Open tavareshugo opened 1 year ago
Initial draft of the timetable (names is to indicate who is doing which slides):
09:45 - 10:15 Introduction to reproducible and scalable bioinformatics analysis - Adam 10:15 - 11:00 Using package managers (slides + practical) - Adam 11:00 - 11:15 Break 11:15 - 12:00 Singularity (slides + practical) - Hugo 12:00 - 12:30 Nextflow (slides) - Raquel 12:30 - 13:30 Lunch 13:30 - 14:30 Nf-core demo and practical - Raquel 14:30 - 15:30 Configuring nextflow on HPC - Hugo 16:00 - 17:00 Q&A
On the live workshop:
09:30 - 09:45 - Welcome 09:45 - 10:10 - Introduction 10:10 - 10:50 - Mamba 10:50 - 11:30 - Mamba Exercise 11:30 - 12:00 - Singularity slides 12:00 - 12:30 - Singularity exercise and wrap-up 12:30 - 13:30 - Lunch 13:30 - 14:15 - Nextflow slides 14:15 - 15:30 - Nextflow exercises (this could be reduced, see #27) 15:30 - 16:00 - Nextflow exercise solution (took a bit too long - don't need to go through the samplesheet python script in such detail) 16:00 - 16:30 - Nextflow on a HPC slides and tmux demo 16:30 - 17:30 - HPC exercise and wrap-up
Titles:
Prerequisite:
Outline:
mamba
)singularity
) - similar to HPC coursesingularity pull
andsingularity run
nextflow
nf-core
focused)--fasta
and--gff
options - ensure reproducibility and uses latest version (or whichever version you wish to use). Discourage usingigenomes
(and why we don't recommend it). Use the reference that matches your downstream needs, e.g. using dbsnp or something like that.Useful resources: