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Copy pathschema_input_reads.json
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234 lines (234 loc) · 9.2 KB
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf-core/seqsubmit/main/assets/schema_input_reads.json",
"title": "nf-core/seqsubmit pipeline - params.input schema",
"description": "Schema for the sample sheet provided with params.input if params.mode is set to 'reads'",
"type": "array",
"items": {
"type": "object",
"properties": {
"id": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "ID must be provided and cannot contain spaces",
"meta": ["id"],
"description": "Unique identifier of this particular data entry. Used as an experiment name"
},
"sample_accession": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Sample accession must be provided and cannot contain spaces",
"description": "ENA sample accession (starting with SAMEA) of the sample used to generate raw reads. Samples must already be submitted to ENA",
"meta": ["sample_accession"]
},
"fastq_1": {
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.(fq|fastq)(\\.gz)?$",
"errorMessage": "FASTQ file must have extension '.fq' or '.fastq' (optionally gzipped)",
"description": "Path to single-end/paired-end forward reads in FASTQ format (optionally gzipped)"
},
"fastq_2": {
"anyOf": [
{
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.(fq|fastq)(\\.gz)?$"
},
{
"type": "string",
"maxLength": 0
}
],
"default": null,
"errorMessage": "FASTQ file for reverse reads must have extension '.fq' or '.fastq' (optionally gzipped)",
"description": "Path to reverse reads in FASTQ format for paired-end data (optionally gzipped). Leave empty for single-end reads"
},
"platform": {
"type": "string",
"enum": [
"BGISEQ",
"CAPILLARY",
"DNBSEQ",
"ELEMENT",
"GENAPSYS",
"GENEMIND",
"HELICOS",
"ILLUMINA",
"ION_TORRENT",
"LS454",
"OXFORD_NANOPORE",
"PACBIO_SMRT",
"TAPESTRI",
"ULTIMA",
"VELA_DIAGNOSTICS"
],
"description": "Sequencing platform. Must be one of the ENA controlled vocabulary values listed in https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#metadata-validation.",
"meta": ["platform"]
},
"instrument": {
"type": "string",
"pattern": "^[^\\n]+$",
"errorMessage": "Instrument must be provided and cannot span multiple lines",
"description": "Sequencer model (e.g., 'Illumina HiSeq 2000', 'PacBio Sequel'). Must be one of the allowed ENA controlled vocabulary values listed in https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#permitted-values-for-instrument",
"meta": ["instrument"]
},
"library_source": {
"type": "string",
"enum": [
"GENOMIC",
"GENOMIC SINGLE CELL",
"TRANSCRIPTOMIC",
"TRANSCRIPTOMIC SINGLE CELL",
"METAGENOMIC",
"METATRANSCRIPTOMIC",
"SYNTHETIC",
"VIRAL RNA",
"OTHER"
],
"description": "Library source type. Must be one of the allowed ENA controlled vocabulary values listed in https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#permitted-values-for-library-source",
"meta": ["library_source"]
},
"library_selection": {
"type": "string",
"enum": [
"RANDOM",
"PCR",
"RANDOM PCR",
"RT-PCR",
"HMPR",
"MF",
"repeat fractionation",
"size fractionation",
"MSLL",
"cDNA",
"cDNA_randomPriming",
"cDNA_oligo_dT",
"PolyA",
"Oligo-dT",
"Inverse rRNA",
"Inverse rRNA selection",
"ChIP",
"ChIP-Seq",
"MNase",
"DNase",
"Hybrid Selection",
"Reduced Representation",
"Restriction Digest",
"5-methylcytidine antibody",
"MBD2 protein methyl-CpG binding domain",
"CAGE",
"RACE",
"MDA",
"padlock probes capture method",
"other",
"unspecified"
],
"description": "Library selection. Must be one of the allowed ENA controlled vocabulary values listed in https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#permitted-values-for-library-selection",
"meta": ["library_selection"]
},
"library_strategy": {
"type": "string",
"enum": [
"WGS",
"WGA",
"WXS",
"RNA-Seq",
"snRNA-seq",
"ssRNA-seq",
"miRNA-Seq",
"ncRNA-Seq",
"FL-cDNA",
"EST",
"Hi-C",
"ATAC-seq",
"WCS",
"RAD-Seq",
"CLONE",
"POOLCLONE",
"AMPLICON",
"CLONEEND",
"FINISHING",
"ChIP-Seq",
"MNase-Seq",
"Ribo-Seq",
"DNase-Hypersensitivity",
"Bisulfite-Seq",
"CTS",
"ChM-Seq",
"GBS",
"MRE-Seq",
"MeDIP-Seq",
"MBD-Seq",
"NOMe-Seq",
"Tn-Seq",
"VALIDATION",
"FAIRE-seq",
"SELEX",
"RIP-Seq",
"ChIA-PET",
"Synthetic-Long-Read",
"Targeted-Capture",
"Tethered Chromatin Conformation Capture",
"OTHER"
],
"description": "Library strategy. Must be one of the ENA controlled vocabulary values listed in https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#permitted-values-for-library-strategy",
"meta": ["library_strategy"]
},
"insert_size": {
"anyOf": [
{
"type": "number",
"minimum": 0
},
{
"type": "string",
"maxLength": 0
}
],
"default": null,
"errorMessage": "Insert size must be a positive number or empty",
"description": "Fragment/insert size for paired-end reads (e.g., 500 for 500 bp inserts). Skip if not applicable.",
"meta": ["insert_size"]
},
"library_name": {
"anyOf": [
{
"type": "string"
},
{
"type": "string",
"maxLength": 0
}
],
"description": "Descriptive library name (optional)",
"meta": ["library_name"]
},
"description": {
"anyOf": [
{
"type": "string"
},
{
"type": "string",
"maxLength": 0
}
],
"description": "Free-text description of the experiment (optional)",
"meta": ["description"]
}
},
"required": [
"id",
"sample_accession",
"fastq_1",
"platform",
"instrument",
"library_source",
"library_selection",
"library_strategy"
]
}
}