| Session 1 |
9:00 |
09:45 |
Introduction to workflow management systems |
| Exercises 1 |
09:45 |
10:15 |
Building a simple analysis workflow with Snakemake |
|
10:15 |
10:30 |
BREAK |
| Session 2 |
10:30 |
11:15 |
Using wildcards to increase scalability |
| Exercises 2 |
11:15 |
12:00 |
Updating the analysis workflow to increase scalability |
|
12:00 |
13:00 |
LUNCH BREAK |
| Session 3 |
13:00 |
13:30 |
Using configuration files to increase transferability |
| Exercises 3 |
13:30 |
14:00 |
Complementing our workflow with a configfile |
| Session 4 |
14:00 |
14:30 |
Combining Snakemake with conda and software containers |
| Exercises 4 |
14:30 |
15:15 |
Updating the analysis workflow to use conda/containers |
|
15:15 |
15:30 |
BREAK |
| Session 5 |
15:30 |
16:15 |
Snakemake in HPC environments |
| Exercises 5 |
16:15 |
17:00 |
Updating our workflow to send jobs via SLURM |