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maxulysse merged 2 commits into from
Oct 13, 2026
Merged

Support list-valued VCF fields in datasheets #160

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1c38702
Support list-valued VCF fields in datasheets
maxulysse Oct 13, 2026
496332c
Update changelog entry with PR number #160
maxulysse Oct 13, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#154](https://github.com/nf-core/references/pull/154) - Added `--hisat2_skip_splice_sites` parameter to skip splice site extraction for prokaryotic genomes
- [#155](https://github.com/nf-core/references/pull/155) - Added species-specific STAR index parameters (`--star_sjdbOverhang`, `--star_genomeSAindexNbases`) with per-genome asset file configuration
- [#159](https://github.com/nf-core/references/pull/159) - Add release roadmap for rnaseq and sarek consumability
- [#160](https://github.com/nf-core/references/pull/160) - Support list-valued VCF fields in datasheets, with positional TBI pairing (null entries trigger index building) and missing `ascat_loci_rt` schema entry

### Changed

Expand Down
63 changes: 27 additions & 36 deletions subworkflows/local/datasheet_to_channel/main.nf
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Expand Up @@ -109,46 +109,18 @@ workflow DATASHEET_TO_CHANNEL {
}

// HANDLING OF VCF
// VCF fields can be a single path or a list of paths, with an optional
// parallel list of indexes (null entries mean the index needs to be built)

dbsnp = datasheet
.filter { meta, _readme -> meta.vcf_dbsnp_vcf }
.map { meta, _readme ->
def meta_extra = record(run_tabix: !meta.vcf_dbsnp_vcf_tbi)
meta_extra += record(type: 'dbsnp', source_vcf: meta.vcf_dbsnp_vcf_source)
[reduceMeta(meta) + meta_extra, files(meta.vcf_dbsnp_vcf, checkIfExists: true)]
}
dbsnp = toVcfChannel(datasheet, 'dbsnp')

germline_resource = datasheet
.filter { meta, _readme -> meta.vcf_germline_resource_vcf }
.map { meta, _readme ->
def meta_extra = record(run_tabix: !meta.vcf_germline_resource_vcf_tbi)
meta_extra += record(type: 'germline_resource', source_vcf: meta.vcf_germline_resource_vcf_source)
[reduceMeta(meta) + meta_extra, file(meta.vcf_germline_resource_vcf, checkIfExists: true)]
}
germline_resource = toVcfChannel(datasheet, 'germline_resource')

known_indels = datasheet
.filter { meta, _readme -> meta.vcf_known_indels_vcf }
.map { meta, _readme ->
def meta_extra = record(run_tabix: !meta.vcf_known_indels_vcf_tbi)
meta_extra += record(type: 'known_indels', source_vcf: meta.vcf_known_indels_vcf_source)
[reduceMeta(meta) + meta_extra, file(meta.vcf_known_indels_vcf, checkIfExists: true)]
}
known_indels = toVcfChannel(datasheet, 'known_indels')

known_snps = datasheet
.filter { meta, _readme -> meta.vcf_known_snps_vcf }
.map { meta, _readme ->
def meta_extra = record(run_tabix: !meta.vcf_known_snps_vcf_tbi)
meta_extra += record(type: 'known_snps', source_vcf: meta.vcf_known_snps_vcf_source)
[reduceMeta(meta) + meta_extra, file(meta.vcf_known_snps_vcf, checkIfExists: true)]
}
known_snps = toVcfChannel(datasheet, 'known_snps')

pon = datasheet
.filter { meta, _readme -> meta.vcf_pon_vcf }
.map { meta, _readme ->
def meta_extra = record(run_tabix: !meta.vcf_pon_vcf_tbi)
meta_extra += record(type: 'pon', source_vcf: meta.vcf_pon_vcf_source)
[reduceMeta(meta) + meta_extra, file(meta.vcf_pon_vcf, checkIfExists: true)]
}
pon = toVcfChannel(datasheet, 'pon')

vcf = channel.empty()
.mix(
Expand All @@ -158,7 +130,6 @@ workflow DATASHEET_TO_CHANNEL {
known_snps,
pon,
)
.flatMap { meta, vcfs -> vcfs instanceof Path ? [[meta, vcfs]] : vcfs.toList().collect { vcf_ -> [meta, vcf_] } }

emit:
ascat_alleles = ascat_alleles // channel: [meta, *.ascat_alleles.txt]
Expand Down Expand Up @@ -195,3 +166,23 @@ def reduceMeta(meta_) {
species: meta_.species,
)
}

// Build a [meta, vcf] channel for one VCF type
// The datasheet field can hold a single path or a list of paths
// Indexes are paired positionally, a null or missing entry means the index has to be built
def toVcfChannel(datasheet, type) {
def vcf_key = "vcf_${type}_vcf"
def tbi_key = "vcf_${type}_vcf_tbi"
def source_key = "vcf_${type}_vcf_source"
datasheet
.filter { meta, _readme -> meta[vcf_key] }
.flatMap { meta, _readme ->
def vcfs = meta[vcf_key] instanceof List ? meta[vcf_key] : [meta[vcf_key]]
def tbis = !meta[tbi_key] ? [] : meta[tbi_key] instanceof List ? meta[tbi_key] : [meta[tbi_key]]
vcfs.withIndex().collect { vcf_, i ->
def meta_extra = record(run_tabix: i >= tbis.size() || !tbis[i])
meta_extra += record(type: type, source_vcf: meta[source_key])
[reduceMeta(meta) + meta_extra, file(vcf_, checkIfExists: true)]
}
}
}
241 changes: 201 additions & 40 deletions subworkflows/local/utils_references/schema_references.json
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,12 @@
"pattern": "^\\S+$",
"errorMessage": "TODO"
},
"ascat_loci_rt": {
"meta": ["ascat_loci_rt"],
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "TODO"
},
"bed12": {
"meta": ["bed12"],
"type": "string",
Expand Down Expand Up @@ -255,17 +261,48 @@
},
"vcf_dbsnp_vcf": {
"meta": ["vcf_dbsnp_vcf"],
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"errorMessage": "DBSNP VCF must be an existing file ending in '.vcf' that does not contain spaces. This file can be bgzipped"
"anyOf": [
{
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
},
{
"type": "array",
"items": {
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
}
}
],
"errorMessage": "DBSNP VCF must be an existing file (or list of existing files) ending in '.vcf' that does not contain spaces. This file can be bgzipped"
},
"vcf_dbsnp_vcf_tbi": {
"meta": ["vcf_dbsnp_vcf_tbi"],
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true,
"errorMessage": "DBSNP VCF index must be an existing file ending in '.vcf.gz.tbi' that does not contain spaces"
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "array",
"items": {
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "null"
}
]
}
}
],
"errorMessage": "DBSNP VCF index must be an existing file (or list of existing files, null entries allowed) ending in '.vcf.gz.tbi' that does not contain spaces"
},
"vcf_dbsnp_vcf_vqsr": {
"meta": ["vcf_dbsnp_vcf_vqsr"],
Expand All @@ -281,17 +318,48 @@
},
"vcf_germline_resource_vcf": {
"meta": ["vcf_germline_resource_vcf"],
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"errorMessage": "Germline Resource VCF must be an existing file ending in '.vcf' that does not contain spaces. This file can be bgzipped"
"anyOf": [
{
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
},
{
"type": "array",
"items": {
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
}
}
],
"errorMessage": "Germline Resource VCF must be an existing file (or list of existing files) ending in '.vcf' that does not contain spaces. This file can be bgzipped"
},
"vcf_germline_resource_vcf_tbi": {
"meta": ["vcf_germline_resource_vcf_tbi"],
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true,
"errorMessage": "Germline Resource VCF index must be an existing file ending in '.vcf.gz.tbi' that does not contain spaces"
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "array",
"items": {
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "null"
}
]
}
}
],
"errorMessage": "Germline Resource VCF index must be an existing file (or list of existing files, null entries allowed) ending in '.vcf.gz.tbi' that does not contain spaces"
},
"vcf_germline_resource_vcf_source": {
"meta": ["vcf_germline_resource_vcf_source"],
Expand All @@ -301,17 +369,48 @@
},
"vcf_known_indels_vcf": {
"meta": ["vcf_known_indels_vcf"],
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"errorMessage": "Known indels VCF must be an existing file ending in '.vcf' that does not contain spaces. This file can be bgzipped"
"anyOf": [
{
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
},
{
"type": "array",
"items": {
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
}
}
],
"errorMessage": "Known indels VCF must be an existing file (or list of existing files) ending in '.vcf' that does not contain spaces. This file can be bgzipped"
},
"vcf_known_indels_vcf_tbi": {
"meta": ["vcf_known_indels_vcf_tbi"],
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true,
"errorMessage": "Known indels VCF index must be an existing file ending in '.vcf.gz.tbi' that does not contain spaces"
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "array",
"items": {
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "null"
}
]
}
}
],
"errorMessage": "Known indels VCF index must be an existing file (or list of existing files, null entries allowed) ending in '.vcf.gz.tbi' that does not contain spaces"
},
"vcf_known_indels_vcf_source": {
"meta": ["vcf_known_indels_vcf_source"],
Expand All @@ -321,17 +420,48 @@
},
"vcf_known_snps_vcf": {
"meta": ["vcf_known_snps_vcf"],
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"errorMessage": "Known snps VCF must be an existing file ending in '.vcf' that does not contain spaces. This file can be bgzipped"
"anyOf": [
{
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
},
{
"type": "array",
"items": {
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
}
}
],
"errorMessage": "Known snps VCF must be an existing file (or list of existing files) ending in '.vcf' that does not contain spaces. This file can be bgzipped"
},
"vcf_known_snps_vcf_tbi": {
"meta": ["vcf_known_snps_vcf_tbi"],
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true,
"errorMessage": "Known snps VCF index must be an existing file ending in '.vcf.gz.tbi' that does not contain spaces"
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "array",
"items": {
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "null"
}
]
}
}
],
"errorMessage": "Known snps VCF index must be an existing file (or list of existing files, null entries allowed) ending in '.vcf.gz.tbi' that does not contain spaces"
},
"vcf_known_snps_vcf_source": {
"meta": ["vcf_known_snps_vcf_source"],
Expand All @@ -341,17 +471,48 @@
},
"vcf_pon_vcf": {
"meta": ["vcf_pon_vcf"],
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"errorMessage": "PON VCF must be an existing file ending in '.vcf' that does not contain spaces. This file can be bgzipped"
"anyOf": [
{
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
},
{
"type": "array",
"items": {
"type": "string",
"exists": true,
"pattern": "^\\S+\\.vcf(\\.gz)?$"
}
}
],
"errorMessage": "PON VCF must be an existing file (or list of existing files) ending in '.vcf' that does not contain spaces. This file can be bgzipped"
},
"vcf_pon_vcf_tbi": {
"meta": ["vcf_pon_vcf_tbi"],
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true,
"errorMessage": "PON VCF index must be an existing file ending in '.vcf.gz.tbi' that does not contain spaces"
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "array",
"items": {
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz\\.tbi?$",
"exists": true
},
{
"type": "null"
}
]
}
}
],
"errorMessage": "PON VCF index must be an existing file (or list of existing files, null entries allowed) ending in '.vcf.gz.tbi' that does not contain spaces"
},
"vcf_pon_vcf_source": {
"meta": ["vcf_pon_vcf_source"],
Expand Down
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