ngless "0.10"
import "parallel" version "0.6"

samples = readlines('MG7S2')
sample = lock1(samples)
input = fastq(sample)

output = preprocess(input, keep_singles=False) using |read|:
   read = substrim(read, min_quality=25)
   if len(read) < 45:
     discard

contigs = assemble(input)
write(contigs, ofile='contigsM7S2.fa')

orfs = orf_find(contigs, is_metagenome=True)
write(contigs, ofile='orfM7S2.fna')