Usage:
The typical command for running the pipeline is as follows:
nextflow run main.nf --reads  "*.fastq.gz" --reference <.fna.gz> --gff <.gff.gz> -profile conda
Mandatory arguments:
  --reads                 FastQ (.gz) input file containg the reads
  --reference             Input File in fasta format (.gz), nucleotide sequences.
  --gff                   Input file in gff (.gz) format, annotations
Optional arguments:
  --paired                Paired end reads
  --noQuali               Disable quality control
  --noCounts              Disable feature counts
  --featureCountsS        FeatureCounts attribute strandedness: unstranded, reverse or forward strandness (default: reverse)
  --g                     FeatureCounts attribute to group features (default: locus_tag)
  --t                     FeatureCounts attribute that should be counted (default: transcript)
  --extraAttributes       FeatureCounts extra attriutes divided by comma (default: gene_name)
  --M                     FeatureCounts: Count multi-mapping reads
  --O                     FeatureCounts: Count reads overlapping features
  --fraction              FeatureCounts: Fractional counts for multi-mapping/overlapping features (must be used together with -M or -O)
  --pubDir                The directory where the results will be stored [def: Results]