Pipelines are data analysis programs, typically comprised of multiple bioinformatics modules chained together. iMaps runs on Nextflow, and each pipeline in iMaps is powered by a single DSL2 Nextflow pipeline, which is open source on examinable on GitHub.

To run a pipeline, you just need to select it from the list on the pipelines page, and provide it with inputs. The inputs to the pipeline are iMaps Data objects, which can either be newly uploaded Data, or Data which was itself produced by previous pipelines. iMaps will filter the Data available to you by those the pipeline can accept for a given input.

In some cases, a pipeline will take as its input not a single Data object, but an Execution object (see next page). In this case it will get access to all the output files of that Execution for that input. This is used when a pipeline needs access to an entire genome description, for example, whose files are generated by the 'Prepare Genome' pipeline.

Once everything is ready, you can run the pipeline. The job may sometimes go to a queue first, but in any case every time you run a pipeline you create an Execution, and you will be immediately taken to the page for that Execution.

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