Amrplusplus

[AroArz]

todo:

1. slurm settings
2. edit input in config.yaml
3. figure out why error message is printed at the end of successful workflow (this is a function of the develop branch and not a result of amrplusplus integration)

[boulund]

We have not utilized this way of referencing script paths in any previous StaG module. I'm not entirely sure that this belongs in the config file, as usage of the script is tightly coupled to the call to the script (in the rule body), so we might as well just hardcode the script path in there... Thoughts?

[AroArz]

Sure its easy to change. My main idea with this type of referencing was if we would ever change the structure of scripts folder we would only need to change the path in config.yaml and not touch the rulefile itself.

[boulund]

I would like to only have stuff that end-users should be able to modify in the config file. You can still use the params section to define the path to the script for each rule just like you currently have, just that you hardcode it in place there instead of keeping it here in the config.

[boulund]

We need to add the license text from https://github.com/meglab-metagenomics/amrplusplus_v2 to the subdirectory where we include their scripts (see e.g. how it looks with KrakenTools)

[boulund]

We also need to write documentation (make a new section in https://github.com/ctmrbio/stag-mwc/blob/amrplusplus/docs/source/modules.rst). We should also make it very clear here that AMRPlusPlus only works with singularity. If a user tries to run this without singularity, the user would likely be presented with strange errors. If possible we should make sure these rules are skipped by Snakemake if the users tries to run without singuarlity (I don't think this is practically possible, however).

[boulund]

Additionally, we need to update the CircleCI tests so the syntax and dag can be automatically validated: https://github.com/ctmrbio/stag-mwc/blob/amrplusplus/.circleci/config.yml

[boulund]

The CHANGELOG also needs to be updated:

https://github.com/ctmrbio/stag-mwc/blob/amrplusplus/CHANGELOG.md#041-unreleased

[AroArz]

How about

Suggested change

	amrplusplus:
	databases:
	megares_fasta: "scripts/amrplusplus/db/megares_modified_database_v2.00.fasta"
	megares_annotation: "scripts/amrplusplus/db/megares_modified_annotations_v2.00.csv"
	amrplusplus:
	megares:
	fasta: "scripts/amrplusplus/db/megares_modified_database_v2.00.fasta"
	annotation: "scripts/amrplusplus/db/megares_modified_annotations_v2.00.csv"

[boulund]

This is starting to look good. I would just like to confirm with you @AroArz that you've successfully tried running this with --use-conda and --use-singularity separately?

[AroArz]

This is starting to look good. I would just like to confirm with you @AroArz that you've successfully tried running this with --use-conda and --use-singularity separately?

[AroArz]

That was not the button I was looking for.. :).

I successfully ran this using --use-singularity and --use-conda on both nas and Uppmax.