Bwa through module rcbio/1.3.3

Start an interactive job, with a walltime of 2 hours, 2000MB of memory. 

Create a working directory on scratch and change into the newly-created directory. For example, for user abc123, the working directory will be

Copy some test data following this page: Build Folder Structures From Sample Sheet for rcbio NGS Workflows page.

Copy the example bwa bash script:

Now you can modify the options as needed. Please reference the bwa user manual if you have any questions.

To edit the bwa script:

To test the pipeline run the following command. Jobs will not be submitted to the scheduler.

To run the pipeline:

To understand how 'runAsPipeline' works, how to check output, how to re-run the pipeline, please visit: Run Bash Script As Slurm Pipeline

Now you are ready to run an rcbio workflow

To instead run the workflow on your own data, transfer the sample sheet to your local machine following this wiki page and modify the sample sheet. Then you can transfer it back to O2 under your account, then go to the build folder structure step.