How to Run the Workflow

Follow these instructions to run the Nextflow Casanovo workflow from your system. Note that your system must remain on for the duration of the running of the workflow. Even though the steps may be running on a remote system (like AWS Batch), your system still orchestrates the running of the steps.

Important

You must set up your system to run Nextflow first. Please see How to Install the Workflow for more information. All commands will be typed in the command line. See How to Install the Workflow for more information about how to get a command line.

Follow these steps to run a workflow:

  1. Create a directory that will be the “home” directory for this search. Example commands:

    cd
mkdir my-nextflow-run
cd my-nextflow-run

    This will create a directory named my-nextflow-run in your home directory and move into that directory.

  2. Copy in or create a pipeline.config file. A template can be found at: https://raw.githubusercontent.com/mriffle/nf-ms-dda-casanovo/main/resources/pipeline.config

    Example command:

    wget https://raw.githubusercontent.com/mriffle/nf-ms-dda-casanovo/main/resources/pipeline.config

    You may edit this config file in two ways:

    Command Line:

    nano pipeline.config

    Use the commands displayed in the bottom of the window to save the file and close the editor when you are done. They will be Control-O and <Enter> to save and Control-X to exit.

    GUI Editor in your Operating System:

    MacOS or Linux: You can directly edit ~/my-nextflow-run/pipeline.config using your favorite GUI editor.

    Windows: The file is a little tricky to find. In your file open dialogue, type in \\wsl$\ and hit enter. This should reveal a Ubuntu-22.04 directory (or something close to it). Go into that and double click on home, then double click on your username, then my-nextflow-run. The pipeline.config file should be present and you can edit it like a normal file.

    Important

    For a complete desciption of all parameters see Workflow Parameters.

  3. Copy in or create a Casanovo params file. A template can be found at: https://raw.githubusercontent.com/mriffle/nf-ms-dda-casanovo/main/resources/casanovo.yaml

    This is the file used to configure Casanovo. It contains many settings that may be reviewed and changed for your particular data.

    Example command:

    wget https://raw.githubusercontent.com/mriffle/nf-ms-dda-casanovo/main/resources/casanovo.yaml

    You may edit this config file in two ways:

    Command Line:

    nano casanovo.yaml

    Use the commands displayed in the bottom of the window to save the file and close the editor when you are done. They will be Control-O and <Enter> to save and Control-X to exit.

    GUI Editor in your Operating System:

    MacOS or Linux: You can directly edit ~/my-nextflow-run/casanovo.yaml using your favorite GUI editor.

    Windows: The file is a little tricky to find. In your file open dialogue, type in \\wsl$\ and hit enter. This should reveal a Ubuntu-22.04 directory (or something close to it). Go into that and double click on home, then double click on your username, then my-nextflow-run. The casanovo.yaml file should be present and you can edit it like a normal file.

  4. Run the workflow.

    Nextflow workflows may be run with a variety of executors. Executors are what run the actual steps of the pipeline; that is, they are the systems on which steps like Casanovo and msconvert will be run. Examples of executors are your local computer, a computer cluster, or AWS Batch. The example below describes how to run the workflow using your local system or AWS Batch as the executor.

    A good first step is to ensure you have the latest version of the workflow. Execute this command:

    nextflow pull -r main mriffle/nf-ms-dda-casanovo

    Then, to run the steps of the workflow on your local computer, execute this command:

    nextflow run -resume -r main mriffle/nf-ms-dda-casanovo -c pipeline.config

    Note

    It is important to only launch one workflow at a time if you are running on your local computer. Launching multiple workflows at once will result in multiple instances of the programs running at once. To run multiple workflows at once on your local system, you will need to implementing a queuing system such as Slurm and use the Slurm executor.

    Alternatively, to run the workflow using AWS Batch, execute a command similar to:

    nextflow run -resume -r main -profile aws mriffle/nf-ms-dda-casanovo -bucket-dir s3://bucket/dir -c pipeline.config

    Important

    You must set up a AWS Batch cluster before running on AWS Batch. See How to Setup and Configure AWS Batch for more details about how to set up a AWS Batch cluster and the resulting parameters to set in your pipeline.config file.

  1. Retrieve results.

    Your results will appear in the results sub directory of your current directory. See Output & Results for more information about the results that are generated.