Got the existing code to work. Now creates a merged uncompressed FastQ file..
Added code to do environment module loading work. Now seems to run cutadapt ok.
Added code to run FastQC and the bowtie alignment
Further additions to the pipeline.py script
Added miRBase reference. Fixed bugs in pipeline. Now aligns to reference and to miRBase properly.
First draft of new HTSeq code. Removed some cruft.
Added code to count miRBase alignments using samtools. Fixed bugs with HTSeq.
Cleaning out zero count lines and sorting counts
Fixed bug in htseq_counts, made initial miRBase alignments in temp dir and forced FastQC version
Merge pull request #4 from ewels/master

WIP. Porting bash pipeline script to python.