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Something I found out about yesterday. I haven't h...
# pipeline-resource-optimization
m
Something I found out about yesterday. I haven't had time to explore yet, but maybe of interest: https://openebench.bsc.es/benchmarking
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m
I'm sure we mentioned it somewhere, maybe in #C066SFL4PL4 or #C06K0KEAMTN
m
Well, I'm getting old and forgetting things. I need to start using it.
I'm listening to the current updates to the Elixir research software ecosystem
m
I did mentioned twice since, but you were the first
I know there are some focus groups on benchmarking in elixir (at least for CNVs), I've been trying to collaborate, but it's a bit of a mess for an outsider
m
Yeah, I think you need to go through an Elxiir node ideally. Maybe Elixir Spain, or Elixir Sweden ( NBIS ) can help out there some how.
m
Can I do so without being part of any Elixir node?
I know IFB quite well too (French node)
m
I don't know. It seems a bit silly that you couldn't, but they definitely make it difficult because of work package reporting I guess.
m
I'll connect with French node at JOBIM by the end of the month, I'll see if there's anything I can do from there
m
I missed the everything you wanted to know about Elixir session that might have answered that
It seems more tools need to be added to bio.tools so they get indexed properly in openebench and people have access to benchmark information. I need to see what kind of benchmarking done though. I was browsing over the busco entry page yesterday, but I didn't get very far
🤯 1
p
'cc @Júlia Mir
m
I realised I'm also in the Elixir slack where I can just ask questions directly if we want feedback. The nice thing about bio.tools is they're also tagged with EDAM ontology. Galaxy has been making community lists of tools based on this meta data so people can look up appropriate tools for their analysis
I definitely need to explore more though when I get a little time
m
Have you seen Claire yesterday @Mahesh Binzer-Panchal?
m
Yes, but I've not spoken directly to her about it
This poster and the other winner were presented on stage at the closing ceremony
m
That's what she mentioned to me
p
@Mahesh Binzer-Panchal your timing with this is impeccable. Been discussing how we can better use bio.tools / ontologies in other parallel meetings yesterday and today.
this 2
@Júlia Mir is going to start building these into the modules 
meta.yml
files today basically 😅
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Galaxy has been making community lists of tools based on this meta data so people can look up appropriate tools for their analysis
Do you have a link for this?
m
@Júlia Mir while you're looking into this, can we bake in bibtex / doi info / citation info properly?
p
"properly"? We already have DOI, no?
j
yes I have it in my mind! I will reach you once I get to this
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m
"properly"? We already have DOI, no?
not enough
p
But tools / you can easily fetch a bibtex ref from the DOI, no?
Copy code
@article{Li_2009, title={The Sequence Alignment/Map format and SAMtools}, volume={25}, ISSN={1367-4803}, url={<http://dx.doi.org/10.1093/bioinformatics/btp352>}, DOI={10.1093/bioinformatics/btp352}, number={16}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard}, year={2009}, month=jun, pages={2078â€"2079} }
j
Maxime had an issue about this, but I can’t find it now 😅
p
simples
j
m
> Galaxy has been making community lists of tools based on this meta data so people can look up appropriate tools for their analysis
Do you have a link for this?
I think it's this: https://github.com/galaxyproject/galaxy_tool_metadata_extractor
m
Thanks @Phil Ewels, but basically I'd want that info in the meta.yml, that way we could automatically add it to the citations in the pipeline / methods description for multiQC
cf my issue
p
And we get all the software used, on run time
How important is this vs. just having all tools in the pipeline?
If it's the latter, then having an nf-core #CE5LG7WMB command to autogenerate a 
.bib
file from every DOI found in every module, and then committing this to the repo, should be fairly easy
(then it'd work offline, which I guess is the main motivation to not do this from the DOIs directly at run time..)
m
So currently we have in the TEMPLATE something that is widely under-used (and that's an understatement) and that people should fill in to mention all the tools used + publication. We (@James Fellows Yates @Edmund ) have been talking about improving and automatizing the way to deal with that, which is why I'm asking for such a way with the bib already built-in the meta.yml, and we could render it all nicely in the final multiQC report, and probably also avoid some duplication with the CITATIONS.md file
p
Yeah, I like it 👍🏻
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