nft-fasta

nf-test plugin to provide support for FASTA files.

Requirements

• nf-test version 0.7.0 or higher

Setup

To use this plugin you need to activate the nft-fasta plugin in your nf-test.config file:

config {
  plugins {
    load "[email protected]"
  }
}

Usage

nft-fasta extends path by a fasta property that can be used to read FASTA files into maps. nft-fasta supports also gzipped FASTA files.

Comparing files

assert path('path/to/fasta1.fasta').fasta == path("path/to/fasta2.fasta'").fasta

Working with individual samples

def sequences = path('path/to/fasta1.fasta.gz').fasta
assert "seq1" in sequences
assert !("seq8" in sequences)
assert sequences.seq1 == "AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC"