A slideshow showing the development of a pluggable pipeline system

1. Pluggable Pipelines Andy Brown New Pipeline Development Wellcome Trust Sanger Institute

3. Possible solution – Make the components of the pipeline pluggable, so that they can be inserted, dropped or the order changed dependent on the project requirements.

5. It just needs to know any variables (e.g. a run folder), the functions it is to run and the order it is to run them in

6. Each function knows nothing apart from what it is to do and what it should return (typically something which alerts the next function/script to know when to run) Flag Waver Function b Function c Function d Function e Function a

12. Functions are only responsible for launching, not checking

13. It is up to the component which is launched to complete fully and properly – not the function!

14. It is also up to the user to only select an order where if one component is dependent on the output of another that it is queued after that

16. It also has the parameters required (i.e. a run folder)

17. Flag waver calls each function in turn, passing in anything which delays the script the function will call (i.e. LSF job ids for dependency)

18. Function calls the object which will launch the component script or do something, giving it any required parameters. (If something is needed to be looked up, the Object should do this, not the Flag Waver or the function).

20. Object returns any information which the next function will require, typically again, LSF job ids.

21. The function passes out of it the returned information if it needs to.

22. Flag waver moves onto next function, or ends

25. create_srf – srf format files have been a standard

26. create_fastq – another format for data

27. create_md5 – md5sum the files for data integrity

28. qc_fastq – run some qc checks on the fastq files

31. The function loads and calls an object module, passing in the requirements.

32. The first is archive_dir. In this case, as nothing is before it, it just creates the directory, and returns no LSF job ids.

34. These are converted into an LSF job dependency string, and passed to the next function, create_fastq

35. This then continues until the list has been through, using LSF to now queue the different scripts to run at an appropriate time.

37. Flag waver – code which just blindly launches through an array of functions in user defined order, passing only minimum data to each

38. Functions know nothing about anything except what they are responsible for calling

39. Responsibility falls to the user to ensure correct order of use, and components to ensure that they complete properly (or error sensibly).