areebapatel / rapid-cns2_nf Goto Github PK

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