Added pbsv_splits to input templates. Updated Zenodo links.

PacificBiosciences · Oct 6, 2023 · ba7126d · ba7126d
1 parent 07bb93b
commit ba7126d
Show file tree

Hide file tree

Showing 8 changed files with 10 additions and 3 deletions.
diff --git a/backends/aws/inputs.aws.json b/backends/aws/inputs.aws.json
@@ -19,6 +19,7 @@
       "data": "s3://dnastack-resources/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta",
       "data_index": "s3://dnastack-resources/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai"
     },
+    "pbsv_splits": "s3://dnastack-resources/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json",
     "tandem_repeat_bed": "s3://dnastack-resources/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed",
     "trgt_tandem_repeat_bed": "s3://dnastack-resources/dataset/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed",
     "hificnv_exclude_bed": {

diff --git a/backends/azure/inputs.azure.json b/backends/azure/inputs.azure.json
@@ -19,6 +19,7 @@
       "data": "/datasetpbrarediseases/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta",
       "data_index": "/datasetpbrarediseases/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai"
     },
+    "pbsv_splits": "/datasetpbrarediseases/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json",
     "tandem_repeat_bed": "/datasetpbrarediseases/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed",
     "trgt_tandem_repeat_bed": "/datasetpbrarediseases/dataset/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed",
     "hificnv_exclude_bed": {

diff --git a/backends/gcp/inputs.gcp.json b/backends/gcp/inputs.gcp.json
@@ -19,6 +19,7 @@
       "data": "gs://pacbio-wdl/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta",
       "data_index": "gs://pacbio-wdl/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai"
     },
+    "pbsv_splits": "gs://pacbio-wdl/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json",
     "tandem_repeat_bed": "gs://pacbio-wdl/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed",
     "trgt_tandem_repeat_bed": "gs://pacbio-wdl/dataset/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed",
     "hificnv_exclude_bed": {

diff --git a/backends/hpc/README.md b/backends/hpc/README.md
@@ -35,13 +35,13 @@ See [the inputs section of the main README](../../README.md#workflow-inputs) for
 
 # Reference data bundle
 
-![https://doi.org/10.5281/zenodo.8381621](https://zenodo.org/badge/DOI/10.5281/zenodo.8381621.svg)
+![https://doi.org/10.5281/zenodo.8415406](https://zenodo.org/badge/DOI/10.5281/zenodo.8415406.svg)
 
-Reference data is hosted on Zenodo at [10.5281/zenodo.8381621](https://zenodo.org/record/8381621).  Download the reference data bundle and extract it to a location on your HPC, then update the input template file with the path to the reference data.
+Reference data is hosted on Zenodo at [10.5281/zenodo.8415406](https://zenodo.org/record/8415406).  Download the reference data bundle and extract it to a location on your HPC, then update the input template file with the path to the reference data.
 
 ```bash
 # download the reference data bundle
-wget https://zenodo.org/record/8381621/files/wdl-humanwgs.v1.0.1.resources.tgz
+wget https://zenodo.org/record/8415406/files/wdl-humanwgs.v1.0.1.resources.tgz
 
 # extract the reference data bundle and rename as dataset
 tar -xzf wdl-humanwgs.v1.0.1.resources.tgz && mv static_resources dataset

diff --git a/backends/hpc/inputs.hpc.json b/backends/hpc/inputs.hpc.json
@@ -19,6 +19,7 @@
       "data": "<local_path_prefix>/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta",
       "data_index": "<local_path_prefix>/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai"
     },
+    "pbsv_splits": "<local_path_prefix>/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json",
     "tandem_repeat_bed": "<local_path_prefix>/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed",
     "trgt_tandem_repeat_bed": "<local_path_prefix>/dataset/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed",
     "hificnv_exclude_bed": {

diff --git a/workflows/cohort_analysis/inputs.json b/workflows/cohort_analysis/inputs.json
@@ -26,6 +26,7 @@
       "data": "File",
       "data_index": "File"
     },
+    "pbsv_splits": "File",
     "hificnv_expected_bed_male": "File",
     "hificnv_expected_bed_female": "File",
     "gnomad_af": "File? (optional)",

diff --git a/workflows/sample_analysis/inputs.json b/workflows/sample_analysis/inputs.json
@@ -13,6 +13,7 @@
       "data": "File",
       "data_index": "File"
     },
+    "pbsv_splits": "File",
     "tandem_repeat_bed": "File",
     "trgt_tandem_repeat_bed": "File",
     "hificnv_exclude_bed": {

diff --git a/workflows/tertiary_analysis/inputs.json b/workflows/tertiary_analysis/inputs.json
@@ -27,6 +27,7 @@
       "data": "File",
       "data_index": "File"
     },
+    "pbsv_splits": "File",
     "tandem_repeat_bed": "File",
     "trgt_tandem_repeat_bed": "File",
     "gnomad_af": "File",