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Exercise 1: Analysis Scripts and Snakemake

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You should see something like this: Snakemake output second rule Check for the output file:

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It will spend some time downloading files and running the analysis code. Then it should hadd the files: Snakemake output third rule

Exercise 2: Setting up your first benchmark with pipelines

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  • GitHub pull request form with the Add a title field Provide a title like “Adding benchmark for …”.

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  • Create draft pull request Since this work is not yet complete, open dropdown menu of the “Create pull requst” button and select “Create draft pull request”

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  • Draft pull request Click “Draft pull request”

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    Check running on GitHub
    Check running on GitHub

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    Check running on eicweb
    Check running on eicweb

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    Job output on eicweb
    Job output on eicweb

    Exercise 3: Filling out your benchmark

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    Your benchmark directory should now look like this: File listing of the completed your_benchmark directory

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    This command should show something like this: Example output of git status listing the new benchmark files

    Exercise 4: Adding a Status Flag

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    At the completion of one of GitLab’s pipelines, the status flags from each benchmark are gathered and summarized like this one: Status flag example

    Exercise 5: Making Useful Figures

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    Example benchmark figure

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    Benchmark explainer

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    Benchmark explainer artifact