RNAseq-pipeline v1.5.1

Version 1.5.1 release.

• Some code cleanup
• Restructured user defined values, split into a section that can be changed called additional configurations
• Following failed verification of necessary software prerequisites, script offers to try installing software
• Improved documentation

RNAseq-pipeline v1.5.0

Version 1.5.0 release.
Overall performance improvements and optimizations. Some QoL changes.

• Removed .sam file to .bam file conversion section, now pipes hisat2 output directly to samtools sort
  • Reduced disk space requirements for all data by 83% (325.1 GB down to 54.0 GB on same dataset)
  • Reduced script runtime on same data set by 27% (130.5 min down to 95.9 min)
• Removed pre-run environment changes section as it is no longer necessary
• Added help flag that prints description of all flags
• Limit number of threads passed to featureCounts to 64

RNAseq-pipeline v1.0.0

Initial functional version of the RNA-seq pipeline. Can only handle bulk RNA-seq data at the moment.