Workshop schedule
Drafts for an in-person workshop of four or five days
The workshop length is decided after the content. These drafts fit the lessons into four or five days of about six teaching hours. The times are computed from the planned length of each part and will be tuned after a first run. Participants do the setup before day 1, including the cache prefetch, so that class time is not spent downloading software. The only large download in class is the lesson 03 data (115 MB).
The core lessons, with time for your own project every day and a show-and-tell at the end.
Day 1: Organize and track
| Time | Session |
|---|---|
| 09:00–09:40 | 01 Introduction (slides) |
| 09:40–10:05 | 03 FAIR |
| 10:05–10:20 | Break |
| 10:20–11:40 | 02 Project organization |
| 12:00–13:00 | Lunch |
| 13:00–13:40 | 03 hands-on |
| 13:40–15:00 | 04 Git §1–6: Git on your laptop and on GitHub |
| 15:00–15:15 | Break |
| 15:15–16:25 | 04 Git §7–10: branches, a conflict, tags, pull requests |
| 16:25–16:55 | Your own project under Git |
Day 2: Environments and reports
| Time | Session |
|---|---|
| 09:00–10:20 | 05 Pixi Part A |
| 10:20–10:35 | Break |
| 10:35–11:55 | 05 Pixi Part B: features, tasks |
| 12:00–13:00 | Lunch |
| 13:00–13:30 | 05 Pixi the Reproduce check on GitHub |
| 13:30–14:10 | 07 Quarto §1–3: a first document |
| 14:10–14:25 | Break |
| 14:25–15:45 | 07 Quarto §4–9: the LTEE report, parameters, formats, notebooks, the report in reproduce |
| 15:45–16:15 | Your own project: Pixi and a report |
Day 3: Containers and workflows
| Time | Session |
|---|---|
| 09:00–10:20 | 08 Containers §1–4: Docker |
| 10:20–10:35 | Break |
| 10:35–11:25 | 08 Containers §5–6: an image from the lock file |
| 11:25–11:55 | Your own project: your environment in a container |
| 12:00–13:00 | Lunch |
| 13:00–14:20 | 09 Snakemake §1–5 |
| 14:20–14:35 | Break |
| 14:35–15:55 | 09 Snakemake §6–11 |
| 15:55–16:35 | 10 Nextflow intro |
Day 4: Document and share
| Time | Session |
|---|---|
| 09:00–10:20 | 11 Documentation |
| 10:20–10:35 | Break |
| 10:35–11:55 | 12 Putting it together §1–2: swap and reproduce |
| 12:00–13:00 | Lunch |
| 13:00–13:30 | 12 Putting it together §3: release with a DOI |
| 13:30–14:15 | Your own project: README, license, citation, fixes from the swap |
| 14:15–14:30 | Break |
| 14:30–15:15 | Own-project show-and-tell |
| 15:15–15:35 | Wrap-up, checklist, next steps |
Not in the four days (self-paced afterwards): 01a Reproducibility reading; 01b Open science reading and the openness audit; 03 Data management Part A: concepts; 05 Part C (pixi global, HPC); 05b Conda comparison; 06 Jupyter; 08 Containers §7: Apptainer; 08 Containers §8–9: registry, provenance; 09 Snakemake lab: the LTEE pipeline, best practices; 09 Snakemake §13: on a Slurm cluster; 10 Nextflow full tutorial; Package and share your tool
All the in-class parts of the course, at a gentler pace, with time for your own project every day and a show-and-tell at the end.
Day 1: Organize and track
| Time | Session |
|---|---|
| 09:00–09:40 | 01 Introduction (slides) |
| 09:40–10:05 | 03 FAIR |
| 10:05–10:20 | Break |
| 10:20–11:40 | 02 Project organization |
| 12:00–13:00 | Lunch |
| 13:00–13:40 | 03 hands-on |
| 13:40–15:00 | 04 Git §1–6: Git on your laptop and on GitHub |
| 15:00–15:15 | Break |
| 15:15–16:25 | 04 Git §7–10: branches, a conflict, tags, pull requests |
| 16:25–16:55 | Your own project under Git |
Day 2: Environments
| Time | Session |
|---|---|
| 09:00–10:20 | 05 Pixi Part A |
| 10:20–10:35 | Break |
| 10:35–11:55 | 05 Pixi Part B: features, tasks |
| 12:00–13:00 | Lunch |
| 13:00–14:00 | 05 Pixi the Reproduce check on GitHub |
| 14:00–14:40 | 06 Jupyter |
| 14:40–14:55 | Break |
| 14:55–15:55 | Your own project: Pixi and a notebook |
Day 3: Reports and containers
| Time | Session |
|---|---|
| 09:00–09:40 | 07 Quarto §1–3: a first document |
| 09:40–11:00 | 07 Quarto §4–9: the LTEE report, parameters, formats, notebooks, the report in reproduce |
| 11:00–11:15 | Break |
| 11:15–12:00 | Your own project: a report in Quarto |
| 12:00–13:00 | Lunch |
| 13:00–14:20 | 08 Containers §1–4: Docker |
| 14:20–14:35 | Break |
| 14:35–15:25 | 08 Containers §5–6: an image from the lock file |
| 15:25–15:55 | 08 Containers §7: Apptainer |
| 15:55–16:10 | Break |
| 16:10–16:55 | Your own project: your environment in a container |
Day 4: Workflows
| Time | Session |
|---|---|
| 09:00–10:20 | 09 Snakemake §1–5 |
| 10:20–10:35 | Break |
| 10:35–11:55 | 09 Snakemake §6–11 |
| 12:00–13:00 | Lunch |
| 13:00–14:10 | 09 Snakemake lab: the LTEE pipeline, best practices |
| 14:10–14:25 | Break |
| 14:25–15:05 | 10 Nextflow intro |
| 15:05–15:50 | Your own project: a first workflow |
Day 5: Share
| Time | Session |
|---|---|
| 09:00–10:20 | 11 Documentation |
| 10:20–10:35 | Break |
| 10:35–11:05 | 12 Putting it together §3: release with a DOI |
| 11:05–11:50 | Your own project: README, license, citation |
| 12:00–13:00 | Lunch |
| 13:00–14:20 | 12 Putting it together §1–2: swap and reproduce |
| 14:20–14:35 | Break |
| 14:35–15:35 | Own-project show-and-tell |
| 15:35–15:55 | Wrap-up, checklist, next steps |
Not in the five days (self-paced afterwards): 01a Reproducibility reading; 01b Open science reading and the openness audit; 03 Data management Part A: concepts; 05 Part C (pixi global, HPC); 05b Conda comparison; 08 Containers §8–9: registry, provenance; 09 Snakemake §13: on a Slurm cluster; 10 Nextflow full tutorial; Package and share your tool