Modified all templates so that singularity images are used instead of conda envs or loaded modules

[victor5lm]

PR checklist

• [X] This comment contains a description of changes (with reason).
• [ ] Make sure your code lints (black and flake8).
• If a new tamplate was added make sure:
  • [ ] Template's schema is added in templates/services.json.
  • [ ] Template's pipeline's documentation in assets/reports/md/template.md is added.
  • [ ] Results Documentation in assets/reports/results/template.md is updated.
• [X] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).
• [ ] If you know a new user was added to the SFTP, make sure you added it to templates/sftp_user.json

PR description

All templates were modified so that, if a conda environment was being used, this environment is replaced by the corresponding singularity image. Furthermore, if module load was used initially in a template, the loaded module is also replaced with the appropriate singularity image, with the same version of the software being employed.

This PR addresses #55 partially.

[saramonzon]

Good job! But it stills needs some tweaking! You need to check for each process which folders need to be mounted, like I've done in the comments of the review, for some examples. Check here for plasmidID:

singularity exec --bind /data/bi/references/ --bind ${scratch_dir} /scratch/bi/singularity-images/depot.galaxyproject.org-singularity-plasmidid-1.6.5--hdfd78af_0.img

references and scratch dir is mounted so the files are available for the image.

You'd probably need to test each of the processed, and see if it works, you can go to any old folder and just try to run the singularity command, you don't need it to complete, just see if it begins.

[jaimeozaez]

buisciii-tools/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon also has a "module load R/4.2.1"