Input Requirements

The pipeline requires two primary input tables and raw sequencing data in FASTQ format.

Sample Table

• Format: CSV file with a header row.

• Required Columns:

  • fastq_filepath — Path to the FASTQ file for each sample.

  • sample_ID — Human-readable sample identifier.

  • control_status — Classification of each sample. Required values:

    • beads_only — Negative control (bead-only immunoprecipitation). At least 2 required when run_zscore_fit_predict = true.

    • library — Library control (optional).

    • empirical — Experimental samples.

• Note: Do not include a column named sample_id (lowercase). The pipeline auto-generates integer sample_id indices.

Example Sample Table

sample_ID	fastq_filepath	control_status
Patient_1_B	reads/patient1_baseline.fastq.gz	empirical
Patient_1_E	reads/patient1_endline.fastq.gz	empirical
neg1	reads/neg_control_1.fastq.gz	beads_only
neg2	reads/neg_control_2.fastq.gz	beads_only

Peptide Table

• Format: CSV file with a header row.

• Required Columns:

  • oligo — The oligonucleotide sequence for each peptide tile. Uppercase characters are used for alignment; lowercase characters are trimmed.

• Optional Columns:

  • peptide_id — Integer index (auto-generated if not provided).

  • Organism — Species or virus name associated with the peptide (used for virus scoring and heatmaps).

  • Species — Species-level grouping.

  • peptide — Amino acid sequence of the peptide tile.

  • pdb_id — PDB structure identifier (used for 3D visualization).

  • id — Unique identifier for merging with oligo metadata.

Example Peptide Table

oligo	Organism	Species	peptide	pdb_id
ATGCGA…	Human coronavirus OC43	Betacoronavirus 1	MSDNGP…	6OHW
GCTAGC…	Influenza A virus	Influenza A virus	DTLCIA…	4LXV

Sequencing Data

• Format: FASTQ files (.fastq.gz or .fastq).

• Platform: Oxford Nanopore Technologies (ONT).

• Compression: Set params.fastq_stream_func = 'zcat' for gzipped files, or 'cat' for uncompressed.

• Location: By default, paths in the sample table are resolved relative to $baseDir. If you provide a custom sample table, paths are resolved relative to $launchDir. Absolute paths are also supported.

Optional Input Files

IEDB Database

• Path: Configured via params.iedb_database.

• Format: TSV file from the Immune Epitope Database.

• Usage: Cross-referenced to annotate enriched peptides with known epitope information.

IEDB Neutralizing Database

• Path: Configured via params.neutralization_db.

• Format: TSV file from the Immune Epitope Database.

• Usage: Cross-referenced to annotate neutralizing peptides with known epitope information.

PDB Structures

• Path: Configured via params.pdb_dir.

• Format: Directory containing .pdb or .cif structure files named by PDB ID.

• Usage: Used by the Streamlit 3D visualization dashboard to render protein structures with mapped epitopes.