introduction to workflow managers for pipelines & getting started with nextflow in bioinformatics

Most bioinformatics roles dealing with large volumes of data will require you to wrap your processing steps (a pipeline!) in a workflow manager. This video introduces you to the key concepts of what a workflow manager is, why it's important and guides you to some helpful resources for getting started with nextflow. Feel free to use the time stamps to skip to what you might find helpful. Enjoy!
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Welcome to Genomics with Georgia! I’m a self-taught bioinformatician/data scientist working in biological research. I share, on this channel, all about getting into this space. If you’re looking for an insight into the field of bioinformatics - start here! Welcome 💗

*TIMESTAMPS*
00:00 = Intro
01:13 = Pipelines recap
02:08 = GATK
03:44 = why use workflow managers
04:52 = examples
07:00 = !!
07:29 = Nextflow intro/why
08:21 = nextflow training
09:46 = key concepts of nextflow
09:56 = processes & channels
11:54 = resume/caching
13:00 = workflows
14:00 = work dir
14:35 = portability
15:25 = action points
16:10 = outro

*Links to mentioned helpful things & resources*
⭐https://www.youtube.com/watch?v=dbOKB3VRpuE&list=PL3xpfTVZLcNgLBGLAiY6Rl9fizsz-DTCT
⭐https://www.nextflow.io/docs/latest/channel.html
⭐https://www.nextflow.io/docs/latest/workflow.html
⭐https://www.nextflow.io/docs/latest/container.html
⭐https://training.nextflow.io/basic_training/
⭐https://carpentries-incubator.github.io/workflows-nextflow/
⭐https://www.ebi.ac.uk/training/online/courses/nextflow/
⭐https://nf-co.re/
⭐https://nextflow.slack.com/join/shared_invite/zt-2fajdfgqa-8YnTY4xEeB07ndXHW04lvQ#/shared-invite/email


*Learn to code like me*
👩‍💻 Learn Python on Codecademy https://www.codecademy.com/catalog/language/python
(Specifically, Learn Python3)
👩‍💻 Learn R https://www.codecademy.com/learn/learn-r
👩‍💻 Learn the command line https://www.codecademy.com/learn/learn-the-command-line
👩‍💻 Code First Girls Uni Kickstarter https://codefirstgirls.com/courses/coding-kickstarter/
👩‍💻 Volunteer with CFG https://codefirstgirls.com/blog/thinking-of-becoming-a-cfg-volunteer-instructor-meet-two-here/
👩‍💻 My article with EI about why undergrads should learn to code https://www.earlham.ac.uk/articles/students-need-their-bioinformatics-game-why-i-am-learning-code-python

*Equipment* *
📸Camera - https://amzn.to/3YjctTP
📸Lens - https://amzn.to/4eFH4Rq
📸Laptop - https://amzn.to/4eFBWfT
📸Hardrive - https://amzn.to/4h5yaOz

*these are affiliate links, I make a small commission but it costs you nothing extra

*Other videos you might like*
- https://www.youtube.com/watch?v=62oxQSo34js&t=58s
- https://www.youtube.com/watch?v=MBBcXjtxAcM&t=28s
- https://www.youtube.com/watch?v=SHpHYmrO8lI&t=710s
- https://www.youtube.com/watch?v=fwQer75K194

*Business Enquiries*
📧 genomicswithgeorgia@gmail.com

*Music Creds*
Bliss by Luke Bergs | https://soundcloud.com/bergscloud/
Creative Commons - Attribution-ShareAlike 3.0 Unported
https://creativecommons.org/licenses/by-sa/3.0/
Music promoted by https://www.chosic.com/free-music/all/

Still Awake by Ghostrifter Official | https://soundcloud.com/ghostrifter-official
Music promoted by https://www.chosic.com/free-music/all/
Creative Commons CC BY-SA 3.0
https://creativecommons.org/licenses/by-sa/3.0/


Magical Forest by MaxKoMusic | https://maxkomusic.com/
Music promoted by https://www.chosic.com/free-music/all/
Creative Commons CC BY-SA 3.0
https://creativecommons.org/licenses/by-sa/3.0/

Disclaimer:
The views and opinions expressed on this channel are my own and do not reflect those of my current or past employers. The content I share is for educational and informational purposes only and should not be considered professional advice. While I strive to provide accurate and up-to-date information on 'omics and career development, I encourage viewers to conduct their own research.