Addition of amrfinderplus to characterization template

BU-ISCIII / buisciii-tools

set of helper tools for bu-isciii management of its core services portfolio.

GNU General Public License v3.0

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Addition of amrfinderplus to characterization template #290

Closed jaimeozaez closed 1 week ago

jaimeozaez commented 1 week ago

Added folder for execution of amrfinderplus inside characterization template. Modified lablog for armfinder, including organism selection stage. Modified lablog_characterization_results, adding links for amrfinder files.

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

Shettland commented 1 week ago

I think that the error that you mentioned here https://github.com/BU-ISCIII/buisciii-tools/pull/290#discussion_r1656964901 using the singularity image could be fixed. But im not sure.

According to the github documentation https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus, --database can be used to use a custom database. This could be used together with -update to download the latest version of the AMRFinderPlus database.

Nonetheless, its better to include it in the template with conda for now; we can try to implement it with singularity later. I'll create an issue mentioning that this should be tested.

jaimeozaez commented 1 week ago

I think that the error that you mentioned here #290 (comment) using the singularity image could be fixed. But im not sure.

According to the github documentation https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus, --database can be used to use a custom database. This could be used together with -update to download the latest version of the AMRFinderPlus database.

Nonetheless, its better to include it in the template with conda for now; we can try to implement it with singularity later. I'll create an issue mentioning that this should be tested.

I tried what you're talking about, but it failed... I downloaded de latest available database and used the custom path when running singularity, but the same error raised up.