These files are example CSV samplesheets. Each has a header row and one row per sample:
| Column | Meaning |
|---|---|
sample |
Sample name used in the pipeline. |
barcode |
Depends on the file (see below). |
fastq.csv — for runs that start from FASTQ reads: barcode is the full path to that sample’s read file. To auto-generate a samplesheet CSV from a folder of FASTQ files, follow the --input note in all_options.md.
POD5.csv — use this samplesheet when starting from raw signal (pod5) data, or from basecalled but not demultiplexed reads (fastq_pass). In both cases, barcode is the barcode label (e.g. barcode01) for that sample. The data directory is set separately in your params file (input_dir), not in the CSV.
all_options.md — pipeline parameters as tables.