Scipediacontent: Scipediacontent moved page Draft Content 836638831 to Wijaya et al 2014a

2021-01-28T19:14:23Z

Scipediacontent moved page Draft Content 836638831 to Wijaya et al 2014a

Scipediacontent: Created page with " == Abstract == In this paper we describe our initial experiences in the Cloud-e-Genome project with moving the whole exome sequencing pipeline from the scripted HPC-based so..."

2021-01-28T19:14:18Z

Created page with " == Abstract == In this paper we describe our initial experiences in the Cloud-e-Genome project with moving the whole exome sequencing pipeline from the scripted HPC-based so..."

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== Abstract ==

In this paper we describe our initial experiences in the Cloud-e-Genome project with moving the whole exome sequencing pipeline from the scripted HPC-based solution to a workflow enactment system running in the cloud. We discuss shortcomings of the existing approach based on scripts and list benefits that a workflow-based solution can provide. Despite the effort it involved to wrap all required tools in the form of workflow blocks and the restrictions of the dataflow model used to represent workflows we expect the migration to significantly improve the current status of the pipeline. Our target is to enable flexibility, traceability and reproducibility of the solution, so that it can better fit the evolution of tools, data and pipeline itself and allow us to run it at national scale. This work will become foundation for the more complete system that includes variant filtering and interpretation for the diagnostic purposes.

== Original document ==

The different versions of the original document can be found in:

* [http://homepages.cs.ncl.ac.uk/paolo.missier/doc/C4Bio.pdf http://homepages.cs.ncl.ac.uk/paolo.missier/doc/C4Bio.pdf]

* [http://xplorestaging.ieee.org/ielx7/6844760/6846423/06846521.pdf?arnumber=6846521 http://xplorestaging.ieee.org/ielx7/6844760/6846423/06846521.pdf?arnumber=6846521],
: [http://dx.doi.org/10.1109/ccgrid.2014.128 http://dx.doi.org/10.1109/ccgrid.2014.128]

* [https://dblp.uni-trier.de/db/conf/ccgrid/ccgrid2014.html#CalaXWM14 https://dblp.uni-trier.de/db/conf/ccgrid/ccgrid2014.html#CalaXWM14],
: [https://eprint.ncl.ac.uk/216149 https://eprint.ncl.ac.uk/216149],
: [https://ieeexplore.ieee.org/document/6846521 https://ieeexplore.ieee.org/document/6846521],
: [https://academic.microsoft.com/#/detail/2025676854 https://academic.microsoft.com/#/detail/2025676854]

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Wijaya et al 2014a - Revision history

Scipediacontent: Scipediacontent moved page Draft Content 836638831 to Wijaya et al 2014a

Scipediacontent: Created page with " == Abstract == In this paper we describe our initial experiences in the Cloud-e-Genome project with moving the whole exome sequencing pipeline from the scripted HPC-based so..."