Automation of the configuration process prior to the execution of viralrecon services.

jaimeozaez commented 1 month ago

Modification of the viralrecon template (lablog_viralrecon) in order to ease the running of this pipeline.
Checking and downloading of required containers.
Checking and downloading of required references.
Setup of configuration files.

Closes #225

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

saramonzon commented 1 month ago

You'll need to test it thoroughly, but it looks pretty good! I think it covers all scenarios :)

saramonzon commented 1 month ago

I think I'd add a question for assembly, mapping or both, in case of "other" virus.

saramonzon commented 1 month ago

Include the module load inside the sbatch. Include comments at the beginning of the script explaining what it does.

Not for this PR, open an issue: include not interative mode

saramonzon commented 1 month ago

LGTM :), @Shettland do the honors and approve it :)