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Hi, I've updated fcs/fcsgx to topic but its contai...
# modules
l
Hi, I've updated fcs/fcsgx to topic but its container doesn't pass the lint. It's a deprecated modules so I don't thinks it's worth moving it to quay.io. What should I do ? https://github.com/nf-core/modules/pull/11522
e
delete xD
m
it already has the registry added, so it will still run correctly. linting is not so important then
👍 1
e
sorry, I mean if it's been deprecated for more than 8 months 😛
l
delete xD
That's what I thought too, but fsc/adaptor has the same issue and isn't deprecated 😅
m
Those modules got caught in partial migration, and I think haven't been updated since. The tool interface changed around a bit and no one has had time to finish getting the modules up to date. I would say get rid of the deprecated module though. Leave fcs/adaptor as it's still used outside nf-core (or I think it is).
👍 1
s
Do we have a graceful handling in nf-core tools for when we delete? If you have an installed module that gets removed, does it give some kind of error that makes sense when you try and nf-core modules update?
m
nope, not yet. can add it. also should throw a warning if it deprecated. can you make an issue please?
s
l
So, should we leave it as is for the moment and wait for nf-core tools to be able to deal with deleted modules ? I've also cleaned fcs/adaptor but it doesn't pass the lint, as it's using 
<http://docker.io/|docker.io/>
m
for the first point yes. for the second, they need to be on quay or wave
or is there a licensing issue?
s
Gah
It is unhelpful to try and enforce these sorts of things via the linting
m
that's what we do with linting, enforce our guidelines
s
Fine for requiring the full prefix, not so helpful for requiring bulk migration to our quay
m
no bulk migration, we just want to have control over our containers/ let everybody update a module.
l
> they need to be on quay or wave > or is there a licensing issue? They do provide a bioconda environment but it only contains run_gx.py, sync_files.py, action_report.py and classify_taxonomy.py. fcs_adaptor ("av_screen_x" command) is not available in it. They might add it later, but no timeline is provided https://github.com/ncbi/fcs/issues/74
m
Yeah, that was what stopped us partial migration.
The implementation of the tool was a mess to start with. They wrote scripts which then wrapped a docker/singularity call and made it impossible to use in nf-core modules so we had to dig down into what it was calling in the first place. Then not everything got moved when they restructured after requests from other nf-core contributors.
l
I see... should we force merge for the moment ? The modules work, it's just the linting of docker.io that fails.
s
I think force merge yes
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