Merge pull request #231 from nf-osi/patch/templates

Patch/templates
nf-osi · Jan 10, 2023 · cba5507 · cba5507
2 parents e7268f2 + 4c58951
commit cba5507
Show file tree

Hide file tree

Showing 4 changed files with 34 additions and 6 deletions.
diff --git a/NF.csv b/NF.csv
@@ -451,6 +451,7 @@ readsMappedPercent,"Percent of mapped reads collected from samtools",,,FALSE,htt
 meanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=mean_coverage,,,,,meanCoverage,Property,Processing,annotationProperty,,,,
 proportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_coverage_10x,,,,,proportionCoverage10x,Property,Processing,annotationProperty,,,,
 proportionCoverage30x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_coverage_30x,,,,,proportionCoverage30x,Property,Processing,annotationProperty,,,,
+isFilteredReads,"Whether the reads in the processed result has been filtered by adding a 'PASS' filter or other filters as determined by the data generator",,,FALSE,Sage Bionetworks,,,,,isFilteredReads,Property,Processing,annotationProperty,,,,
 head,The head is the anterior-most division of the body.,"","",FALSE,http://purl.obolibrary.org/obo/UBERON_0000033,bodyPart,,"","",Head,Class,Biosample,Body_Part,Body_Part,"","",""
 lymph node,A bean-shaped organ surrounded by a connective tissue capsule.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C12745,organ,,"","",Lymph_Node,Class,Biosample,Body_Part,Organ,"","",""
 kidney,One of the two bean-shaped organs located on each side of the spine in the retroperitoneum.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C12415,organ,,"","",Kidney,Class,Biosample,Body_Part,Organ,"","",""
@@ -768,14 +769,14 @@ concentrationNaCl,"Numeric value for NaCl concentration","",,FALSE,,parameter,,,
 concentrationNaClUnit,"Unit used for the NaCl concentration, e.g. mM","mg/mL,mM",,FALSE,,parameter,,,,concentrationNaClUnit,Property,Sample,annotationProperty,,,,
 Component,"Category of metadata manifest; provide the same one for all items/rows.",,,TRUE,https://w3id.org/biolink/vocab/category,,,,,,,,,,,,
 genomicsAssayTemplateNormalized,"Generic template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,,
-genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,,
-genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
+genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,,
+genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
 WGSTemplate,"Template for describing raw data from Whole Genome Sequencing (WGS)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WGS_Template,Class,Template,Template,Assay_Template,,,
 WESTemplate,"Template for describing raw data from Whole Exome Sequencing (WES)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,targetCaptureKitID,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WES_Template,Class,Template,Template,Assay_Template,,,
 RNASeqTemplate,"Template for describing raw data from (bulk) RNA-sequencing",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,targetDepth,comments",TRUE,Sage Bionetworks,template,,,,RNA_Seq_Template,Class,Template,Template,Assay_Template,,,
 ScRNASeqTemplate,"Template for describing raw data from single-cell RNA-sequencing (scRNA-seq)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,ScRNA_Seq_Template,Class,Template,Template,Assay_Template,,,
 ProcessedAlignedReadsTemplate,"Template for describing aligned reads output data (i.e. BAM)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,averageInsertSize,averageReadLength,averageBaseQuality,pairsOnDifferentChr,readsDuplicatedPercent,readsMappedPercent,meanCoverage,proportionCoverage10x,proportionCoverage30x,readDepth,totalReads,workflow,genomicReference,comments",TRUE,Sage Bionetworks,template,,,,Processed_Aligned_Reads_Template,Class,Template,Template,Assay_Template,,,
-ProcessedVariantCallsTemplate,"Template for describing either germline or variant calls output data (i.e. VCF/MAF)",,"Component,Filename,resourceType,progressReportNumber,specimenID,dataType,assay,individualID,workflow,comments",TRUE,Sage Bionetworks,template,,,,Processed_Variant_Calls_Template,Class,Template,Template,Assay_Template,,,
+ProcessedVariantCallsTemplate,"Template for describing either germline or variant calls output data (i.e. VCF/MAF)",,"Component,Filename,resourceType,progressReportNumber,specimenID,dataType,assay,individualID,isFilteredReads,workflow,comments",TRUE,Sage Bionetworks,template,,,,Processed_Variant_Calls_Template,Class,Template,Template,Assay_Template,,,
 ProcessedExpressionTemplate,"Template for describing expression output data",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,individualID,specimenID,parentSpecimenID,modelSystemName,workflow,expressionUnit,comments",TRUE,Sage Bionetworks,template,,,,Processed_Expression_Template,Class,Template,Template,Assay_Template,,,
 imagingAssayTemplate,"Generic template for describing data from an imaging type assay (IHC, etc). This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assayTarget,individualID,parentSpecimenID,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template,Class,Template,Template,Assay_Template,,,
 imagingAssayTemplateExtended,"Template for describing data from an imaging type assay (IHC, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assayTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,

diff --git a/NF.jsonld b/NF.jsonld
@@ -11164,6 +11164,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:IsFilteredReads",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "Whether the reads in the processed result has been filtered by adding a 'PASS' filter or other filters as determined by the data generator",
+            "rdfs:label": "IsFilteredReads",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "schema:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "isFilteredReads",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Head",
             "@type": "rdfs:Class",
@@ -17710,6 +17727,9 @@
                 {
                     "@id": "bts:ParentSpecimenID"
                 },
+                {
+                    "@id": "bts:IsXenograft"
+                },
                 {
                     "@id": "bts:RunType"
                 },
@@ -17765,6 +17785,9 @@
                 {
                     "@id": "bts:ParentSpecimenID"
                 },
+                {
+                    "@id": "bts:IsXenograft"
+                },
                 {
                     "@id": "bts:ExperimentalCondition"
                 },
@@ -18140,6 +18163,9 @@
                 {
                     "@id": "bts:IndividualID"
                 },
+                {
+                    "@id": "bts:IsFilteredReads"
+                },
                 {
                     "@id": "bts:Workflow"
                 },

diff --git a/modules/Processing/annotationProperty.csv b/modules/Processing/annotationProperty.csv
@@ -11,3 +11,4 @@ readsMappedPercent,"Percent of mapped reads collected from samtools",,,FALSE,htt
 meanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=mean_coverage,,,,,meanCoverage,Property,Processing,annotationProperty,,,,
 proportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_coverage_10x,,,,,proportionCoverage10x,Property,Processing,annotationProperty,,,,
 proportionCoverage30x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_coverage_30x,,,,,proportionCoverage30x,Property,Processing,annotationProperty,,,,
+isFilteredReads,"Whether the reads in the processed result has been filtered by adding a 'PASS' filter or other filters as determined by the data generator",,,FALSE,Sage Bionetworks,,,,,isFilteredReads,Property,Processing,annotationProperty,,,,
diff --git a/modules/Template/Template.csv b/modules/Template/Template.csv
@@ -1,13 +1,13 @@
 Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote
 genomicsAssayTemplateNormalized,"Generic template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,,
-genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,,
-genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
+genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,,
+genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
 WGSTemplate,"Template for describing raw data from Whole Genome Sequencing (WGS)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WGS_Template,Class,Template,Template,Assay_Template,,,
 WESTemplate,"Template for describing raw data from Whole Exome Sequencing (WES)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,targetCaptureKitID,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WES_Template,Class,Template,Template,Assay_Template,,,
 RNASeqTemplate,"Template for describing raw data from (bulk) RNA-sequencing",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,targetDepth,comments",TRUE,Sage Bionetworks,template,,,,RNA_Seq_Template,Class,Template,Template,Assay_Template,,,
 ScRNASeqTemplate,"Template for describing raw data from single-cell RNA-sequencing (scRNA-seq)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,ScRNA_Seq_Template,Class,Template,Template,Assay_Template,,,
 ProcessedAlignedReadsTemplate,"Template for describing aligned reads output data (i.e. BAM)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,averageInsertSize,averageReadLength,averageBaseQuality,pairsOnDifferentChr,readsDuplicatedPercent,readsMappedPercent,meanCoverage,proportionCoverage10x,proportionCoverage30x,readDepth,totalReads,workflow,genomicReference,comments",TRUE,Sage Bionetworks,template,,,,Processed_Aligned_Reads_Template,Class,Template,Template,Assay_Template,,,
-ProcessedVariantCallsTemplate,"Template for describing either germline or variant calls output data (i.e. VCF/MAF)",,"Component,Filename,resourceType,progressReportNumber,specimenID,dataType,assay,individualID,workflow,comments",TRUE,Sage Bionetworks,template,,,,Processed_Variant_Calls_Template,Class,Template,Template,Assay_Template,,,
+ProcessedVariantCallsTemplate,"Template for describing either germline or variant calls output data (i.e. VCF/MAF)",,"Component,Filename,resourceType,progressReportNumber,specimenID,dataType,assay,individualID,isFilteredReads,workflow,comments",TRUE,Sage Bionetworks,template,,,,Processed_Variant_Calls_Template,Class,Template,Template,Assay_Template,,,
 ProcessedExpressionTemplate,"Template for describing expression output data",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,individualID,specimenID,parentSpecimenID,modelSystemName,workflow,expressionUnit,comments",TRUE,Sage Bionetworks,template,,,,Processed_Expression_Template,Class,Template,Template,Assay_Template,,,
 imagingAssayTemplate,"Generic template for describing data from an imaging type assay (IHC, etc). This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assayTarget,individualID,parentSpecimenID,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template,Class,Template,Template,Assay_Template,,,
 imagingAssayTemplateExtended,"Template for describing data from an imaging type assay (IHC, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assayTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,