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Big big thanks to <@U07EFJBC4UR> and <@U07CBTL827N...
# funcscan
j
Big big thanks to @Haidong Yi and @Xinpeng Zhang a CAZyme screening subworkflow has been integrated into 
dev
of funcscan! I will start preparing for a release - so for those who have asked for this it's coming very soon!
❤️ 1
nf core party 3
party parrot 4
@Haidong Yi @Xinpeng Zhang would you do the honour of picking the release name? Funcscan release names follow national food dishes - we've had German Rollmops, British beans on toast, Brazilian Escondidinho, Egyptian Hoshari, and French Chocolatine... Any suggestions?
🎉 2
e
FYI, we will have a new nf-core module soon to predict cazymes...in case you want to add that to funcscan as well (for proteins though)
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i'll do it for #C084HP11VPF. This is the software: https://github.com/lczong/CAALM
preparing for a first release + PyPI / bioconda etc..
x
That sounds so interesting! Thank you for giving us this chance. Since we're working on CAZymes, how about Chinese Baozi or Mantou, which are two traditional Chinese foods with carbohydrates? How about @Haidong Yi’s opinion
❤️ 3
j
I love it! (Also because myself and my family love Baozi 😬)
🎉 1
I will assume Baozi for now unelss @Haidong Yi says otherwise during the release review period 🙂
h
Thank you everyone for making this happen. Baozi works for me pretty well.
baozi 1
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j
@Haidong Yi @Xinpeng Zhang question for you both, from when I was testing the pipeline on our 'full test' data: https://github.com/nf-core/funcscan/pull/523#issuecomment-4152941342
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e
if anybody wants to have an early-go on 
caalm
, feel free to review my PR 😄 : https://github.com/nf-core/modules/pull/11087 (cpu-only mode first -will be needed as a fallback)
✏️ 1
x
Hi James, thank you for reporting this issue. I'm looking into it and will reply to you as soon as possible! @James Fellows Yates
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j
@Xinpeng Zhang wondering if you happened to have any updates on this or not? We can quite easily update the module so the Nextflow knows that the 
*_synteny_pdf
directory is optional, but I wanted to make sure that this was inded the case
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x
It's kinda optional results. Not all results are shown in that folder.
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j
OIk then I will update the module to make it optional 🙂
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@Xinpeng Zhang I've been trying to do this all through today, but the tests are taking a horrible amount of time (I think to download the database? I'm not sure): https://github.com/nf-core/modules/pull/11242 Do you have any idea what could be happening? All I needed to run was 
nf-core modules test rundbcan --update --profile docker
Is there any chance you could finish the PR with updating the snapshots?
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x
Hi James, thank you for the effort for updating it! I’m attending a workshop and will check it asap!
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j
Tahnk you!
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@Xinpeng Zhang just small reminder of the above about the failing tests, in case you have a bit more time now?
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x
@James Fellows Yates Hi James, yes, I'm working on this today. So sorry for the long delay 😞.
I'll update a new version with a new improvement, and then hope we can fix this issue as well.
j
Ok! Thank you :D, let me know and I can also update the module
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x
I've included some updates in the dev branch and am running tests. Once it passes, I'll update it to the bioconda, and it may take one or two days to be merged on the bioconda and Docker.
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Thank you so much for your help with the long-term process 😄!
j
You're welcome! And updates @Xinpeng Zhang? I have review/merge rights on bioconda so can do that quickly for you if you yourself don't have such permissions 🙂
x
That would be great! Thank you James! I’m running a test and once everything passes I’ll submit to the bioconda and let you know.
salute 1
@James Fellows Yates Hi James, I just published the v5.2.9 and it will be on bioconda soon after the autobump. I'll also double-check if it still has the nf-core module issue. Thank you so much for your help!
j
OK I found the autobump, approved and merged!
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x
Thank you James!
j
I'll see if I can do a lazy search and replace on the module PR quickly now 😉
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x
i think the singularity may need one or two days to be uploaded.
j
Yes, the singularity image should be there in about 24h, but if docker/conda works then should be all fine (just have to reexecute the tests once it's availalbe)
x
gotcha
most of those passed, and there were issues about the md5 in test_STP_hmm_results.tsv and test_total_cgc_info.tsv
should we update the snapshot to fix it?
j
Aha nice!
Yes
But fantastic 😄
Is it the same change across all tests?
Hrm no, ok yeah would need to be a full snapshot upodate... is taht something you could do?
OR would you prefer me to do so?
x
yes I could do it👍 will work on it now and double-check it to make sure if it is acceptable
thank you James!
j
🎉
I thin kyou should be able to push directly to my branch
x
okay👍
Hi James, I've submitted it, and it looks all passed.
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j
Looks greaT!
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I'll put a remidner to re-run the singularity tests tomrorow and the nrequest review 🙂
x
thank you James! I think the program speed is much faster than before.
j
🎉
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