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* Create wrapper scripts for each tool
|
|
TODO
|
|
* Create param files for each tool
|
|
======
|
|
* Update peak calling and remove duplicates modules from dummy values
|
|
* Update wrapper scripts walltime / memory to correctly reflect request values.
|
|
|
|
* Update peak calling and remove duplicates modules from dummy values.
|
|
|
|
* Refactor modules code.
|
|
|
|
|
|
|
|
Database
|
|
|
|
===========
|
|
* Code to insert results into MongoDB and GridFS (Python classes and wrapper scripts)
|
|
* Code to insert results into MongoDB and GridFS (Python classes and wrapper scripts)
|
|
* Create Genome collection in MongoDB
|
|
* Job definitions to load data into database
|
|
* Create the Modules class
|
|
|
|
* Pegasus stdout handling for certain tools (bwa, samtools, zcat, sort, etc.) |
|
Helper Scripts
|
|
\ No newline at end of file |
|
================
|
|
|
|
* Script to generate param.yaml file
|
|
|
|
* Script to generate workflow with provided inputs
|
|
|
|
|
|
|
|
Polishing
|
|
|
|
===========
|
|
|
|
* Update pegasus stduout/stderr redirection |
|
|
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\ No newline at end of file |