2022-08-16 19:46:22 +00:00
|
|
|
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*$"
|
|
|
|
|
run_accession:
|
|
|
|
|
type: string
|
|
|
|
|
description: "Run accession number."
|
|
|
|
|
instrument_platform:
|
|
|
|
|
type: string
|
|
|
|
|
description: "Name of the platform that sequenced the samples."
|
|
|
|
|
enum:
|
|
|
|
|
[
|
|
|
|
|
"ABI_SOLID",
|
|
|
|
|
"BGISEQ",
|
|
|
|
|
"CAPILLARY",
|
|
|
|
|
"COMPLETE_GENOMICS",
|
|
|
|
|
"DNBSEQ",
|
|
|
|
|
"HELICOS",
|
|
|
|
|
"ILLUMINA",
|
|
|
|
|
"ION_TORRENT",
|
|
|
|
|
"LS454",
|
|
|
|
|
"OXFORD_NANOPORE",
|
|
|
|
|
"PACBIO_SMRT",
|
|
|
|
|
]
|
|
|
|
|
fastq1:
|
|
|
|
|
type: ["string", "null"]
|
2022-09-15 16:31:49 +00:00
|
|
|
description: "Optional FASTQ file for read 1 of paired-end sequenced libraries."
|
2022-08-16 19:46:22 +00:00
|
|
|
pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
|
|
|
|
|
fastq2:
|
|
|
|
|
type: ["string", "null"]
|
2022-09-15 16:31:49 +00:00
|
|
|
description: "Optional FASTQ file for read 2 of paired-end sequenced libraries."
|
2022-08-16 19:46:22 +00:00
|
|
|
pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
|
|
|
|
|
fasta:
|
|
|
|
|
type: ["string", "null"]
|
2022-09-15 16:31:49 +00:00
|
|
|
description: "Optional FASTA file."
|
2022-08-16 19:46:22 +00:00
|
|
|
pattern: "^[\\S]+.(fa\\.gz|fasta\\.gz)$"
|
|
|
|
|
required:
|
|
|
|
|
- sample
|
|
|
|
|
- run_accession
|
|
|
|
|
- instrument_platform
|
|
|
|
|
files:
|
|
|
|
|
- fastq1
|
|
|
|
|
- fastq2
|
|
|
|
|
- fasta
|
|
|
|
|
required:
|
|
|
|
|
- samples
|
2022-09-27 13:32:51 +00:00
|
|
|
- run_accession
|
|
|
|
|
- instrument_platform
|
