Merge pull request #375 from nf-osi/patch/fixes-and-reconfig

Patch/fixes and reconfig
nf-osi · Dec 5, 2023 · c5e3232 · c5e3232
2 parents 1591954 + ee34dfb
commit c5e3232
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Showing 6 changed files with 77 additions and 34 deletions.
diff --git a/NF.jsonld b/NF.jsonld
@@ -1544,6 +1544,8 @@
       "@id" : "bts:NEBNextmRNALibraryPrepReagentSetforIllumina"
     }, {
       "@id" : "bts:Omni-ATAC"
+    }, {
+      "@id" : "bts:QuantSeqFWDV2withUDI"
     }, {
       "@id" : "bts:Smart-seq2"
     }, {
@@ -1687,7 +1689,7 @@
   }, {
     "@id" : "bts:assayTarget",
     "@type" : "rdfs:Class",
-    "rdfs:comment" : "The HUGO gene symbol that represents the target assayed.",
+    "rdfs:comment" : "Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.",
     "rdfs:label" : "assayTarget",
     "rdfs:subClassOf" : [ ],
     "schema:isPartOf" : {
@@ -5876,6 +5878,8 @@
       "@id" : "bts:comments"
     }, {
       "@id" : "bts:platform"
+    }, {
+      "@id" : "bts:assayTarget"
     }, {
       "@id" : "bts:auxiliaryAsset"
     } ],
@@ -7287,6 +7291,8 @@
       "@id" : "bts:comments"
     }, {
       "@id" : "bts:platform"
+    }, {
+      "@id" : "bts:assayTarget"
     }, {
       "@id" : "bts:auxiliaryAsset"
     }, {
@@ -7362,6 +7368,8 @@
       "@id" : "bts:comments"
     }, {
       "@id" : "bts:platform"
+    }, {
+      "@id" : "bts:assayTarget"
     }, {
       "@id" : "bts:auxiliaryAsset"
     }, {
@@ -7606,6 +7614,8 @@
       "@id" : "bts:comments"
     }, {
       "@id" : "bts:platform"
+    }, {
+      "@id" : "bts:assayTarget"
     }, {
       "@id" : "bts:auxiliaryAsset"
     }, {
@@ -20161,6 +20171,17 @@
     },
     "sms:displayName" : "10",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:QuantSeqFWDV2withUDI",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "QuantSeqFWDV2withUDI",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "QuantSeq FWD V2 with UDI",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:B6.129(Cg)-Nf1tm1Par/J",
     "@type" : "rdfs:Class",

diff --git a/dca-template-config.json b/dca-template-config.json
@@ -0,0 +1,27 @@
+{
+  "manifest_schemas": [
+      {"display_name": "Whole Genome Sequencing Assay", "schema_name": "WGSTemplate", "type": "file"},
+      {"display_name": "Whole Exome Sequencing Assay", "schema_name": "WESTemplate", "type": "file"},
+      {"display_name": "RNA Sequencing Assay", "schema_name": "RNASeqTemplate", "type": "file"},
+      {"display_name": "Single-cell RNA Sequencing Assay", "schema_name": "ScRNASeqTemplate", "type": "file"},
+      {"display_name": "Epigenetics Assay", "schema_name": "EpigeneticsAssayTemplate", "type": "file"},
+      {"display_name": "Other Genomics Assay", "schema_name": "GenomicsAssayTemplate", "type": "file"},
+      {"display_name": "Extended Genomics Assay", "schema_name": "GenomicsAssayTemplateExtended", "type": "file"},
+      {"display_name": "Imaging Assay", "schema_name": "ImagingAssayTemplate", "type": "file"},
+      {"display_name": "MRI Assay", "schema_name": "MRIAssayTemplate", "type": "file"},
+      {"display_name": "Pharmacokinetics Assay", "schema_name": "PharmacokineticsAssayTemplate", "type": "file"},
+      {"display_name": "Proteomics Assay", "schema_name": "ProteomicsAssayTemplate", "type": "file"},
+      {"display_name": "Plate-Based Reporter Assay", "schema_name": "PlateBasedReporterAssayTemplate", "type": "file"},
+      {"display_name": "Update Milestone Report", "schema_name": "UpdateMilestoneReport", "type": "file"},
+      {"display_name": "Clinical Assay Template", "schema_name": "ClinicalAssayTemplate", "type": "file"},
+      {"display_name": "Processed/Aligned Sequencing Reads", "schema_name": "ProcessedAlignedReadsTemplate", "type": "file"},
+      {"display_name": "Processed Variant Calls", "schema_name": "ProcessedVariantCallsTemplate", "type": "file"},
+      {"display_name": "Processed Expression Data", "schema_name": "ProcessedExpressionTemplate", "type": "file"},
+      {"display_name": "FACS Template", "schema_name": "FlowCytometryTemplate", "type": "file"},
+      {"display_name": "Light Scattering Assay", "schema_name": "LightScatteringAssayTemplate", "type": "file"},
+      {"display_name": "Protocol Resource", "schema_name": "ProtocolTemplate", "type": "file"}
+    ],
+  "main_fileview" : "syn16858331",
+  "community" : "NF",
+  "schematic_service": "v1"
+}
diff --git a/modules/Assay/Parameter.yaml b/modules/Assay/Parameter.yaml
@@ -61,47 +61,50 @@ enums:
     permissible_values:
       10x:
         description: 10x Genomics library preparation
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       CEL-seq:
         description: CEL-Seq library preparation
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       Drop-Seq:
         description: Drop-Seq library preparation
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       GTAC@WUSTL in-house prep:
         description: Non-stranded library prep that uses a TruSeq-like (in-house) library design (includes cDNA generation, end-repair, A-tailing, ligation, and PCR amplification with unique dual indexing)
       IDT xGen Exome Research Panel:
         description: ''
-        meaning: https://www.idtdna.com/pages/products/next-generation-sequencing/targeted-sequencing/hybridization-capture/predesigned-panels/xgen-exome-research-panel-v2
+        source: https://www.idtdna.com/pages/products/next-generation-sequencing/targeted-sequencing/hybridization-capture/predesigned-panels/xgen-exome-research-panel-v2
       Illumina TruSeq DNA Nano:
         description: ''
       KAPA HyperPrep Kit PCR-free:
         description: KAPA HyperPrep Kits offer a streamlined library preparation protocol that combines several enzymatic steps and eliminates bead cleanups to significantly reduce library preparation time and improve consistency.
-        meaning: https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/library-preparation/kapa-hyperprep/ordering.html
+        source: https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/library-preparation/kapa-hyperprep/ordering.html
       KAPA RNA HyperPrep Kit with RiboErase (HMR):
         description: The KAPA RNA HyperPrep Kits utilize novel chemistry that enables the combination of enzymatic steps and fewer reaction purifications, resulting in a truly streamlined solution for the preparation of high-quality RNA-seq libraries.
-        meaning: https://rochesequencingstore.com/catalog/kapa-rna-hyperprep-kit-with-riboerase-hmr/
+        source: https://rochesequencingstore.com/catalog/kapa-rna-hyperprep-kit-with-riboerase-hmr/
       KAPA mRNA HyperPrep Kit:
         description: The KAPA mRNA HyperPrep Kit is a highly efficient library preparation kit designed for generating stranded RNA-seq libraries with low input amounts and reduced bias.
-        meaning: https://sequencing.roche.com/global/en/products/group/kapa-rna-hyperprep-kits.html
+        source: https://sequencing.roche.com/global/en/products/group/kapa-rna-hyperprep-kits.html
       NEBNext mRNA Library Prep Reagent Set for Illumina:
         description: NEBNext mRNA Library Prep Reagent Set for Illumina
-        meaning: https://www.neb.com/products/e6100-nebnext-mrna-library-prep-reagent-set-for-illumina
+        source: https://www.neb.com/products/e6100-nebnext-mrna-library-prep-reagent-set-for-illumina
       Omni-ATAC:
         description: Omni-ATAC-seq library preparation
-        meaning: https://protocolexchange.researchsquare.com/article/nprot-6107/v1
+        source: https://protocolexchange.researchsquare.com/article/nprot-6107/v1
+      QuantSeq FWD V2 with UDI:
+        description: Prep kit for next-gen sequencing with low-abundance samples. For analysis, note that this only provides gene-level counts, not transcript-level.
+        source: https://www.lexogen.com/quantseq-fwd-udi-v2/
       Smart-seq2:
         description: Smart-seq 2 library preparation
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       Smart-seq4:
         description: Smart-seq4 library preparation
-        meaning: https://www.takarabio.com/products/next-generation-sequencing/single-cell-rna-and-dna-seq/smart-seq-v4-for-mrna-seq
+        source: https://www.takarabio.com/products/next-generation-sequencing/single-cell-rna-and-dna-seq/smart-seq-v4-for-mrna-seq
       TruSeq:
         description: TruSeq library preparation
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       TruSeq standard total RNA library kit:
         description: ''
-        meaning: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-total-rna.html
+        source: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-total-rna.html
       unknown: 
         description: information not provided
   MRISequenceEnum:
@@ -118,19 +121,19 @@ enums:
     permissible_values:
       bulk cell:
         description: All cells from bulk sample
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       bulk nuclei:
         description: All nuclei from bulk sample
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       mitochondria:
         description: Mitochondria only
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       single cell:
         description: Single cell
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       single nucleus:
         description: Single nuclei
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
   ProteinExtractSourceEnum:
     permissible_values:
       cell lysate:
@@ -141,7 +144,7 @@ enums:
         meaning: http://purl.obolibrary.org/obo/NCIT_C13226
       mitochondria:
         description: Mitochondria only
-        meaning: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
+        source: https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json
       nuclear extract:
         description: Nuclear extracts contain proteins in nuclear compartment of the cell
         meaning: http://purl.obolibrary.org/obo/NCIT_C19832
@@ -159,18 +162,16 @@ enums:
     permissible_values:
       forward:
         description: Read 1 (or unpaired read) comes from the forward strand and read 2 (if applicable) comes from the reverse strand
-        meaning: 'FALSE'
       reverse:
         description: read 1 (or unpaired read) comes from the reverse strand and read 2 (if applicable) comes from the forward strand
-        meaning: 'FALSE'
   RunTypeEnum:
     permissible_values:
       pairedEnd:
         description: A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.
         meaning: http://purl.obolibrary.org/obo/OBI_0001852
       singleEnd:
         description: A library preparation that results in the creation of a library of 5' ends of DNA.
-        meaning: Sage Bionetworks
+        source: Sage Bionetworks
   StrandednessEnum:
     permissible_values:
       FirstStranded:

diff --git a/modules/Template/Data.yaml b/modules/Template/Data.yaml
@@ -470,6 +470,7 @@ classes:
     description: General template for describing imaging data.
     slots:
     - platform
+    - assayTarget
     - auxiliaryAsset
     annotations:
       requiresComponent: ''
@@ -481,6 +482,7 @@ classes:
       - in vivo bioluminescence
       - gel filtration chromatography
       - laser speckle imaging
+      - photograph
       - positron emission tomography
       - spatial frequency domain imaging
       - western blot

diff --git a/modules/props.yaml b/modules/props.yaml
@@ -38,7 +38,7 @@ slots:
     range: AssayEnum
     required: true
   assayTarget:
-    description: The HUGO gene symbol that represents the target assayed.
+    description: Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.
     required: false
   author:
     description: The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.

diff --git a/tests/generate/basic_templates.sh b/tests/generate/basic_templates.sh
@@ -1,8 +1,7 @@
 #!/bin/bash
 # Test generate GoogleSheets templates
 
-CONFIG=https://raw.githubusercontent.com/nf-osi/NF_data_curator/staging/www/config.json
-TEST_CONFIG=config.json
+TEST_CONFIG=../../dca-template-config.json
 CREDS=creds.json
 DATA_MODEL_PATH=../../NF.jsonld
 DATA_MODEL=NF.jsonld
@@ -23,17 +22,10 @@ else
   exit 1
 fi
 
-# Setup config
-if [ -f "$TEST_CONFIG" ]; then
-  echo "Local $TEST_CONFIG present, running test with this local config..."
-else 
-  echo "Getting $CONFIG to use as test config..."
-  wget $CONFIG -O $TEST_CONFIG
-fi
 
 TEMPLATES=($(jq '.manifest_schemas[] | .schema_name' $TEST_CONFIG | tr -d '"'))
 #TITLES=($(jq '.manifest_schemas[] | .display_name' $TEST_CONFIG | tr -d '"'))
-echo "✓ Retrieved config with ${#TEMPLATES[@]} templates..."
+echo "✓ Using config with ${#TEMPLATES[@]} templates..."
 
 # Setup data model
 cp $DATA_MODEL_PATH $DATA_MODEL