ARMS checklist

[kmexter]

For the ARMS samples we will use the https://www.ebi.ac.uk/ena/browser/view/ERC000025 checklist but we will want to add our own things to do
This issue is for us to decide what should be added and where we can add values as URLs rather than strings

[cpavloud]

Related issues

emo-bon/observatory-profile#43

emo-bon/observatory-profile#20

[kmexter]

This is also relevant for the ENA uploading process, @bulricht and @marc-portier

[kmexter]

This is a 2026 Q2-Q3 to do

[cpavloud]

Ok, @isanti @kmexter sample submission for ARMS batch 3 is done!
It wasn't very straightforward, but at least it's finished :)

FYI, one thing to note, regarding the automatic creation of sample accession:
the term sequence quality check must be equal to one of the allowed values: ["manual","none","software"]
so we cannot use "basic Genoscope QC" to populate that field
To overcome it now, I renamed the term to sequence_quality_check, which made it a custom field and I was able to keep what we originally had included there.

There were missing latitude and longitude values for Getxo A3, so whenever they are provided, we should update the samples in ENA.

There were missing *latitude, longitude and environmental medium values for Buoy Vida BuoyVida, so whenever they are provided, we should update the samples in ENA.

depth was missing for Svalbard, so whenever it is provided, we should update the samples in ENA.

Luckily very few fields were mandatory in this checklist (because we had some NA values).
But the submission needed to be done, so I proceeded.

This is what I submitted:
Checklist_GSC-MIxS miscellaneous natural or artificial environment_ERC000025_ARMS_batch3.tsv

And this is my (dirty and not documented) R script to create the checklist (saved as a .txt and not as .R because GitHub doesn't allow all kinds of attachments)
ARMS_ENA_submission.txt

And this is the file containing the ENA sample accessions (to be sent to Genoscope when we want the sequences to be submitted/released)
arms_batch3_sample_accessions.tsv

[kmexter]

grand - I can raise a new QC and/or ENA worflow issue to document that ena bit, can @isanti check out the missing entries and raise a flag on those stations?
@cpavloud would you say that this checklist is complete, or does it need discussions (I will only raise the issue on QC and ENA workflows once you give me the go-ahead)

[cpavloud]

Complete in terms of "we don't need to add more column names"?
At the moment I think yes.

[kmexter]

new issue raised on emo-bon/ena-sample-registration-action#14

[isanti]

I wrote to the stations to give this information and will follow up here when there are updates.

[isanti]

There were missing latitude and longitude values for Getxo A3, so whenever they are provided, we should update the samples in ENA.

done

depth was missing for Svalbard, so whenever it is provided, we should update the samples in ENA.

done

[cpavloud]

Samples corrected :)