nextflow.config

manifest {
  description = "A RNA seq fusion pipeline for tumor/normal or tumor sample"
  nextflowVersion = "> 20.07.1"
}

includeConfig 'configs/modules.config'

process.shell = ['/bin/bash', '-euo', 'pipefail']

profiles {
  hopper  {
    singularity {
      enabled = true
      runOptions = '--bind /fs1/  --bind /local/ --bind /fs2/ --bind /mnt/beegfs/'  
    }
    process {
      queue       =   params.queue
      executor    =   'slurm'
    }  
  }

  lennart {
    singularity {
      enabled = true
      runOptions = '--bind /fs1/  --bind /local/ --bind /fs2/'  
    } 
  }
}

params {

  // results dir //
  resultsdir                          = "/fs1/results"
  dev                                 = false
  dev_suffix                          = ''
  if (params.dev) {
    dev_suffix                        = '_dev'
  }

  outdir = "${params.resultsdir}${params.dev_suffix}"
  subdir = "solid_ST_RNA"
  tmp_dir = "/local/scratch/"
  crondir = "${params.outdir}/cron/"

  /*
  Sumsampling parameters
  */
  subsampling = true
  // change the reads later to 65000000
  // 09-02-2023 change the reads to 10000000
  subsampling_number = 100000000

  /*
  Arriba parameters
  */
   refbase = "/fs1/paul/RareDisease_RNA_workflow/star_hg38_nochr_index/"

  //refbase = "/fs1/resources/ref/hg38/data/star_refGenome_index/star_ref_index"

  fasta = "/fs1/resources/ref/hg38/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set_nochr.fna"

  fastaIndex = "/fs1/resources/ref/hg38/fasta/"

  gtf = "/fs1/saile/prj/RareDisease_RNA_workflow/resources/gencode.v38.annotation_nochr.gtf"
  
  blacklists = "/fs1/saile/prj/runarriba/blacklist_hg38_GRCh38_v2.3.0.tsv.gz"

  knownfusions = "/fs1/saile/prj/runarriba/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz"

  proteinDomains = "/fs1/saile/prj/runarriba/protein_domains_hg38_GRCh38_v2.3.0.gff3"

  cytobands = "/fs1/saile/prj/arriba_v2.3.0/database/cytobands_hg38_GRCh38_v2.3.0.tsv"

  /*
  Starfusion parameters
  */
  pairEnd = true // Currently run in the pairedEND mode with 2x150 bp setup

  refbase2 = "/fs1/saile/prj/rnafusion/references/starfusion/ctat_genome_lib_build_dir/"

  /*
  Fusion Catcher parameters
  */
  fusioncatcher = "/fs1/saile/prj/rnafusion/references/fusioncatcher/human_v102/"

  /*
  IGH-DUX4 workflow parameters
  */
  ighDux4 = "/fs1/saile/prj/nextflow_rnaseqfus/data/IGH_DUX4-reg_grch38.bed"


  /*
  MET and EGFR exon skipping
  */
  metEgfr =  "/fs1/saile/prj/rnafusion/references/exon_skipping/Twist_RNA_Design5.hg38.annotated.bed"

  /*
  Filter genes based on the designed geneprobes
  */

  stgenePanel_file = "/fs1/saile/prj/nextflow_ST_rnaseqfus/resources/ST_RNA_genes.tsv"

  /*
  QC parameters
  */
  hg38_sizes = '/fs1/resources/ref/hg38/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set_nochr.chrom.sizes'

  ref_rseqc_bed = '/fs1/resources/ref/hg38/data/RseQC/Homo_sapiens.GRCh38.79.bed'

  ref_bed = '/fs1/resources/ref/hg38/data/provider/HPA_1000G_final_38.bed'

  ref_bedXY = '/fs1/resources/ref/hg38/data/provider/xy_38.bed'

}



trace {
    overwrite = true
}