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Run the whole pipeline!

Step 11: Running the pipeline

Once you've decorated the entire Snakefile, you should be able to run through the whole workflow using either the rule name:

snakemake -p make_vcf -j 2

or by using the file name:

snakemake -p variants.vcf -j 2

Recollect that Snakemake will execute the first rule in the Snakefile by default. We can use this feature by creating a default rule called all at the top of the Snakefile:

rule all:

    input: "variants.vcf"

and run:

snakemake -p all -j 2

This rule runs through the entire workflow with a single command! This is much better than running each command one by one!

The final snakemake workflow looks like this:


The diagram above is called a directed acyclic graph (DAG) and it is how snakemake interprets the workflow from the Snakefile. You can read more about the syntax information on the snakemake documentation.

To generate a DAG file, we need Graphviz, a graph visualization software, and dot to create directed graphs. We can use conda to create a new environment with the required packages.

# initialize and reset the bash with conda
conda init bash
source .bashrc

# create a new environment and install Graphviz
conda create -y -n graphs graphviz

# activate conda environment
conda activate graphs

# create dag png file
snakemake --dag variants.vcf | dot -Tpng > vc_workflow_dag.png

Step 12: Looking at VCF files

Finally, let's look at the output!

less variants.vcf

We can look at the alignment by running the alignment viewer in samtools:

samtools tview -p ecoli:4202391 SRR2584857.sorted.bam ecoli-rel606.fa

Navigating samtools tview

  • Access the help menu in samtools tview by hitting shift key and ? key.
  • Exit help menu by hitting q key
  • Go to a specific position location in the alignment by hitting / key.


Exit (snaketest) conda environment to return to (base) environment:

conda deactivate

Hopefully, you have now:

  • learned how to write basic workflows with Snakemake rules
  • learned variable substitution for Snakemake rules
  • learned wildcard matching for Snakemake rules
  • understood why workflow systems can help you do your computing more easily!

Key Points

  • Snakefile defines a Snakemake workflow
  • the rules specify steps in the workflow
  • at the moment (and in general), they run shell commands
  • you can "decorate" the rules to link the dependencies between rules
  • basic decoration comes in the form of input: and output: which are lists of one or more files, quoted, separated by commas
  • the rules are connected by matching filenames
  • tabs are important syntax feature in Snakemake

Last update: May 19, 2021