nextflow.config

/*
 * Copyright (c) 2013-2023, Seqera Labs.
 *
 * 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 = '>=23.10.0'
}

/* 
 * default params 
 */
 
params.outdir = "results"
params.reads = "${projectDir}/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.multiqc = "${projectDir}/multiqc"

/* 
 * defines execution profiles for different environments  
 */ 

profiles {
  standard {
    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
  }

  'all-reads' {
    params.reads = "${projectDir}/data/ggal/ggal_*_{1,2}.fq"
  }

  'wave' {
    // note: requires nextflow 24.03.0-edge or later
    wave.enabled = true
    wave.strategy = 'conda'
    wave.freeze = true
  }

  'wave-mirror' {
    // note: requires nextflow 24.09.0-edge or later
    wave.enabled = true
    wave.strategy = 'container'
    wave.mirror = true
    wave.build.repository = 'quay.io'
  }

  'docker' {
    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
    docker.enabled = true
  }

  'singularity' {
    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
    singularity.enabled = true
    singularity.autoMounts = true
  }

  'conda' {
    conda.enabled = true
    conda.channels = 'seqera,conda-forge,bioconda,defaults'
  }
  
  'slurm' {
    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
    process.executor = 'slurm'
    singularity.enabled = true
  }
  
  'batch' {
    params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
    params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
    process.executor = 'awsbatch'
    process.queue = 'nextflow-ci'
    workDir = 's3://nextflow-ci/work'
    aws.region = 'eu-west-1'
    aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
  }

  's3-data' {
    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
    params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
    params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
  } 

  'google-batch' {
      params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
      params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
      params.multiqc = 'gs://rnaseq-nf/multiqc'
      process.executor = 'google-batch'
      process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
      workDir = 'gs://rnaseq-nf/scratch' // <- replace with your own bucket!
      google.region  = 'europe-west2'
  }

  'gs-data' {
      process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
      params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
      params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
  }

  'azure-batch' {
    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
    workDir = 'az://nf-scratch/work'
    process.executor = 'azurebatch'
    process.queue = 'nextflow-ci' // replace with your own Azure pool name

    azure {
      batch {
        location = 'westeurope'
        accountName = "$AZURE_BATCH_ACCOUNT_NAME" 
        accountKey = "$AZURE_BATCH_ACCOUNT_KEY"
        autoPoolMode = true
        deletePoolsOnCompletion = true
      }

      storage {
        accountName = "$AZURE_STORAGE_ACCOUNT_NAME"
        accountKey = "$AZURE_STORAGE_ACCOUNT_KEY"
      }
    }
  }
}