You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a tab-separated file with 6 columns, and a header row. See usage docs.
An example of properly formatted input files can be found at the nf-core/test-datasets.
For example, this is the input used for a hybrid assembly in testing:
ID R1 R2 LongFastQ Fast5 GenomeSize
ERR044595 https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz https://github.com/nf-core/test-datasets/raw/bacass/nanopore/subset15000.fq.gz NA 2.8m
ID: The identifier to use for handling the dataset e.g. sample name
R1: The forward reads in case of available short-read data
R2: The reverse reads in case of available short-read data
LongFastQ: The long read FastQ file with reads in FASTQ format
Fast5: The folder containing the basecalled fast5 files
GenomeSize: The expected genome size of the assembly. Only used by the canu assembler.
Missing values (e.g. Fast5 folder in case of short reads) can be omitted by using a
NA in the TSV file. The pipeline will handle such cases appropriately then.