tonyyzy / RNASeq

A framework for RNA-seq data analysis workflows

RNASeq

Notes

DESeq2 requires metadata sample name to match gene_count_matrix sample name will handle this in workflow to make things consistent

Session status definition

0 session initialised
1 session submitted (no change to conditions/samples/workflows allowed pass this stage)
2 workflow generated
3 workflow submitted to run
4 workflow finished

Some libraries needed to setup local dependencies

sudo apt-get install zlib1g-dev
sudo apt-get install libncurses5-dev
sudo apt-get install libbz2-dev
sudo apt-get install liblzma-dev

Testing

We use python and pytest as the testing framework. All the tests are stored in ./tests. Before committing a new test, you should test your test locally first.

Assuming you have all dependencies met

run $ pytest ./tests

You should see something similar to the following:

$ pytest tests
============================= test session starts ==============================
platform linux -- Python 3.6.3, pytest-3.3.0, py-1.5.2, pluggy-0.6.0
rootdir: /home/travis/build/tonyyzy/RNASeq, inifile:
collected 1 item
tests/test_STAR_index_nodocker.py .                                      [100%]
=========================== 1 passed in 2.01 seconds ===========================
The command "pytest tests" exited with 0.

Backend data structure

rnaseq  
|  
|-- Genome_Index  
|               |-- H. Sapiens  
|               |             |-- fasta  
|               |             |-- annotation  
|               |             |-- STAR_index  
|               |             |-- HISAT2_index  
|               |              
|               |-- P. Yoelii  
|-- data  
|       |  
|       |-- Session ID  
|                     |-- workflow1  
|                     |            |-- cwl file  
|                     |            |-- yml file
|                     |            |-- analysis result directories
|                     |-- fastq  
|                     |        |-- file1.fastq  
|                     |        |-- file2.fastq  
|                     |  
|                     |-- genome  
|                              |-- fasta  
|                              |-- annotation  
|  
|-- RNASeq (repository)