## Download and run a workflow I've added all of the code we ran from this morning's [k-mer genome-resolved taxonomy tutorial](https://hackmd.io/0ErEGoopTHaSwyRVoDovdg?view) into a workflow file. Let's download a couple files: ``` cd ~/kmers curl -JLO https://raw.githubusercontent.com/mblstamps/stamps2023/main/workflows/Snakefile curl -JLO https://raw.githubusercontent.com/mblstamps/stamps2023/main/workflows/plot-sourmash-sankey.R ``` Let's activate our `smash` environment from earlier and install one more bit of software we need: ``` conda activate smash mamba install -c conda-forge -c bioconda snakemake-minimal ``` First, let's see what steps will be run: ``` snakemake -p -n ``` Now, let's run these steps: ``` snakemake -p --cores 4 ``` ## What are we even running? We're running a snakemake workflow! [intro to snakemake](https://ngs-docs.github.io/2023-snakemake-book-draft/chapter_0.html) We've given snakemake all of the steps we need to run, and told it how they interact. ## Workflow systems, in general ![](https://hackmd.io/_uploads/r1KDljT52.png) From: [Streamlining data-intensive biology with workflow systems](https://academic.oup.com/gigascience/article/10/1/giaa140/6092773) ## Resources - Paper: [Streamlining data-intenstive biology with workflow systems](https://academic.oup.com/gigascience/article/10/1/giaa140/6092773) - [ANGUS 2019 lesson on GitHub](https://angus.readthedocs.io/en/2019/github.html) - Snakemake Resources - Titus is writing a snakemake book! - [intro blog post](http://ivory.idyll.org/blog/2023-snakemake-slithering-section-1.html) - [draft book](https://ngs-docs.github.io/2023-snakemake-book-draft/) - [Anvi'o snakemake workflows](https://merenlab.org/2018/07/09/anvio-snakemake-workflows/)