Updated config for larger files

[erflynn]

Updated memory,time requirements for many of the steps to enable it to run on 6 larger JDM samples. Also adjusted the config files to reduce redundancy in specification, and set memory max for Java to task-1.

[erflynn]

A minor comments for a future commit

• In the README mention sample_sheet is a .csv (png does not provide this info)
• In terms of the config set up:
  • you can have the -c config/base.config default included by either putting it in the run script or in .nextflow.config so it's included -- it's a little clunky to have to add this. See Amadeo's single cell config pipeline setup
  • I would prefer the params you have to edit every time (e.g. results_directory, input, etc) to be part of a separate config file that someone prepares for each run rather than part of the list of diretories, this is also difficult because this is a tracked file
  • tmp_dir could have a default
  • ?could make -profile hpc default for DSCo users?
  • would be good to create a test profile for the toy fastqs (the mini ones I shared)
• run_pipeline.sh script instructions are wrong in comments, also should have a resume setup that works if someone is running multiple nextflow pipelines (this one works but only if someone is running one instance)

[AlaaALatif]

@erflynn thanks for the PR and your comments. I have pushed additional commits to this PR that address several of your comments:

• -c config/base.config is included as default inside the run script, the user no longer needs to specify this
• added an additional config file named user_directories.config containing parameters that the user has to specify every time
• added a separate config file named references.config containing paramters for the reference genome
• added a default location for tmp_dir in config/user_directories.config
• fixed various instructions inside the run_pipeline.sh script
• changed the name of the parameter input to input_sample_sheet inside user_directories.config to be more verbose and intuitive to the user