Hi what is the purpose of the files on this line a...
# referencesn
Nicolas Vannieuwkerke
03/26/2025, 10:02 AMHi what is the purpose of the files on this line and all lines after that? https://github.com/nf-core/modules/blob/565c264868ccfe46a4c87a4ab3f812298c307597/subworkflows/nf-core/utils_references/schema_references.json#L42
(I'm trying to get a better understanding in order to update the JSON schema)
m
Maxime Garcia
03/26/2025, 10:08 AMso currently these files are tar in sarek
Maxime Garcia
03/26/2025, 10:08 AMbut I think we can actually provide folders instead
n
Nicolas Vannieuwkerke
03/26/2025, 10:08 AMOkay so these should be directories or tarzipped files? 😛 All of the following path values too?
m
Maxime Garcia
03/26/2025, 10:09 AMoooh
Maxime Garcia
03/26/2025, 10:09 AMshall we hope on a call so I can explain the logic?
Maxime Garcia
03/26/2025, 10:09 AMsorry did not catch all the question
Maxime Garcia
03/26/2025, 10:09 AMI was blinded by
ascat_allelesn
Nicolas Vannieuwkerke
03/26/2025, 10:09 AMYeah good idea 😉
l
Luuk Harbers
03/26/2025, 10:10 AMIve been running and implementing ASCAT on some future pipelines as well so maybe I can add to this if something is unclear what these files are used for and what is the most convenient type (zip vs folder for instance)
🎉 1
m
Maxime Garcia
03/26/2025, 10:11 AMl
Luuk Harbers
03/26/2025, 10:14 AMSo let me know if you have any questions/want to discuss about how it would actually be easiest to use ascat reference files in pipelines
m
Maxime Garcia
03/26/2025, 10:18 AM@Luuk Harbers so my current implementation in references can auto-extract references
l
Luuk Harbers
03/26/2025, 10:22 AMI haven't had the time to look into the exact implementation of nf-core/references yet. I guess this shows it? https://github.com/nf-core/references/blob/dev/subworkflows/local/yaml_to_channel/main.nf
Where it downloads the associated files and puts it in a channel or am i simplifying too much?
Luuk Harbers
03/26/2025, 10:24 AMIf this is the implementation and output as illustrated in that subworkflow, that seems perfect to me
Copy code
emit:
ascat_alleles // channel: [meta, *.ascat_alleles.txt]Luuk Harbers
03/26/2025, 10:24 AMBetter than the current, downloading a
.zipm
Maxime Garcia
03/26/2025, 10:27 AMso yaml_to_channel is just transforming the yaml genome sheet in a channel
Maxime Garcia
03/26/2025, 10:28 AMthis is where the auto-extract happen: https://github.com/nf-core/references/blob/dev/main.nf#L222-L252
l
Luuk Harbers
03/26/2025, 10:31 AMAh I see, neat, thanks a lot!
Looking forward to 1.0.0 and some more info on how to use it on other pipelines!
PS: Sorry for hijacking this thread :')
m
Maxime Garcia
03/26/2025, 10:31 AMHijacking discussions is my middle name
Maxime Garcia
03/26/2025, 10:38 AMutils_referencesn
Nicolas Vannieuwkerke
03/26/2025, 10:39 AMAwesome! I'll give it a go after lunch!
m
Maxime Garcia
03/26/2025, 10:39 AMTHANKS