To get DAG:
snakemake --profile profiles/aws --forceall --dag | dot -Tpdf > dag.pdf
To get rule graph:
snakemake --profile profiles/aws --forceall --rulegraph | dot -Tpdf > rulegraph.pdf
To get file graph:
snakemake --profile profiles/aws --forceall --filegraph | dot -Tpdf > filegraph.pdf
To run pipeline:
snakemake --profile profiles/aws/ all
To modify pipeline:
Change sample download table, or change the reference genomes in the config.