Improve usage readability within editor
Move aligned directory back from $TMP_DIR, where it did not belong.
Reworked tmp directory creation/location a bit
Determine number of cores available locally or on a slurm node
Initial commit of python script for counting/binning by size
Grab functionality directly from htseq-count script
Grab functionality directly from htseq-count script
Removed ridiculously extraneous whitespace from counts.py
Added .gitignore
Modified counts.py to return counts
Tmp save counts to yaml file
Add counts.py support for working with BAM files
Route stdout from counts.py to /dev/null
Rewriting pipeline in python
Added docstrings, chmod +x
Added RunDirectory class, positional args, num_cores checking
Merge fastq files, deal with compressed data
Fixed datetime formatting bug
Code cleanup
Merge branch 'master' of ssh://github.com/mariogiov/miRNA_processing