Teaching Reproducible Data Analysis for HPC Users -- The Snakemake Teaching Alliance

Read full text
Authors: Petersen, Malte, Hellmann, Sören Lukas, Böker, Florian, Brand, Fabian, Sharma, Aasish Kumar, Pleico, Martin Leandro, Köster, Johannes, Meesters, Christian
Cited by: 0

Abstract

1.4.0 (2026-08-26) Features accomodating a new site: Goethe University Frankfurt (77c962a) added custom images to use for different purposes (f2db4bc) added image for onboarding chapter (20b4f57) added images to create a pair programming intro slide (3ca099b) added missing images (8e8261c) added slide introducing the pair programming concept (af911dc) added slides about software stack and example run (6e09a2e) added stats about slurm plugin downlaods (bbf2bb3) added two example configs using the new pair programming option (93769cf) cleaner config (61e78d7) configuration for Frankfurt (e45cf97) configuration for Frankfurt (ab7f66c) exchanged slide with easier approach and appeal for support before starting on Snakemake (74e1f4f) finished slides about software envs (b47704d) finished the 'About Snakemake' section (756fa5e) first step toward admin intro - profile slides (88c1a0d) half-ready admin intro to Snakemake (37be23b) included the pair programming option everywhere (d68880f) intro to admins (5e3cfe2) introducing data mangament part - still with redundant AI-slop intro image (737e201) introducing Snakemake syntax highlighting (1183395) pair programming slide (3a8c385) snakemake profile and slurm partition profile are introduced (2597c7b) stable title (414c795) structure color for sketch slide (17d7c4b) using cc compatible image in Why Workflows section (2c667f9) using public domain images (0ace41b) Bug Fixes added missing word (5148840) added question to avoid unpleasent surprises (a470394) added question to teaching elsewhere to prevent teaching somewhere, where workflow management is not welcomed (7acf415) added the cluster_profile parameter to the ci config (25126e9) choosing blue in boxes (95879de) correct color section for section underlyning (3520ecd) correctly considering section boundaries for mini tocs (b5380e6) deleted accidental text between slides (5750378) deleted annoncement slides - does not belong into admin talk (433152d) deleted config for MogonII - cluster does not exist anymore (80cdef9) deleted old slide set for profiles - now per site (eb9afa6) exchanged an AI rendered image by a wikipedia free image (a857623) missing image (56e204b) possible fix for missing PDF artifact (da34d90) possible fix for missing PDF artifact (9d8a8c2) preserving beamer's frametitle layout, if no logo is given (5055c16) Snakemake logo display and yaml listing syntax highlighting (e67bb7a) software setup for the tutorial workflow (41d715b) software setup for the tutorial workflow (c3037af) typo / syntax error (144483e) typo / syntax error (9f4d5fa) typo / syntax error (2f086af)

Publication details

Journal / source
Zenodo (CERN European Organization for Nuclear Research)
Publication date
26 August 2026