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Creating a pipeline

Guiding principles

Most (bioinformatics?) projects start small, and grow over time. From that perspective it is advisable to give the organization of your project some thought on forehand.

When using Moa the separate analysis steps of a pipeline each reside in a directory. The output data of each analysis usually resides in the same directory or a subdirectory thereof. Moa has templates that assist in downloading and organizing data. This has as result that all project data in a Moa project will be organized in a directory tree on your filesystem. Such a tree must represent both the data in logical way as well as the analysis pipeline organization.

Although there are likely multiple ways of achieving a healthy organization of a Moa project, this manual proposes the following organization:

  • On the highest levels organize your project according to fundamental divisions in the project or data source. For example, if you work with data from multiple organisms, that might be a good top level division.
  • On lower levels start organizing your annotation pipeline. Since most

Setting up new jobs - moa new

Creating a new job is done with the moa new command.

Running a pipeline

Running one job

Running a series of jobs

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