jpalpant / rnaseqflow

A Python library to make preprocessing of RNA-seq files more convenient

What Is It?

An open-source Python library to make preprocessing of RNAseq files more convenient

CircleCI build status:

TravisCI build status:

Complete documentation available on Read the Docs

Copyright and License

For the complete copyright and licensing information see LICENSE

Copyright 2015 Justin Palpant

This file is part of the RNAseqflow program.

RNAseqflow is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

RNAseqflow is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with RNAseqflow. If not, see http://www.gnu.org/licenses/.

rnaseqflow's Issues

Add at least one pairwise file trimming stage

The main motivator for continuing development to 0.2.0 was the need for trimming fastq files in pairs - so called "pair-end" or PE mode. This mode is available with several softwares, including trimmomatic and possibly fastq-mcf. Investigate this possibility and write a WorkflowStage subclass that trims files in pairs (R1 and R2 together).

Test 0.2.0 interface

Work out all bugs in the 0.2.0 interface, including bugs with PyPI installation

MergeSplitFiles needs file 000

MergeSplitFiles does not work because it does not find a part numbered 000 in the test data. Attempt to reproduce this bug and figure out why it still passes the tests.

Create documentation

The project currently has no usable documentation aside from the help command, which makes it not a very good Python project. Create publically available documentation for the project.

Improve documentation and testing

The documentation is rather rough, although existent, and test coverage is well below 100%. Work on tests and docs until they are more complete in advance of 0.2.1

Create more complete user documentation

Documentation is strong for the Python library but weak for the CLI. Fill in the documentation there.

Tests not passing with circle.yml

Using the circle.yml file and trying to cache fastq-mcf did not work because files are cached on a per-branch basis.

Make some check to see if files were cached and if they were not go through the process of making them for the cache.

FastQMCFTrimPairs does not handle solo files

When given a solo file, FastQMCFTrimPairs raises a StopIteration error that is uncaught, likely related to the method used for finding the paired file. Find and fix.