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dkj committed Sep 11, 2023
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Expand Up @@ -11,22 +11,22 @@ There are two main pipelines:

and the daemons which automatically start these pipelines.

Processing is performed as a appropriate for the entire run, for each lane in
the sequencing flowcell, or each tagged library (within a pool on the flowcell).
Processing is performed as appropriate for the entire run, for each lane in the
sequencing flowcell, or each tagged library (within a pool on the flowcell).

## Batch Processing and Dependency Tracking with LSF or wr

With this system, all of a pipeline's job for its steps are submitted for
With this system, all of a pipeline's jobs for its steps are submitted for
execution to the LSF, or wr, batch/job processing system as the pipeline is
initialised. As such, a _submitted_ pipeline does not have a orchestration
initialised. As such, a _submitted_ pipeline does not have an orchestration
script or daemon running: managing the runtime dependencies of jobs within an
instance of a pipeline is delegated to the batch/job processing system.

How is this done? The job representing the start point of a graph is submitted
to LSF, or wr, in a suspended state and is resumed once all other jobs have been
submitted thus ensuring that the execution starts only if all steps are
successfully submitted to LSF, or wr. If an error occurs at any point, all
submitted jobs, apart from the start job, are killed.
successfully submitted to LSF, or wr. If an error occurs at any point during job
submission, all submitted jobs, apart from the start job, are killed.

## Pipeline Creation

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