Hi <@U02JS8EFMMJ>, Thanks for the input on crispre...
# crisprseqs
sathya jali
08/28/2025, 12:36 PMHi @Júlia Mir, Thanks for the input on crispresso2 pipeline. I am happy to collaborate on integrating crispresso2 to crisprseq pipeline. https://github.com/nf-core/proposals/issues/75. please let me know how to proceed on this. https://github.com/sathyasjali/nf-core-crispresso
j
Júlia Mir
08/29/2025, 6:52 AMHello @sathya jali, happy to have you on board!
I see that you have a crispresso2 module but it is not in the nf-core/modules repo, is this correct?
I think the first step would be to add the module to nf-core
Júlia Mir
08/29/2025, 6:53 AMdo you find good execution times when you use the crisprsesso2 module? I have always thought that it would be better to split what the code is doing into chunks (and each of this into nf-core/modules), to improve the speed and scalability of the tool
Júlia Mir
08/29/2025, 6:53 AMdo you think this is doable and worth it?
Júlia Mir
08/29/2025, 6:54 AMif you want we could also schedule a short meeting to discuss the best way to implement all this into the pipeline 🙂
s
sathya jali
08/29/2025, 4:50 PMHi @Júlia Mir, Thank you! Y Thank you! You’re right — the CRISPResso2 module isn’t in the nf-core/modules repo yet. I’ll work on submitting it there first.
For now, execution times look fine for single-sample runs. Testing the modular approach is definitely possible, but will take some time to implement cleanly. Its is definitely worth doing it.
Once the CRISPResso2 module is reviewed and approved, I’d be happy to set up a short call to discuss next steps for modularization.
I really appreciate the opportunity to collaborate on this.
j
Júlia Mir
08/29/2025, 5:39 PMnice! 👏🏻 let me know if you need a review 🙂
s
sathya jali
08/30/2025, 5:00 AMI have created PR for the module. Could you please review it when you get a chance. https://github.com/nf-core/modules/pull/8973 Thank you!