nextflow.config

manifest {
  name = 'Sage-Bionetworks-Workflows/nf-synapse'
  author = 'Brad Macdonald'
  homePage = 'https://github.com/Sage-Bionetworks-Workflows/nf-synapse'
  description = 'Synapse Operations for Nextflow'
  mainScript = 'main.nf'
  nextflowVersion = '>=22.04.0'
  version = '0.0.1'
  defaultBranch = 'main'
}

profiles {
	conda { process.conda = "$baseDir/environment.yml" }
	docker { docker.enabled = true }
}

process {
  maxErrors     = '-1'
  maxRetries    = 5
  errorStrategy = { task.attempt <= 5 ? 'retry' : 'finish' }
  
  cpus     = 1
  memory   = 6.GB
  time     = 24.h

  withLabel: synapse {
    container = 'sagebionetworks/synapsepythonclient:v4.2.0'
  }
  withLabel: aws {
    container = 'ghcr.io/sage-bionetworks-workflows/aws-cli:1.0'
  }
}

params {
	// Config options
  custom_config_version      = 'master'
  custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
}

// Load nf-core custom profiles from different institutions
try {
  includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
  System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}