biohpc.config

singularity {
  enabled = true
  runOptions = ''                             // Please do NOT use "--disable-cache" in this runOptions. 
                                              // Starting from version 2.0.0, the astrocyte_cli will clean up the cache automatically.
  // runOptions = '--bind /vagrant:/vagrant'  // Use this one for vagrant development env only
  cacheDir = "$baseDir/images/singularity"    // Singularity images specified in `workflow_containers` of astrocyte_pkg.yml will be saved to 
                                              // this folder automatically, before running the workflow. The images will be renamed as
                                              // "NAME-TAG.img", e.g. ubuntu-latest.img, centos-centos8.img, r-4.1.1.img, etc.
}

process {
  executor = 'slurm'
  queue = 'super'
  clusterOptions = '--hold'
  beforeScript= 'ulimit -Ss unlimited'

  // Process specific configuration
  withName: trackStart {
    executor = 'local'
  }

  withName: checkDesignFile {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/py36:1.0.0'
    executor = 'local'
  }
  withName: trimReads {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    cpus = 32
  }
  withName: alignReads{
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    queue = '256GB,256GBv1'
    cpus = 32
  }
  withName: filterReads{
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    queue = '128GB,256GB,256GBv1'
  }
  withName: experimentQC {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    queue = '128GB,256GB,256GBv1'
  }
  withName: convertReads {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    queue = '128GB,256GB,256GBv1'
  }
  withName: crossReads {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    cpus = 32
  }
  withName: defineExpDesignFiles {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/py36:1.0.0'
    executor = 'local'
  }
  withName: poolAndPsuedoReads {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/py36:1.0.0'
    executor = 'local'
  }
  withName: callPeaksMACS {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    queue = '128GB,256GB,256GBv1'
  }
  withName: plotProfile {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    queue = '128GB,256GB,256GBv1'
    cpus = 32
  }
  withName: consensusPeaks {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    executor = 'local'
  }
  withName: peakAnnotation {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/r:3.3.2'
    executor = 'local'
  }
  withName: diffPeaks {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/r:3.3.2'
    cpus = 32
  }
  withName: motifSearch {
    executor = 'local'
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/motif-search:meme-5.5.4'
    //cpus = 32
  }
  withName: multiqcReport {
    container = 'docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/bicf/chipseq_analysis/chipseq:1.0.0'
    executor = 'local'
  }
}

params {
  // Reference file paths on BioHPC
  genomes {
    'GRCh38' {
      bwa = '/project/shared/bicf_workflow_ref/human/GRCh38'
      genomesize = 'hs'
      chromsizes = '/project/shared/bicf_workflow_ref/human/GRCh38/genomefile.txt'
      fasta = '/project/shared/bicf_workflow_ref/human/GRCh38/genome.fa'
      gtf = '/project/shared/bicf_workflow_ref/human/GRCh38/gencode.v25.chr_patch_hapl_scaff.annotation.gtf'
      geneNames = '/project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt'
    }
    'GRCh37' {
      bwa = '/project/shared/bicf_workflow_ref/human/GRCh37'
      genomesize = 'hs'
      chromsizes = '/project/shared/bicf_workflow_ref/human/GRCh37/genomefile.txt'
      fasta = '/project/shared/bicf_workflow_ref/human/GRCh37/genome.fa'
      gtf = '/project/shared/bicf_workflow_ref/human/GRCh37/gencode.v19.chr_patch_hapl_scaff.annotation.gtf'
      geneNames = '/project/shared/bicf_workflow_ref/human/GRCh37/genenames.txt'
    }
    'GRCm38' {
      bwa = '/project/shared/bicf_workflow_ref/mouse/GRCm38'
      genomesize = 'mm'
      chromsizes = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genomefile.txt'
      fasta = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genome.fa'
      gtf = '/project/shared/bicf_workflow_ref/mouse/GRCm38/gencode.vM20.annotation.gtf'
      geneNames = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genenames.txt'
    }
  }
}

trace {
  enabled = true
  file = 'pipeline_trace.txt'
  fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
}

timeline {
  enabled = true
  file = 'timeline.html'
}

report {
  enabled = true
  file = 'report.html'
}


env {
  http_proxy = 'http://proxy.swmed.edu:3128'
  https_proxy = 'http://proxy.swmed.edu:3128'
  all_proxy = 'http://proxy.swmed.edu:3128'
}

manifest {
  mainScript = 'main.nf'
  version = '2.0.1'
  nextflowVersion = '>=19.07.0'
}