Bulk rnaseq dynamic resource allocation

[AlaaALatif]

• memory (RAM) resources dynamically allocated for each process step based on input file sizes
• dynamically handles both single-end and paired-end datasets, especially for earlier process steps that use the FASTQ reads as input
• tested with two different datasets, containing inputs of various sizes, without failure
• quality-of-life improvements to the configuration files

[erflynn]

This looks great! very exciting to be making the switch to more dynamic resource allocation. Will test it out more when I am back week of 10/16.

[erflynn]

@AlaaALatif -- update here, tested on files 0.75-18.5GB and this completed. I think fine to merge, but you may want to fine tune some steps more for less resources if not needed.

[AlaaALatif]

Tested branch pipeline against a dataset with 2 samples and another dataset with 1 sample only, without any errors.

@erflynn thank you for providing resource usage information from your dataset, and fixing issues with dynamic resource allocation @amadeovezz thank you for writing a bare-bones example of dynamic resource allocation using Nextflow, and testing the pipeline @lzemelko thank you for fixing a bug to handle datasets consisting of one sample only, and testing the pipeline

Looking good to me! Going to merge this and delete the branch shortly after.