@Mxrcon and @abhi18av super excited about this one! Thank you very much!

I changed the merge branch to dsl2, I'm going to play around with it this weekend! (haha super super excited about this!)

Some things we know that would be changed during the course of this review

• Shrim the module folders (Readme, bin, template folders etc)
• Enhance the utils to accomodate further channel manipulation
• Combine modules into sub-workflows to allow other people to choose parts they'd like to use
• Refactor to use path instead of file

@abhi18av I can take care of the usage of path instead of file! you can focus on the other tasks!

Thank you @rpetit3 for taking time to this!

Quick question, for the module bins (https://github.com/bioinformatics-lab/bactopia/tree/dsl2-modules/modules/blast/blast_genes/bin). Is it ok to delete the scripts that won't be used by the module? (e.g. update-tools.sh)

I think the answer is "yes, it's ok to remove unused scripts", but want to verify. If the answer is yes, I can go through and delete the unused scripts.

Yes, you are right it's okay to delete those module level bin folders if the script isn't used in that module.

Though in light of nextflow-io/nextflow#1798, if the NF script main.nf is invoked from the base directory (or outside) the module will find those scripts in bin folder.

However, if you wish to test only that module, then it's best to invoke NF from that particular module itself and in that case the module level bin would be used by that process.

For module specific scripts I'll put them in the module bin folder and not the main bactopia/bin folder.

Like you mentioned, for testing it will be great and it should prevent maintaining duplicates (if shared across modules it will be duplicated (example: merge-blast-json.py is shared across the blast processes)).

For testing and help on my end, I had a question. On the bioinformatics-lab/bactopia repo, which branch are we aiming to get into bactopia, bioinformatics-lab/dsl2-modules or bioinformatics-lab/dsl2?

I'm assuming the route is bioinformatics-lab/dsl2-modules --> bioinformatics-lab/dsl2 --> bactopia/dsl2 --> bactopia/master

Thank you!

I suggest that we continue working on the dsl2-modules branch since it doesn't contain changes to the main.nf and therefore we can include the modules and then iteratively swap them into the main.nf file piece-by-piece.

Therefore, we can simply follow

bioinformatics-lab/dsl2-modules --> bactopia/dsl2 --> bactopia/master

What do you think?

Sounds good! Thank you for clearing that up.

Next question, would you prefer my contributions come into bioinformatics-lab/dsl2-modules until ready to merge this PR into bactopia/dsl2, or go ahead and get this merged so my contributions can be made directly to bactopia/dsl2?

go ahead and get this merged so my contributions can be made directly to bactopia/dsl2

I think that this makes more sense, as we can have a central point of reference. What do you think @Mxrcon ?

I think that this makes more sense, as we can have a central point of reference. What do you think @Mxrcon ?

I completely agree, we can track your changes on your branch and we could discuss the points mentioned by @abhi18av after you make them!

Sounds like a plan! Llet me fix the conflicting main.nf then I'll get this merged

This might actually be easier on your end since I cannot edit the files.

I think at the moment if you just use the most recent main.nf (unless there are DSL2 specific changes in the dsl2-modules version, I didn't notice any), this should fix the conflict.

Once merged, I'll bring the bactopia/dsl2 branch up to v1.7.1 (the PR I closed on your end)

Okay, I've rebased this branch on the master v1.7.1 and resolved the merge conflicts.

@rpetit3 , for collaborating further #228 (comment) , how do you think that we should proceed?

Would it make sense to use a Github project to track the work to be done/in-progress/done ?

I've started a Bactopia v2 project here https://github.com/bactopia/bactopia/projects/1

For now we can make the focus getting DSL2 fully implemented, then there's a bunch I'll want to get in as well (more bactopia tools, other random issues)

Oh, makes sense - thanks for the initiative 👍