If the input source type is set to Directory and subdirectories, all FASTQ files in the subdirectories are used as input data. This functionality can be used, e.g., to process MinKNOW data without a report json file, e.g., after copying some directories to another place.

The pipeline can handle multiple FASTQ files per directory, so there is no need to merge the files before. Use the following settings to use the Directory and subdirectories input source type and to use the directory names as sample names:

• Select Oxford Nanopore WGS genomic, single-end reads as Procedure Details.
• Open the Advanced Input Source Options
• Select Use Regular Expression and enter .*\\([^\\]+)\\([^\\]+)
• Select Use complete file path

With these settings, the directory names will be used as sample names. If the directory contains a run details file then this file is read for the samples.