Bring master branch up to date

[ManavalanG]

Pull request

This PR will merge current version of joss_manuscript to the master branch to bring it up to date, and then we will cut a new release. Note that joss_manuscript branch will not be deleted and it will continue to serve as the branch to be used for JOSS reviews.

This PR includes several PRs as follows:

• Autocreate user-provided dirpath if they don't exist #67
• Swtich singularity+conda setup to singularity setup for snakemake tasks #70
• Check mount paths exist #72
• Create sbatch args using cluster config file #73
• Adds system testing workflow to github actions #75
• Refactors to account for user's environment-specific SLURM setup #80

Changelog corresponding to this PR is listed below:

2023-06-22 Manavalan Gajapathy

• Refactors CLI script to accounting for user's environment specific slurm args requirements when submitting job to
  slurm (CLI script not accounting for user's environment specific slurm args requirements #76)
• Removes CLI option --rerun_failed and instead configures it via snakemake-slurm profile
  (src/slurm/slurm_profile/config.yaml)
• Removes --subtasks_slurm option and --snakemake_slurm as they were redundant
• Checks if tool dependencies are available in user environment.
• Adds time resource to configs/snakemake_cluster_config.json
• Removes PR trigger from system testing github actions.
• Tests if singularity is working as expected in user machine

2023-05-31 Manavalan Gajapathy

• Adds system testing as github actions workflow

2023-05-18 Manavalan Gajapathy

• Constructs snakemake's sbatch command using args and values from cluster config file supplied via
  --cluster_config.
• Updates doc to include cluster config as a requirement

2023-05-09 Manavalan Gajapathy

• Adds a verification step in the CLI wrapper script to check if the file/dirpaths to be mounted to singularity already
  exist as expected (Verify singularity mount paths exist #71)
• Resolves dirpaths of datasets in the workflow config file to obtain their full path

2023-04-10 Manavalan Gajapathy

• Refactors snakemake pipeline to fully run jobs in direct singularity containers. No more creation of conda environment
  using singularity containers! (Removing use of conda env for tasks within snakemake pipeline #69)

2023-04-04 Manavalan Gajapathy

• Retires use of cheaha-specific env variable $USER_SCRATCH
• Auto-creates user-provided dir structures for --outdir, --tmp_dir, and --log_dir

Please fill in the checklist below and comment as needed.

• Was code modified? Briefly describe. Yes, but changes were already reviewed as part of earlier PRs
• Was documentation modified? Briefly describe. Yes, but changes were already reviewed as part of earlier PRs
• Is this a bug-fix? Briefly describe. Yes, but changes were already reviewed as part of earlier PRs
• Is this a feature addition? Briefly describe. Yes, but changes were already reviewed as part of earlier PRs
• Did you modify QuaC-Watch config file? If so, did you modify multiqc template
  configs/multiqc_config_template.jinja2 and script src/quac_watch/create_mutliqc_configs.py as necessary? No
• Did you perform system-level testing manually as described in master readme doc? Did it pass completely? If not why? Yes
• Updated Changelog.md file with change logs in recommended format?

Anything else reviewer should know?

[wilkb777]

LGTM