areebapatel / rapid-cns2_nf Goto Github PK
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License: MIT License
Rapid-CNS v2
License: MIT License
Dear @areebapatel ,
As i was waiting for a response for the first issue, I tried deploying the pipeline in a local machine. I did come across alot of errors that are more of bugs concerning the variables in calling the processes in main.nf
file vs how they are actually named in the respective ./nextflow/*.nf
files. Kindly look into it to make the necessary updates.
Additionally, there is a problem in the basecalling.nf
, the runtime:
keyword in
runtime:
docker pod5Docker
cpus runtime_attributes.nThreads
memory "${runtime_attributes.gbRAM} GB"
time 10.hours
keeps being flagged as invalid, so i replaced :
with {}
brackets as shown:
runtime {
docker pod5Docker
cpus runtime_attributes.nThreads
memory "${runtime_attributes.gbRAM} GB"
time 10.hours
}
Subsequently, the whole reportRendering.nf file in include { reportRendering } from './nextflow/reportRendering.nf'
is missing from the .nextflow
directory.From there, I could not proceed anymore. I request the addition of the reportRendering.nf
file so I can proceed.
Thanks,
George
Hi @areebapatel
I just came across this wonderful tool you made and I am trying to deploy it. I was wondering if the support for job schedulers highlighted in the nextflow.config
file (LSF and SLURM) are the only limited ones or any scheduler can be used. This is because my particular HPC uses PBS as a job scheduler. Please advice
George
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