Palmetto-related tweaks

[bentsherman]

This PR adds a number of tweaks that emerged as a result of me testing GEMmaker 2.0 on Palmetto. I will briefly describe them here:

• Added a pbspro profile, similar to the old pbs profile, which provides a few basic settings specific to PBS Pro, including the Palmetto cluster which is used by many GEMmaker users.
• Changed the singularity profile to also mount the work/GEMmaker folder, which allows GEMmaker to work properly whenever the work directory resides outside of the launh directory.
• Added a new helper script retrieve_sra_spots.py which obtains the total number of spots in an SRA sample by parsing the metadata file. The spots is in turn saved as a trace directive in download_runs for the purpose of predicting resource usage. This script is very niche but it could also be generalized to extract any attribute from a metadata file.
• Added a max_jobs param which controls the number of samples processed in parallel. Previously this behavior was controlled by max_cpus which already controls something else and was therefore confusing.
• Renamed the multithreaded label to process_medium to take advantage of the new labels provided by nf-core.
• Renamed noclean profile to test_noclean for consistency with the other testing profiles.

I apologize for the conglomeration of changes but it's a bunch of small changes so I figure it would be easier to hash them out in one thread. Let me know if I need to change anything to stay consistent with nf-core guidelines.

[bentsherman]

@spficklin I have moved all of the Palmetto-specific settings into a separate config file. Please review my remaining concern about the start_first_batch process.

[bentsherman]

@spficklin I think we've resolved everything. No more Palmetto-specific settings but a bunch of fixes and aesthetic improvements that I made while testing the pipeline on Palmetto. It's ready to merge.

[spficklin]

Changes looked good and it ran fine on my end.... Merging!