This repository hosts the final code and data needed for the Snakemake tutorial.
Run in VScode using binder: 
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- 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- png instead of svg histogram (easier to view)
- latest code-server (
4.5.0) is not working with mybinder
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Tencent