description: A schema for validation of samplesheet.csv for taxprofiler pipeline.
imports:
  - https://schema.databio.org/pep/2.1.0.yaml
properties:
  samples:
    type: array
    items:
      type: object
      properties:
        sample:
          type: string
          description: "Sample identifier."
          pattern: "^\\S*$"
        run_accession:
          type: string
          description: "Run accession number."
        instrument_platform:
          type: string
          description: "Name of the platform that sequenced the samples."
          enum: ["ABI_SOLID", "BGISEQ", "CAPILLARY", "COMPLETE_GENOMICS", "DNBSEQ", "HELICOS", "ILLUMINA", "ION_TORRENT", "LS454", "OXFORD_NANOPORE", "PACBIO_SMRT"]
        fastq1:
          type: string
          description: "FASTQ file for read 1."
          pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
        fastq2:
          type: string
          description: "FASTQ file for read 2."
          pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
        fasta:
          type: string
          description: "Path to FASTA file."
      required:
        - sample
        - run_accession
        - instrument_platform
      files:
        - fastq1
        - fastq2
        - fasta
required:
  - samples
