Include MetaBinner/SemiBin2 as inputs to DASTool

[AlexHoratio]

Happy Yuletide, developers of nf-core! 😊

As a gift I bring you this PR: MetaBinner/SemiBin2 should be included as inputs to DASTool when available. I believe this fixes it by replicating the existing pattern for other binners (just tested on my own data, appears to work).

PR checklist

• This comment contains a description of changes (with reason).

[jfy133]

Thank you @AlexHoratio !

I've not tested, but looks simple enough to me. I'll let someone else from @nf-core/nf-core-mag to double check :)

[jfy133]

of the tests:

1. Is checkM2 database download time out
2. The second is a a snapshot update required for assembly_input - @AlexHoratio you will need t orun nf-test test --tag test_assembly_input --profile +docker --update-snapshot (or something along this lines), to incorporate teh FASTA2CONTIGBIN output for semi2bin into the sanpshot :)

[prototaxites]

This looks fine to me also, but I just want to double-check - are the contig headers of the bins from these new binners compatible with DAS_Tool? Some binners for whatever reason rename contigs, but these bin refinement tools need the original contig names to remain in place.

[AlexHoratio]

This looks fine to me also, but I just want to double-check - are the contig headers of the bins from these new binners compatible with DAS_Tool? Some binners for whatever reason rename contigs, but these bin refinement tools need the original contig names to remain in place.

I just double-checked some of my outputs, and I can't find any evidence of the contigs being renamed, and it does seem to mix with DASTool appropriately.

Also, that snapshot update test is still failing... I think that's my fault for trying to run it on my under-powered local machine. I'll try it again in a moment.

[jfy133]

Don't worry @AlexHoratio the failing test isn't you

Zenodo is 403ing for some reason when downloading the CheckM2 database.. not to do with you I think :)

[dialvarezs]

Zenodo is 403ing for some reason when downloading the CheckM2 database.. not to do with you I think :)

It seems that Zenodo is blocking aria2 UA 🙃. It doesn't work for me either, but it does when changing UA, e.g. --user-agent="Wget/1.21.4" .

[jfy133]

@AlexHoratio sorry taken so long to get to this. We refactored somewhat the DAS_Tool steps in another PR, so there were some merge conflicts I've tried to resolve. Please have a look to make sure I didn't make sure

Otherwise I think the nf-test snapshot may still need updating, but we w ill see

(checkM issues should be resolved now!)

[AlexHoratio]

Awesome, well that is a good refactor 😊 I believe the test_assembly_input snapshot should now be updated again.

[jfy133]

Is that something you have capacity to do, or should one someone take over @AlexHoratio ?

[AlexHoratio]

If you just need me to test the pipeline on some real data and see if this PR currently works, I have just done that, and it appears to do so.. all binners still occur appropriately in DASTool outputs.

Anything else may lie beyond my Nextflow know-how 🥲

[jfy133]

Works for me! Thank you @AlexHoratio ! LGTM!