yes, please open PRs in seqsubmit repo if you will try uploading chromosomes 🙏 we will help!

v1.0.0 - PR ready for reviews -> github.com/nf-core/seqsubmit/pull/72 amazing effort by @Ekaterina Sakharova and @Sofiia Ochkalova nf core party

Btw, please ping me here on Slack if/when you want a rereview, I'm stil l in the process of moving to Spain so not checking my github notifications regularly

@James Fellows Yates do we deserve removing “block releases” rule for seqsubmit? I have merged all fixes to main

<- this guy did it

First release, massive effort from @Ekaterina Sakharova and @Sofiia Ochkalova 👏 🎉

<!here> ✨we have released seqsubmit ✨ github.com/nf-core/seqsubmit/…/1.0.0 to be continued seqsubmit logo light🙌

Does the 1.0 release support submitting co-assemblies or is that still to come?

One other question - does the pipeline support submission of eukaryotic mags? I have a whole bunch of these in my dataset…

Sorry Jim! It doesn't support Euks ATM

There is an issue for this github.com/nf-core/seqsubmit/issues/40 - maybe during the hackathon we get someone to implement it 🙂

seqsubmit talk today at 2.30 UTC+1 on nf-core summit nextflow partyseqsubmit logo lightnf core scroll

@Sofiia Ochkalova or someone else can you look at this one for me when you have a sec please 🙂 I don't have powers to assign it to anyone anymore meow cry github.com/EBI-Metagenomics/mgnify-pipelines-toolkit/pull/164

I’m checking it

@Varsha Kale I think Sonya didn’t wait for tests 😁 lint is failing, fix it please at some point github.com/EBI-Metagenomics/mgnify-pipelines-toolkit/…/38735703045 I have launched container creation

Sorry Kate, I'm rushing ahead github.com/EBI-Metagenomics/mgnify-pipelines-toolkit/pull/165

I can fix lint here

image.png

hack ladies, github.com/nf-core/seqsubmit/pull/106 please tests failed because of ena problems

Does anyone have a direct line to ENA to check two thing for me? Can multiple BAMS be submitted and is it usual? Docs say it can be done for samples that are always intended to be analysed together but that will be so slow if they are huge... do they still support tar.gz archives for fast5 data. They said they would remove this as it's hard to validate what is in the archive. I would very much like to not support it 😆

@Ekaterina Sakharova what's goint on with branch merging We have 2 branches that we soon want to merge to dev merged

I guess we first need to wait for you to merge a waterfall of your PRs 😃

github.com/nf-core/test-datasets/pull/2332 new test data!

@Varsha Kale Can you please open draft PR from your fork to seqsubmit repo?

Done. It won't work yet until container is updated (sorry if this sent already my internet is rubbish)

We just came back from the ENA internal feedback meeting. They are planning major updated to the website, submissions and etc. A few things that are related to submission and affect us: 1. The chromosome flat file (that Kate has been implementing support for in genome_uploader and @Varsha Kale has been working on as well) will be deprecated for assembly submissions in 3 months time. They are replacing it with a JSON in fasta header (see the photo), so we will need to rewrite this code once again sadpanda 2. I raised our "one contig" bins/MAGs problem and tried to persuade them that it's not sustainable in the long run. The answer was that they would be glad to cancel this rule, but it's required by NCBI as well and if ENA will start to accept one contig assemblies, it will affect the mirroring. So before they change anything, there should be a broader meeting with INSDC to discuss this change.

So the user has to modify the fasta?

thank you so much for pushing the 1 contig thing 💪

💫 seqsubmit now supports raw reads upload in bam format as well 💫 now in

dev

thanks to @Varsha Kale on hackathon

Hi all, hope you don't mind me joining the channel! Thank you for starting this pipeline and making ENA submission less painful 😄 I've seen the repo and checked the issues, if I understood well the pipeline at the moment works for raw data submission and metagenome assemblies, right? I was wondering if someone is already working on genome assembly submission (not metagenome). If not, I'd be happy to help on this as I will have to submit tons of assemblies in the next months and I thought it might be better to contribute to something already created rather than building my own pipeline. Let me know 😊