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]