon going to work every hackathon is a bit different in kind of how I set up this is a fairly relaxed one but we have kind of a rough kind of idea of how we're going to split this up and organize ourselves so we do everything with NF Core with Slack where all of our kind of discussions happen or our kind of community consensus and decisions so jump on Slack if you're not there already and join the hackathon channels which you're most interested in and basically chat with everyone and just kind of keep up to date with what the group's doing it's a good kind of place to start and when you're ready to actually start doing some work we have GitHub projects boards which are basically a way to organize GitHub issues across multiple repositories so if you go to the NF Core organization on GitHub and click projects at the top you'll see there's a bunch of different projects as a board for each one of the hackathon themes so jump on there and you'll find a column on the left saying to do with lots and lots of things to choose from have a scroll through there have a read through some are big some are small some are easy if you're a newcomer some will hopefully be labeled as first-timers only which are ones which we think would be a good place for newcomers to start and but also just just you know have take your pick basically and grab something that you think looks interesting once you found one which you think that you can do go to that issue and so click on that issue and follow through and you can assign yourself to it on the right hand side if you're a member of the NF Core GitHub organization and this is important because this means that the anyone else who's looking at the the boards and the issues will see that you're working on this and won't also start working on the same issue so it basically kind of claims it as yours and stops anyone else so try not to assign yourself to loads of issues because of course that stops other people from working on them so just try and have one the whole time that you're assigned on all right then it's time to write some code and so the usual kind of workflow applies here and we have a talk from a couple of days ago if you're not quite sure how it's normally looks for NF Core so check it out on our website for GitHub contribution basics but basically do your work do your coding on your own fork of that repository make a pull request and get it improved I should note here that the hackathon is always quite focused on writing code but a big part of it is also reviewing other people's code so especially if you're feeling a bit more comfortable with NF Core please try and dedicate a bit of time to looking at other people's pull requests and going through and doing some reviews if you're not completely comfortable you don't have to merge stuff but just doing reviews writing comments checking fever recording testing hours is really helpful we always have a big big backlog of pull requests to go through after every hackathon so any help there is very very welcome welcome okay each project has a document on a website called HackMD the links for all of these are on the website and on Slack and once you finish your little task hop on to HackMD and just make a note of it little description and we're going to use this in those group kind of wrap up sessions for the project leader to summarize what everyone's been doing so if you don't write it there then other people won't know that you've done it and it's also useful for us to write up after the event so it's quite important it's quite easy to forget so please try and try and keep that in the back of your mind as you go along and then yeah basically let people know what you've done have a little little celebrate little shout about it on Slack and find your next project and keep hacking oh yeah I should have put this in first really so it's a Slack if you've seen any talk by me or anyone else and then I've called before this will be old news but you can get your invite to Slack if you're not already there I think we gave out this link on on Slack so I'm assuming everyone will be there but hop on to the Slack organization so the main channel we have for the hackathon is called Hackathon March 2021 but then we also have a bunch of kind of other channels to try and split up the discussion like I said there's quite a lot of us so it'd be very noisy if everyone's chatting at once in that main channel so we've got a project channel for each of the kind of project themes and then we've got one called Help I'm not sure how much we'll use that I'm assuming most people use the main hackathon channel for kind of general stuff but maybe if if you're feeling that you're being drowned out a bit you can hop there and kind of wave your hand and ask for help honorable notion mentioned also to a new channel that Maxime made a couple of days ago called a Spotify playlist so we have a shared collaborative Spotify playlist for the hackathon which is set up and there's even a Slack integration so you can just do slash add and then the name of your favorite song and it will be added to that playlist so if you're feeling motivated or you want to change the style of the playlist a bit get in and get involved there's also details about how to listen to the playlist on that channel okay a new thing we're trying this time is the idea of having some mentors within the hackathon this is basically for people who are new and they need help and don't really know where to turn we've had people volunteer through the registration to be mentors and I've put these to the emoji and because we've reversed all the hackathon mentors to set their their Slack little status as a little a little wizard or an age so uh so that these people are hopefully easy to kind of identify within Slack and you can ask for help and kind of get feedback from them so feel free to ping anyone you see with this this emoji and try and get help from them and also we'll try and just jump in whenever we see anyone asking for help we've specifically tried to make sure that there is at least some some mentors in all the different kind of relevant time zones so if you're working in Asia or in the Americas and and over your attains are in bed then hopefully you'll still have some people online who are there to help and it won't be completely left out by yourself it's going to be a bit quieter those hours I suspect but I'm hoping that we can keep keep those poor requests trickling in 24 hours a day for the next three days just a quick word on on safety um so we have this is a big event we have a lot of people now and so we need to kind of be a little bit more careful and one of the things we've done quite recently uh with a lot of input from Anuka especially uh in the NFCore outreach team is to rewrite our code of conduct and by being here today and being involved in the hackathon you are implicitly agreeing that you're going to abide by our code of conduct please check out it's it's not very long it's very easy to read and just kind of sets out what our expectation staff at the NFCore community and that's up on the NFCore website and we also have a few extras added to the hackathon event web page which are just specific for the event and but basically it kind of boils down to being sensible really um the schedule doesn't have any breaks written in um because we don't know what time zone you're in so just you know be kind to yourself remember time to eat um don't don't trial other people don't be mean um try to not share the the zoom and the jitzy links on on social media just to avoid other people kind of zoom bombing us um youtube of course is fine uh and if you're going to take any screenshots or or anything like that please just ask people before you do so just so that you're not posting stuff on the web without people's consent uh and we put this as part of the sign up just to get gage people's kind of feeling on this and there are a little wedge of people there who are not really very keen on being photographed which is completely fine so just this is just a reminder just to ask people before you do that if you're going to as much to myself as anyone else um if you're if you're in need of help then uh Renuka here is our safety officer and of course a new thing for us um so she's the number one person to go and go and talk to if you've got any concerns whatsoever um Mike he was in the states um and he's uh agreed to be a backup for if Renuka's um asleep and uh failing that when there's also the core team and any mentors so you can go to if you'd like to have any support or help or have any questions um lots of people here are beginners and you've said that you're kind of interested in getting up to speed with NF core and next flow um a little bit different to previous hackathons in the past we've we've had the hackathon interspersed with lots of talks and kind of training materials whereas this time we're really trying to make the hackathon purely about writing code really um so to offset that we've been running this new course of weekly um talks every Tuesday afternoon or every Tuesday lunchtime if you're in Europe um called NF core bytesize which we've been streaming to the web and putting them onto the NF core website so if you go to the events page on the on the NF core website you'll find all of these and all of them have youtube videos attached and most of them are about 15 minutes long that's what we aim for so they're nice and short and we've specifically picked these previous seven talks as the kind of things which we would have talked about at the hackathon previously kind of up getting people up and running um if you're new to NF core and new to next flow so uh please have a look at those if you're new that's a great place to start and a great place great way to spend your time doing a hackathon to to get up to speed we also have a youtube channel where all these are and there's a lot of talks there which might be of interest as well especially have a look at the playlists uh we maintain a playlist of videos of talks that we've done on other people's youtube accounts and quite a few training events and things there so that's also lots of good material for you to dig into um uh if you're new to next flow and you want to pick up next flow rather than something specific to NF core check out um secure the guys uh who who maintain uh next flow they've put up all of their training materials online and they're a fantastic resource so have a look at that that link and you'll be a next flow wizard in no time and just generally check the NF core website we have lots of documentation and help there so dig through usage and dig through developers and see if you can find anything we also have a page called uh resources i think which is all about next flow um training materials from across the web okay i'm going to start wrapping up so a big uh big thanks to Chan Zuckerberg initiative we are very grateful to them to to fund us as part of their central open source software for science that EOS grants which are quite a quite a very kind of um progressive uh grants actually to specifically focus on on something which has previously been difficult to find to grant money for so we're very very thankful to them um many of you should also be thankful for to them if you're you're wearing your your your goody bags today um and but also it's not just that i mean they they help us out in lots of ways and and that grant money goes to lots of things within NF core so we're very thankful for them but especially for today's hackathon and uh if you are wearing some NF core stash some of the good stuff um be aware that in Slack we've got a special emoji to celebrate that and get them on now get them ready because i think we're probably going to do a group photo of everyone in the second wearing your your NF core socks so be prepared okay and with that i'd just like to say you're very very welcome thank you for joining us i hope you have an excellent time in the next few days have a lot of fun make some friends and uh and i'm going to pass on to james i think who is going to talk to us a little bit about some of the social aspects that we're going to have in the hackathon in the coming days so i think we saw Maxime actually but yeah sorry it's fine it's the same uh yeah so uh basically welcome everyone it's uh great to be with uh everyone once again and it feels like it feels like we are almost like seeing just seeing like so many people is good and i really like that uh yes so first of all i just wanted to highlight you that the main social chat will be the main hackathon Slack channel so as if you need like really like to speak to anyone uh go there uh for the Spotify playlist so yes Phil already mentioned that so it's Spotify playlist that we started during our first hackathon so for those who were lucky enough not to be there you know as a chance as well to listen to to this playlist and you can even add some more songs the command is very simple slash add and then you specify the track name it works in in every channel but i recommend to do that in the Spotify playlist specific channel that way we don't uh we don't flood the main Slack channel James i think it's back to you and then throughout the three days we're going to be trialing some more fun and games so one thing i'm going to try is a NF call bingo so i'll post the link in the Slack channel just now and it's also on the website below the schedule table so you can feel free to open that up and keep that open throughout the the event and if you get yeah bingo five in a row post on again the hackathon channel and you might be in for winning some goodies then also on wednesday as Phil mentioned earlier we have the social events so uh five to six p.m on uh c.e.d again just schedule the website for the link and during that we'll be having a NF call quiz like that happened at the last hackathon and also Maxime set up another little fun thing we're going to do during the social event which yes sorry it's me again uh sorry sorry uh yes so we also set up an escape room uh so we did that at our previous hackathon that was just as well and it was quite fun and uh yes because i win that i think like they put me in charge like to find an escape room so that i i don't win again back to you James yeah and then finally as probably this is when we will have the most number of people available like Phil said we want to take a group photo with everyone showing off their their socks um so phil and alex if you can get your exactly so maxime is is demonstrating how this is going to go so if phil and alex gonna get their screenshot and uh windows ready maybe you say in slack when you're ready and if there's anyone who doesn't want to be featured in the in the group photo please turn off your your cameras now so we'll wait for alex and phil to say if they're ready i've got three pages on on zoom there's too many people alex maybe you can do well let's go through i'll do do page at a time i need to put my own socks up ready first page ready one two three okay let's get the second page oh no there's a five second countdown delay i messed it up i love everyone keep your muscles warm up oh i'm doing this so badly alex how's it going right let's try it again ready three two one wonderful okay i'm gonna stop now that's fine all right thank you very much um and then i guess next we'll be moving on to the group distribution and maybe deserve a start sure thanks um yeah so for the group distribution we will just um in in the next minutes we will just split into different rooms but for now we will all introduce a bit what each group is all about um so i'll be one of the leaders of the the pipelines team together with maxine and in our team with will be all about contributing to already existing pipelines in nf core or if someone's interesting interested in adding another pipeline to nf core we can also discuss how this process goes so if you want to contribute to existing pipelines or develop your own pipeline or so just join our team and we'll be talking about that great um i just remembered also the nf core badge which i've only just put mine on uh yeah so we one of the other projects is we've called framework and uh that basically refers to anything that's not a pipeline uh and not not dsl2 not module um so it's the website repository it's nf core tools to help our command line tools um it's doing github auto great github automation for for in a template for any of the pipelines things like this um kind of stuff that's not a pipeline um we've got a few kind of big things going on in that project a few few big things we want to take up and lots and lots of little tidying tasks so especially if you want to get involved in some python or some web stuff then then come and drop in and just take a break from the next flow code for a little bit um and we'll be there uh alex yeah um so james and me are going to work a bit on documentation hopefully and we are actually hoping that a couple people are joining as well so our idea was actually to move on with some of the aspects that have been previously introduced in nf core so for example we have a couple of points open that uh would need some actual care for a lot of pipelines for example we introduced the jason schema that we would like to work on to have that spread out across multiple pipelines but there's also work involved that we want to make a bit more tutorials available to the user community because there's currently a lack especially in some aspects where we don't really have nice user tutorials so we're looking for people to help help us 80 uh and working on these types of documentation tasks and we already put up a lot of tasks in the in the project board and in the hack and d so i'm happy to see if people are interested in working on that yeah hello everyone um welcome and thank you for being here so i'm going to be leading them the dsl two modules group uh there's a bunch of us there actually that are clued up with this um kevin hosey gregor um patrick uh a bunch of us are there and willing to help out a few things that would be nice um given that with with this particular project um the tasks are quite a bit fragmented for example like adding a module or adding documentation for a module um so it would be great if you can just update the hack md document whenever you've you've done something so just so we can keep track instead of having to look in in different places and then that will serve as a sort of a summary um a lot of the functionality we've added for the sot modules is is is fresh off the press in the latest nf core tools release it'd be great if you can attempt to break it because um it just means that we can fix it uh it's all it's all literally just been released last week a lot of it is working if you want to add a module i would definitely recommend checking out the docs in the main read me of the nf core modules repo i've again updated that on thursday i think use the tools there because it will make it so much easier to add modules um and hopefully once you get into a routine of adding them um it will um become more and more trivial and also help us to identify issues and stuff so please use use nf core tools install and use that to add the modules lint and all sorts of other functionality um for those of you that are interested in using um or implementing a dsl2 pipeline there is a template for it um all of you may not know that it's it's on the dsl2 template branch of nf core tools and i literally just have updated it yesterday as well i just need to fix some linting once we get that into the dsl2 branch we may um we had some brief discussion this morning that we may put that on dev um and so you you should be able to then install it directly from there and and develop your pipeline so hopefully that should be ready and that will look like the rna seek which also now is a bit outdated actually the dev on rna seek is more up to date all the dev and viral recon um and yeah please make sure that all the documentation and stuff is up to date um it's all literally been put together so any feedback comments help updating stuff um would be amazing um i'll try i'll try and be on the jitsie link just in case anyone needs me um pretty much all day so yeah thank you any questions just fire away on slack brilliant yeah okay i think that's that's it for this welcome talk well we're going to keep it short so um as we said there's um on join on slack join your project groups that you're interested in you can be a multiple projects it's no problem um but right now pick your favorite one go there there's a link for for jitsie for the video chat um that we're going to all dive straight into right now and then in each of the projects we're going to go into a little bit more detail about the kinds of tasks and the setup more of what harshal was just talking about so to get you up to speed with how to contribute to these um if in doubt please please shout and and maybe if we have any any burning questions right now you can you can um raise your hand or unmute yourself maybe um but if if not we'll crack on and we can take everything on slack great okay welcome everyone that's hack and uh speak to you all soon