Version-3.0 release

[abhi18av]

This PR marks the release of v3.0 of BACTpipe.

[abhi18av]

Pre-flight checklist

• [x] Update the Nextflow to latest edge release on your env (to accomodate the stub feature)
• [ ] Test the pipeline on the HPC

Please let me know when these are done and then the coding tasks for this release are done.

[thorellk]

I installed the nextflow version 20.10.0 build 5430 on the HPC now. However, we are in the middle of a maintenance window for the HPC right now and cannot submit jobs atm. It should be done by tomorrow hopefully.

[abhi18av]

@thorellk , that's the last stable release.

Could you also install the edge release in addition to the usual stable one. Here's how you can do this.

wget https://github.com/nextflow-io/nextflow/releases/download/v21.01.0-edge/nextflow-21.01.0-edge-all
chmod +x nextflow-21.01.0-edge-all
# Add this new binary to the $PATH or move this binary to /usr/local/bin/ 

[thorellk]

Great that you are reviewing the details @boulund! I think I have updated all documentation to be in line with the changes that we have done. Unfortunately our HPC is down atm but I will make a hopefully final test run as soon as it is back to business!

[boulund]

I rewrote rename_fasta.py quite substantially. It still doesn't have any error handling, but it should work just the same,

[boulund]

sendsketch_to_prokka.py needs to be similarly rewritten. It should use argumentparser to parse args and provide useful help and error messages if arguments are missing.

I think the parsing needs to be improved at least a bit as well. It's performing a very blind kind of parsing now, not ensuring that the values it reads are valid at all.

[thorellk]

@boulund, would you be able to help @emilio-r with that? I think it would be valuable for him to get someone showing and explaining those aspects.

[boulund]

@boulund, would you be able to help @emilio-r with that? I think it would be valuable for him to get someone showing and explaining those aspects.

I'd love to, but I don't think I'll have more time to spend on this today unfortunately. Maybe next week?

[emilio-r]

@boulund That would suit me better as well as my availability isn't that good for the afternoon today. Let's talk on Monday and work something out?

[thorellk]

Ok, should we wait with the 3.0 release until that it done or should we polish that afterwards?

[boulund]

Either is fine by me, I guess it can be included in 3.1 later .

It just occurred to me that this PR merges into master and not into develop. I think for future developments we should prepare releases to/on the develop branch first, so we can easily preview the automatically built documentation on readthedocs before merging the release into the main branch.

[emilio-r]

I agree with @boulund. Any updates to that script (or similar) can be seen as adding more polish. Everything seems to work as intended right now (at least it did last time we were able to access the HPC properly...) and that polish may just as well be included in a future 3.1 patch.

[thorellk]

I am fine with pushing this to master as soon as @abhi18av and @boulund consider it ready!

[thorellk]

Ok, let's do this then. Keep your fingers crossed ;)

[abhi18av]

Yayyy! 👏 👏

So happy to see v3 being done!

Thanks for allowing me to be a part of this project @thorellk @boulund @emilio-r 😊

[abhi18av]

It just occurred to me that this PR merges into master and not into develop. I think for future developments we should prepare releases to/on the develop branch first, so we can easily preview the automatically built documentation on readthedocs before merging the release into the main branch.

Now that the 3.E branch has been merged (and deleted) - I'll create the develop branch.