Hi, sorry I am a little confused, and I think the ...
# airrflowj
James O'Brien
02/07/2025, 4:15 PMHi, sorry I am a little confused, and I think the documentation has been updated.
If I am planning on running this pipeline on Takara SMART-BCR with UMIs. I think that I use the clontech_umi_bcr in the profile option.
Do I need to provide any other parameters - previously there was an expectation to use c-primers and linker sequences.
I plan to run this on a HPC, using singularity via SLURM - the FASTQ files total a size of around 60gb, and was run on a P2 flow cell. Is there any guidance on the amount of resources I need to request on the HPC to process this?
Thank you in advance for the advice.
s
ssnn
02/11/2025, 9:54 AMHi James. Yes, setting the profile should work. There is an example in the documentation here. I will come back to answer the resources part of the question, after I have inspected configuration files that we have used in our cluster.
ssnn
02/11/2025, 10:37 AMI forgot this: Immancatation is moving to GitHub. If you need the c region primers for human and mouse are now here.
ssnn
02/11/2025, 10:49 AMWe use this nf-core institutional profile to allocate for resources in our cluster https://github.com/nf-core/configs/blob/master/conf/mccleary.config. You can use it like this `-profile clontech_umi_bcr,mccleary`` or you can use it as inspiration to create a new profile for your cluster.
j
James O'Brien
02/12/2025, 12:00 PMGreat - thanks for responding. The institution profile has worked fine and request appropriate resources.
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