nextflow.config

// your workflow parameters
params {
  codename = 'quick-rnaseq'
  outdir = "./results"

  // experiment information
  experiment.samplesheet = "./testdata/samplesheet.csv"
  experiment.contrasts = [['case', 'control'],['control','case']]

  // transcriptome information 
  transcriptome.reference = ""
  transcriptome.decoys = ""

  // reads trimming
  fastp.args = ""
    
  // salmon parameters
  salmon.index.args = '--gencode'
  salmon.quant.libtype = 'A'
  salmon.quant.args = '--validateMappings --gcBias'

  // summarize_to_gene parameters
  summarize_to_gene.counts_from_abundance = 'no'
  summarize_to_gene.organism_db = 'org.Hs.eg.db'

  // counts transform can be rlog or vst
  qc.pca.transform = 'rlog'
  qc.ma.lfc_threshold = 0
  qc.sample.transform = 'rlog'

  // differential gene expression parameters
  dge.lfc_threshold = 0
  dge.fdr = 0.05

  // gene ontology analysis parameters
  gene_ontology.organism_db = 'org.Hs.eg.db'
  gene_ontology.gene_id = 'ensembl'
  gene_ontology.remove_gencode_version = 'yes'
  gene_ontology.fdr = 0.05

}

// include basic process configuration options
includeConfig 'conf/base.config'