nextflow.config

/*
 * Copyright (c) 2013-2019, Centre for Genomic Regulation (CRG).
 *
 * This Source Code Form is subject to the terms of the Mozilla Public
 * License, v. 2.0. If a copy of the MPL was not distributed with this
 * file, You can obtain one at http://mozilla.org/MPL/2.0/.
 *
 * This Source Code Form is "Incompatible With Secondary Licenses", as
 * defined by the Mozilla Public License, v. 2.0.
 *
 */
 
manifest {
  description = 'Proof of concept of a RNA-seq pipeline implemented with Nextflow' 
  author = 'Paolo Di Tommaso'
  nextflowVersion = '>=19.10.0'
}

/* 
 * defines execution profiles for different environments  
 */ 

profiles {
  standard {
    process.container = 'nextflow/rnaseq-nf:latest'
  }
  
  slurm {
    process.container = 'nextflow/rnaseq-nf:latest'
    process.executor = 'slurm'
    singularity.enabled = true
  }
  
  batch {
    params.reads = 's3://cbcrg-eu/ggal/lung_{1,2}.fq'
    params.transcriptome = 's3://cbcrg-eu/ggal/transcriptome.fa'
    
    workDir = 's3://cbcrg-eu/work'
    process.container = 'nextflow/rnaseq-nf:latest' 
    process.executor = 'awsbatch'
    process.queue = 'demo'
    
    aws.region = 'eu-west-1'
    aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
  }
  
  gls {
      params.transcriptome = 'gs://random-nf-work-bucket/rnaseq/data/transcript.fa'
      params.reads = 'gs://random-nf-work-bucket/rnaseq/data/gut_{1,2}.fq'
      params.multiqc = 'gs://random-nf-work-bucket/rnaseq/multiqc'
      process.executor = 'google-lifesciences'
      process.container = 'nextflow/rnaseq-nf:latest'
      workDir = 'gs://random-nf-work-bucket/work'
      google.region  = 'europe-west2'
  }  

  conda {
    process.conda = "$baseDir/conda.yml"
  }  
}