Hi! I am currently processing 296 single-cell TCR/BCR sequencing datasets using airrflow pipeline. First, I used the pipeline to run scTCR-seq data. HDuring the execution of the

Submitted process > NFCORE_AIRRFLOW:AIRRFLOW:SINGLE_CELL_QC_AND_FILTERING:SINGLE_CELL_QC (all_single_cell)

step, the workflow appears to be unexpectedly stalled. According to the log file, the task initiated at 2025-08-13 235618 has not completed after 8+ hours of runtime. Could you confirm whether this duration is within expected parameters for such data volume?

Hi @Suchen Li, the error message you shared in the execution report html indicates that the process was killed due to it going over the time request limit:

Error executing process > 'NFCORE_AIRRFLOW:AIRRFLOW:SINGLE_CELL_QC_AND_FILTERING:SINGLE_CELL_QC (all_single_cell)'

Caused by:
  Process exceeded running time limit (8h)

You can update the time, memory and CPU request of processes by providing a configuration file with the parameter

-c

to the command. E.g.

nextflow run …. -c custom.config

. Then provide inside the config:

process{
  withName:SINGLE_CELL_QC{
    time = 24.h
    memory = 64.GB
    cpus = 16
  }
}

You can start by updating the time request only, but this is an example that increases also the requested memory and cpus. As you are running the pipeline with a high amount of samples, you might need to increase the requested resources for several processes. Let me know if you run into any other issues, happy to help. Also, when you perform the anlaysis for TCR, you should set the clonal threshold to zero with:

--clonal_threshold 0

Thanks for your kind help!