nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  vjmarteau/nf-scRNAseq-Gpx4-mouse Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

manifest {
    name             = 'vjmarteau/nf-scRNAseq-Gpx4-mouse'
    author           = 'Valentin Marteau'
    description      = 'nf-pipeline for scRNAseq Gpx4 deficient mice data analysis'
    nextflowVersion  = '>=22.04'
    version          = 'v0.1'
}

// Global default params, used in configs
params {

  // Choose between "symlink" - absolute path, "rellink" -relative path, "link " -hard link, "copy"
  publish_dir_mode = "copy"

  // Workflow flags
  resDir        = "${baseDir}/results"
  input_path    = "/data/projects/2021/Grabherr-scRNAseq-mouse/40_nfcore_scrnaseq_v2-0-0_mm39"
  samplesheet   = "${baseDir}/tables/samplesheet.csv"
  cell_cycle_genes = "${baseDir}/tables/regev_lab_cell_cycle_genes_mouse.txt"
  marker_genes  = "${baseDir}/tables/marker_genes.csv"
  progeny       = "${baseDir}/tables/progeny_mouse_2022-12-12.csv"
  dorothea      = "${baseDir}/tables/dorothea_mouse_AB_2022-12-12.csv"
  GOI           = "${baseDir}/tables/genes_of_interest.txt"
}

includeConfig 'conf/modules.config'


conda {
    useMamba = true
    enabled = true
}

singularity {
    enabled = true
    runOptions = "--no-home --env NUMBA_CACHE_DIR=/tmp/\$USER/numba_cache_dir" // "--no-home" prevents using packages stored in local home dir
    autoMounts = true
}

profiles {

    standard {
        process.executor = 'local'
    }

    cluster {
        process.executor = 'sge'
        process.penv = 'smp'
        process.queueSize = 600
        process.clusterOptions = { '-V -S /bin/bash -q all.q@apollo-0[0-9]' }
        
    }
}