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Error with applying reference file for genetic ancestry #234

Answered by smlmbrt
jasamack asked this question in Q&A
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Hi @jasamack - it seems like something is going wrong with the pvar/sorting? I also use the Cambridge HPC but have never used conda (only singularity). If you could try my singularity config that might sort it? You would use -c in nextflow and point to a file with similar contents (adapted for your needs):

prams {
  config_profile_description = 'Cambridge HPC cluster profile.'
  config_profile_contact = 'Sam Lambert'
  config_profile_url = "https://docs.hpc.cam.ac.uk/hpc"
}
singularity {
  enabled = true
  autoMounts = true
  cacheDir = "$HOME/rds/hpc-work/cache_nxf_singularity"
}
process {
    executor = 'slurm'
        clusterOptions = '-p icelake-himem -A [YOUR ACCOUNT, CHANGE]'
      …

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Answer selected by jasamack
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