test links

.gitattributes

@@ -5,8 +5,7 @@ src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38
 src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38 -filter=lfs -diff=lfs -merge=lfs -text
 src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38 -filter=lfs -diff=lfs -merge=lfs -text
 src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38 -filter=lfs -diff=lfs -merge=lfs -text
-
 #Otherwise, track everything in large
 src/test/resources/large/** filter=lfs diff=lfs merge=lfs -text
 src/main/resources/large/** filter=lfs diff=lfs merge=lfs -text
-
+*.psd filter=lfs diff=lfs merge=lfs -text

scripts/variantstore/variant_annotations_table/README.md

@@ -1,8 +1,8 @@
 # Creating the Variant Annotations Table
 
 ### The VAT pipeline is a set of WDLs
-- [GvsCreateVAT.wdl](scripts/variantstore/wdl/GvsCreateVAT.wdl)
-- [GvsValidateVAT.wdl](scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl)
+- [GvsCreateVAT.wdl](/scripts/variantstore/wdl/GvsCreateVAT.wdl)
+- [GvsValidateVAT.wdl](/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl)
 
 The pipeline takes in a jointVCF and outputs a table in BigQuery.
 
@@ -12,14 +12,14 @@ The pipeline takes in a jointVCF and outputs a table in BigQuery.
 
 ### Run GvsCreateVAT:
 
-Most of the inputs are constants — like the reference, or a table schema — and dont require any additional work (and paths can be found in the [example inputs json](scripts/variantstore/wdl/GvsCreateVAT.example.inputs.json)). However for the specific data being put in the VAT, three inputs need to be created.
+Most of the inputs are constants — like the reference, or a table schema — and dont require any additional work (and paths can be found in the [example inputs json](/scripts/variantstore/wdl/GvsCreateVAT.example.inputs.json)). However for the specific data being put in the VAT, three inputs need to be created.
 
 The first two of these inputs are two files — one of the file/vcf/shards you want to use for the VAT, and their corresponding index files. These are labelled as `inputFileofFileNames` and `inputFileofIndexFileNames` and need to be copied into a GCP bucket that this pipeline will have access to (eg. this bucket: `gs://aou-genomics-curation-prod-processing/vat/`) for easy access during the workflow.
 The third input is the ancestry file from the ancestry pipeline which will be used to calculate AC, AN and AF for all subpopulations. It needs to be copied into a GCP bucket that this pipeline will have access to. This input has been labelled as the `ancestry_file`.
 
 Most of the other files are specific to where the VAT will live, like the project_id and dataset_name and the table_suffix which will name the VAT itself as vat_`table_suffix` as well as a GCP bucket location, the output_path, for the intermediary files and the VAT export in tsv form.
 
-The provided [example inputs json](scripts/variantstore/wdl/GvsCreateVAT.example.inputs.json) indicates all of the inputs.
+The provided [example inputs json](/scripts/variantstore/wdl/GvsCreateVAT.example.inputs.json) indicates all of the inputs.
 
 
 ### Notes: