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Samplesheet Reference

The samplesheet is a CSV passed via samplesheet, resolved against sample_base_dir.

Required columns

Column Meaning
sample_id Unique identifier for the sample.
filename Path to the input FASTA file, resolved relative to sample_base_dir.

Optional columns

Column Default Meaning
group sample_id Files sharing a group are merged into a single alignment.
skip_trim false Skip trimming for this file (already trimmed).
skip_filter false Skip functional filtering for this file (already filtered).

Files that skip a step rejoin their group before the next non-skipped step: skip-trim files rejoin before filtering, skip-filter files rejoin before alignment. The global skip_trim / skip_functional_filter params force the corresponding skip for all files, on top of any per-row flags.

See sample_data/samplesheet_grouped.csv for an example that merges two files into one alignment.

Extra columns

Any other column is carried through as per-sample metadata (e.g. cap_name, visit_id) and is not interpreted by the pipeline itself — use it for whatever bookkeeping you need downstream.