nextflow.config

resume = true

process {
  errorStrategy = 'finish'
}

profiles {
  slurm {
    process {
      executor = 'slurm'
      module = 'apptainer'

      withLabel: gpu    { clusterOptions = '--gres=gpu:1' }
      withLabel: guppy  { module = 'guppy' }
    }
  }

  apptainer {
    apptainer {
      enabled = true
      autoMounts = true
    }
  }

  docker {
    docker {
      enabled = true
    }
  }
}

// containers
process {
  withLabel: artic      { container = 'quay.io/biocontainers/artic:1.2.3--pyhdfd78af_0' }
  withLabel: fastp      { container = 'quay.io/biocontainers/fastp:0.23.4--hadf994f_2' }
  withLabel: fastqc     { container = 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0' }
  withLabel: git        { container = 'ghcr.io/dialvarezs/containers/utils:20230817' }
  withLabel: multiqc    { container = 'quay.io/biocontainers/multiqc:1.15--pyhdfd78af_0' }
  withLabel: nextclade  { container = 'nextstrain/nextclade:2.14.0' }
  withLabel: python     { container = 'ghcr.io/catg-umag/ncov2019-ont-nf/pandas-scibioxl:20230821' }
  withLabel: pangolin   { container = 'quay.io/biocontainers/pangolin:4.3--pyhdfd78af_2' }
  withLabel: samtools   { container = 'quay.io/biocontainers/samtools:1.17--hd87286a_1' }
  withLabel: snpeff     { container = 'quay.io/biocontainers/snpeff:5.1d--hdfd78af_0' }
}