Snakemake tutorial with data

This repository hosts the final code and data needed for the Snakemake tutorial.

Run in VScode using binder: (refresh if you get at 500 error code)

To try

snakemake --help
snakemake -n # --dryrun
snakemake -n - # --printshellcmd
snakemake --cores 1 # execute locally with N cores
snakemake --report report.html # after running snakemake, create a report
snakemake --dag | dot -Tpng > dag.png # look at directed acyclic graph (DAG) of jobs 
snakemake -n --forceall # force re-run, otherwise everything was done
snakemake --forceall --use-conda --conda-frontend mamba # run with newly create environments
snakemake --print-compilation > snakemake.py # inspect python script generated based on Snakefile

Questions/Topics raised

• explain what wildcards of a rule are
• tutorial is a simple read-alignment pipeline
• What are ancient, temp, pipe statements etc around file names

If you want to revert changes with the possibility to replay them, use git stash

git stash --all

CHANGELOG

• png instead of svg histogram (easier to view)
• latest code-server (4.5.0) is not working with mybinder