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1. Reproducible Workflows using Snakemake and Singularity
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1. Reproducible Workflows using Snakemake and Singularity
2. Introduction
3. Snakemake Intro Tutorial using Binder
4. Snakemake Tutorial on Cyverse Cloud
4.1. Tutorial on Jetstream cloud
5. Working Locally
6. Awesome
7. Credits
8. Coming Soon
9. Introduction
10. Why Snakemake?
10.1. Snakemake Advantages:
11. Why Containers?
12. Snakemake Basic Tutorial
13. Background
14. Getting started - your first Snakefile
14.1. Updating the Snakefile to track inputs and outputs
14.2. Forcibly re-running things
15. Multiple rules
16. A first refactoring: adding a better default rule
17. A second refactoring: doing a bit of templating
18. Refactoring 3: templating output files, too
18.1. Adding some more files
18.2. Rerunning snakemake
19. Building out the workflow
19.1. Providing input files explicitly to the multiqc rule
19.2. Refactoring this to make it slightly more concise –
19.3. Digression: what files does snakemake check in order to decide about rerunning?
19.4. Making a
clean
rule
19.5. Digression: running things in parallel
19.6. Doing more things in our workflow.
20. More advanced snakemake
20.1. Dry run
20.2. Running things in parallel, revisited
20.3. Specifying software required for a rule
20.4. Outputting the entire workflow diagram
20.5. Snakemake Report
20.6. Adding in some Python…
21. Final thoughts - writing your own snakefile
21.1. Dealing with complexity
22. Thinking about workflows - a strong(er) argument
23. Go forth and Workflow!
24. Snakemake Tutorial on CyVerse cloud
25. Accessing The Atmosphere Cloud
26. Login & Launch Instance
27. SSH Secure-Login
28. Instance Maintenance
28.1. Atmosphere Dashboard
28.2. Suspend Instance
28.3. Delete Instance
29. Additional Features
29.1. Did you know you can access a shell terminal and a web-desktop via your browser ???
30. Advanced Topics
30.1. Atmosphere Advanced Topics
31. Advanced Topics
32. Transferring Data to and from an Instance
32.1.
Transferring Data using iCommands
33. Creating custom Atmosphere Images
34. ssh-rsa-key for password-less login
35. Tmux & Screen
36. SSH Remote host ID Changed Error
37. Workflow Management using Snakemake
37.1. Learning Objectives
37.2. Setup
37.3. Introduction to Snakemake
37.4. Starting with Snakemake
37.5. Creating a pipeline with snakemake
37.6. Using Snakemake to process multiple files
37.7. Snakemake Additional Features
37.8. Advanced Snakemake
37.9. Resources
38. Singularity
39. Awesome List of Resources
40. Reproducibility Toolkit
41. Local Setup instructions
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