Rename source and source_version datasheet meta fields

CHANGELOG.md

@@ -70,6 +70,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#163](https://github.com/nf-core/references/pull/163) - Update nf-schema to 3.0.0 and migrate `paramsHelp`, `paramsSummaryLog`, and `paramsSummaryMap` to their single-options-map signatures
 - [#164](https://github.com/nf-core/references/pull/164) - Replace `update_references_file` string rewriting with nf-schema `allowParamsSubstitution`, so datasheets can carry `${params.references_base_path}` placeholders
 - [#165](https://github.com/nf-core/references/pull/165) - Document `--references_base_path`, multiple genomes, and the asset file format in `docs/usage.md`
+- [#166](https://github.com/nf-core/references/pull/166) - Rename the datasheet `source`, `source_version`, and derived `source_vcf` meta fields to `reference_source`, `annotation_version`, and `annotation_source` (#65)
 
 ### Removed
 

README.md

@@ -82,10 +82,10 @@ Datasheets are stored in [references-datasheets](https://github.com/nf-core/refe
 - genome: GRCh38_chr21
   fasta: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa"
   gtf: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.gtf"
-  source_version: "CUSTOM"
+  annotation_version: "CUSTOM"
   readme: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md"
-  source: "nf-core/references"
-  source_vcf: "GATK_BUNDLE"
+  reference_source: "nf-core/references"
+  annotation_source: "GATK_BUNDLE"
   species: "Homo_sapiens"
   vcf: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
 ```

docs/CONTRIBUTING.md

@@ -201,8 +201,8 @@ Each output type has its own path declaration using the `file >>` syntax.
 Output paths follow this structure:
 
 ```text
-${meta.species}/${meta.source}/${meta.genome}/Sequence/<tool>/<version>/
-${meta.species}/${meta.source}/${meta.genome}/Annotation/<type>/
+${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/<tool>/<version>/
+${meta.species}/${meta.reference_source}/${meta.genome}/Annotation/<type>/
 ```
 
 When adding a new output, add a corresponding entry to the `output {}` block in `main.nf`.

docs/usage.md

@@ -157,12 +157,12 @@ A datasheet is a YAML list with one entry per genome. `genome` is the only requi
 ```yaml
 - genome: GRCh38_chr21
   species: Homo_sapiens
-  source: nf-core
+  reference_source: nf-core
   fasta: https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa
 
 - genome: GRCh38_chr22
   species: Homo_sapiens
-  source: nf-core
+  reference_source: nf-core
   fasta: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta
 ```
 
@@ -182,7 +182,7 @@ An entry lists what a genome already provides. Only `genome` is required; the pi
 ```yaml
 - genome: GRCh37
   species: Homo_sapiens
-  source: GATK
+  reference_source: GATK
 
   # Genome and annotation
   fasta: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta

main.nf

@@ -60,7 +60,7 @@ workflow NFCORE_REFERENCES {
 
     ncbi_download_input = fasta_download_input.to_download
         .mix(gff_download_input.to_download, gtf_download_input.to_download)
-        .map { meta, _file -> [meta.source_version, [meta.reference, meta]] }
+        .map { meta, _file -> [meta.annotation_version, [meta.reference, meta]] }
         .groupBy()
         .map { acc, entries ->
             def ref_types = entries.collect { entry -> entry[0] }
@@ -395,137 +395,137 @@ output {
     }
     ascat_alleles {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/ascat/"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/ascat/"
         }
     }
     ascat_loci {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/ascat/"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/ascat/"
         }
     }
     ascat_loci_gc {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/ascat/"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/ascat/"
         }
     }
     ascat_loci_rt {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/ascat/"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/ascat/"
         }
     }
     bowtie1_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/BowtieIndex/1.3.1"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/BowtieIndex/1.3.1"
         }
     }
     bowtie2_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/Bowtie2Index/2.5.2"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/Bowtie2Index/2.5.2"
         }
     }
     bwamem1_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/BWAIndex/0.7.18"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/BWAIndex/0.7.18"
         }
     }
     bwamem2_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/BWAmem2Index/2.2.1"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/BWAmem2Index/2.2.1"
         }
     }
     chr_dir {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/chr"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/chr"
         }
     }
     dragmap_hashmap {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/dragmap/1.2.1"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/dragmap/1.2.1"
         }
     }
     fasta {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/WholeGenomeFasta/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/WholeGenomeFasta/${file.fileName}"
         }
     }
     fasta_dict {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/WholeGenomeFasta/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/WholeGenomeFasta/${file.fileName}"
         }
     }
     fasta_fai {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/WholeGenomeFasta/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/WholeGenomeFasta/${file.fileName}"
         }
     }
     fasta_sizes {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/WholeGenomeFasta/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/WholeGenomeFasta/${file.fileName}"
         }
     }
     gtf {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Annotation/Genes/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Annotation/Genes/${file.fileName}"
         }
     }
     gff {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Annotation/Genes/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Annotation/Genes/${file.fileName}"
         }
     }
     hisat2_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/Hisat2Index/" + (meta.source_version == 'unknown' ? '' : meta.source_version) + "/2.2.3"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/Hisat2Index/" + (meta.annotation_version == 'unknown' ? '' : meta.annotation_version) + "/2.2.3"
         }
     }
     intervals_bed {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Annotation/intervals/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Annotation/intervals/${file.fileName}"
         }
     }
     kallisto_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/KallistoIndex/" + (meta.source_version == 'unknown' ? '' : meta.source_version) + "/0.52.0/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/KallistoIndex/" + (meta.annotation_version == 'unknown' ? '' : meta.annotation_version) + "/0.52.0/${file.fileName}"
         }
     }
     msisensorpro_list {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Annotation/msisensorpro/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Annotation/msisensorpro/${file.fileName}"
         }
     }
     rsem_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/RSEMIndex/" + (meta.source_version == 'unknown' ? '' : meta.source_version) + "/1.3.1"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/RSEMIndex/" + (meta.annotation_version == 'unknown' ? '' : meta.annotation_version) + "/1.3.1"
         }
     }
     salmon_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/SalmonIndex/" + (meta.source_version == 'unknown' ? '' : meta.source_version) + "/2.7.0"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/SalmonIndex/" + (meta.annotation_version == 'unknown' ? '' : meta.annotation_version) + "/2.7.0"
         }
     }
     snapaligner_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/snap"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/snap"
         }
     }
     splice_sites {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/SpliceSites/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/SpliceSites/${file.fileName}"
         }
     }
     star_index {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/STARIndex/" + (meta.source_version == 'unknown' ? '' : meta.source_version) + "/2.7.11b"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/STARIndex/" + (meta.annotation_version == 'unknown' ? '' : meta.annotation_version) + "/2.7.11b"
         }
     }
     transcript_fasta {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Sequence/TranscriptFasta/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Sequence/TranscriptFasta/${file.fileName}"
         }
     }
     vcf_tbi {
         path { meta, file ->
-            file >> "${meta.species}/${meta.source}/${meta.genome}/Annotation/${meta.source_vcf}/${file.fileName}"
+            file >> "${meta.species}/${meta.reference_source}/${meta.genome}/Annotation/${meta.annotation_source}/${file.fileName}"
         }
     }
 }

subworkflows/local/datasheet_to_channel/main.nf

@@ -161,8 +161,8 @@ def reduceMeta(meta_) {
     record(
         id: meta_.id,
         genome: meta_.genome,
-        source: meta_.source,
-        source_version: meta_.source_version,
+        reference_source: meta_.reference_source,
+        annotation_version: meta_.annotation_version,
         species: meta_.species,
     )
 }
@@ -181,7 +181,7 @@ def toVcfChannel(datasheet, type) {
             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])
+                meta_extra += record(type: type, annotation_source: meta[source_key])
                 [reduceMeta(meta) + meta_extra, file(vcf_, checkIfExists: true)]
             }
         }

subworkflows/local/utils_references/schema_references.json

@@ -20,18 +20,18 @@
                 "default": "unknown",
                 "errorMessage": "Website of origin of the reference must be a valid URL or 'unknown'"
             },
-            "source": {
-                "meta": ["source"],
+            "reference_source": {
+                "meta": ["reference_source"],
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Source of genome cannot contain spaces"
+                "errorMessage": "Reference source of the genome cannot contain spaces"
             },
-            "source_version": {
-                "meta": ["source_version"],
+            "annotation_version": {
+                "meta": ["annotation_version"],
                 "type": "string",
                 "pattern": "^\\S+$",
                 "default": "unknown",
-                "errorMessage": "Source version used to create annotation files (gff/gtf related files) cannot contain spaces"
+                "errorMessage": "Annotation version used to create annotation files (gff/gtf related files) cannot contain spaces"
             },
             "species": {
                 "meta": ["species"],

tests/assets/GRCh38_chr21_placeholder.yml

@@ -4,5 +4,5 @@
 - genome: GRCh38_chr21
   fasta: ${params.references_base_path}/GRCh38_chr21/GRCh38_chr21.fa
   mito_name: MT
-  source: nf-core
+  reference_source: nf-core
   species: Homo_sapiens