From 34278b5d033ce7aa51c51b4338c1c35eec8cebe9 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Fri, 31 Oct 2025 10:38:03 -0400
Subject: [PATCH 01/28] :sparkles: use the updated docker with new sample name
 option

---
 tools/autogvp_annotate_cavatica.cwl | 3 ++-
 tools/autogvp_annotate_custom.cwl   | 3 ++-
 workflows/autogvp.cwl               | 3 +++
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/tools/autogvp_annotate_cavatica.cwl b/tools/autogvp_annotate_cavatica.cwl
index bfbc87e..b24f078 100644
--- a/tools/autogvp_annotate_cavatica.cwl
+++ b/tools/autogvp_annotate_cavatica.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.3'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.4'
 
 baseCommand: []
 arguments:
@@ -27,6 +27,7 @@ inputs:
   intervar_file: { type: 'File', inputBinding: { position: 2, prefix: "--intervar" }, doc: "input intervar file" }
   variant_summary: { type: 'File', inputBinding: { position: 2, prefix: "--variant_summary" }, doc: "variant_summary file (format: variant_summary_2023-02.txt)" }
   output_basename: { type: 'string?', default: "test", inputBinding: { position: 2, prefix: "--output" }, doc: "String to use as base for output filenames" }
+  sample_id: {type: 'string', inputBinding: { position: 2, prefix: "--sample_id" }, doc: "Input sample bioassay id."}
   cpu: { type: 'int?', default: 1, doc: "CPUs to allocate to this task" }
   ram: { type: 'int?', default: 2, doc: "GB of RAM to allocate to this task" }
 outputs:
diff --git a/tools/autogvp_annotate_custom.cwl b/tools/autogvp_annotate_custom.cwl
index f4a1bfd..06a1bf6 100644
--- a/tools/autogvp_annotate_custom.cwl
+++ b/tools/autogvp_annotate_custom.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.3'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.4'
 
 baseCommand: []
 arguments:
@@ -27,6 +27,7 @@ inputs:
   intervar_file: { type: 'File', inputBinding: { position: 2, prefix: "--intervar" }, doc: "input intervar file" }
   variant_summary: { type: 'File', inputBinding: { position: 2, prefix: "--variant_summary" }, doc: "variant_summary file (format: variant_summary_2023-02.txt)" }
   output_basename: { type: 'string?', default: "test", inputBinding: { position: 2, prefix: "--output" }, doc: "String to use as base for output filenames" }
+  sample_id: {type: 'string', inputBinding: { position: 2, prefix: "--sample_id" }, doc: "Input sample bioassay id."}
   cpu: { type: 'int?', default: 1, doc: "CPUs to allocate to this task" }
   ram: { type: 'int?', default: 2, doc: "GB of RAM to allocate to this task" }
 outputs:
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index f89fde0..cfb2998 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -77,6 +77,7 @@ inputs:
   multianno_file: {type: 'File', doc: "ANNOVAR multianno file"}
   output_colnames: {type: 'File', doc: "File with column name information."}
   output_basename: {type: 'string?', default: "out", doc: "String to use as the basename for stored outputs."}
+  sample_id: {type: 'string', doc: "Input sample bioassay id."}
   selected_clinvar_submissions: {type: 'File?', doc: "ClinVar variant file with conflicts resolved. If not provided, this file will
       be generated in the workflow"}
   variant_summary_file: {type: 'File?', doc: "ClinVar variant summary file"}
@@ -127,6 +128,7 @@ steps:
         source: [selected_clinvar_submissions, select_clinvar_subs/clinvar_submissions]
         pickValue: first_non_null
       output_basename: output_basename
+      sample_id: sample_id
       cpu: annotate_cpu
       ram: annotate_ram
     out: [annotation_report]
@@ -144,6 +146,7 @@ steps:
         source: [selected_clinvar_submissions, select_clinvar_subs/clinvar_submissions]
         pickValue: first_non_null
       output_basename: output_basename
+      sample_id: sample_id
       cpu: annotate_cpu
       ram: annotate_ram
     out: [annotation_report]

From 1fe4cfc4c96f0071d538ede5dadf51f2e3b06ede Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Fri, 31 Oct 2025 10:58:21 -0400
Subject: [PATCH 02/28] :memo: update links to our repo

---
 README.md                                     |  4 +-
 workflows/autogvp.cwl                         |  2 +-
 ...d3b-diskin-pathogenicity-preprocess-wf.cwl | 42 +++++++++----------
 3 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/README.md b/README.md
index bea778f..97a1059 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Pathogenicity Preprocessing Workflow
-To run, please see the [CAVATICA app](https://cavatica.sbgenomics.com/public/apps/cavatica/apps-publisher/d3b-diskin-pathogenicity-preprocess-wf). Each version should correspond with a git release. This repo makes use of the git submodule feature for ease of code maintenance. To properly retrieve all relevant code:
+This repo makes use of the git submodule feature for ease of code maintenance. To properly retrieve all relevant code:
 ```sh
-git clone  https://github.com/d3b-center/D3b-Pathogenicity-Preprocessing
+git clone  https://github.com/childrens-bti/D3b-Pathogenicity-Preprocessing-CNH
 git submodule init
 git submodule update
 ```
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index cfb2998..ff1184f 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -175,7 +175,7 @@ hints:
 - class: sbg:maxNumberOfParallelInstances
   value: 2
 "sbg:links":
-- id: 'https://github.com/d3b-center/D3b-Pathogenicity-Preprocessing/releases/tag/v1.2.0'
+- id: 'https://github.com/childrens-bti/D3b-Pathogenicity-Preprocessing-CNH/releases/tag/v1.0.0'
   label: github-release
 sbg:license: Apache License 2.0
 sbg:publisher: KFDRC
diff --git a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
index ec0597f..d93ad77 100644
--- a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
+++ b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
@@ -4,26 +4,26 @@ id: d3b-diskin-pathogenicity-preprocess-wf
 label: Pathogenicity Preprocessing Workflow
 doc: |-
   # Pathogenicity Preprocessing Workflow
-  To run, please see the [CAVATICA app](https://cavatica.sbgenomics.com/public/apps/cavatica/apps-publisher/d3b-diskin-pathogenicity-preprocess-wf). Each version should correspond with a git release. This repo makes use of the git submodule feature for ease of code maintenance. To properly retrieve all relevant code:
+  This repo makes use of the git submodule feature for ease of code maintenance. To properly retrieve all relevant code:
   ```sh
-  git clone  https://github.com/d3b-center/D3b-Pathogenicity-Preprocessing
+  git clone  https://github.com/childrens-bti/D3b-Pathogenicity-Preprocessing-CNH
   git submodule init
   git submodule update
   ```
   ## Prequisite
-  It is recommended to have first run the [Kids First Germline Annotation Workflow](https://github.com/kids-first/kf-annotation-tools/blob/v1.1.0/docs/GERMLINE_SNV_ANNOT_README.md) first.
+  It is recommended to have first run the [Kids First Germline Annotation Workflow](https://github.com/kids-first/kf-annotation-tools/blob/v1.1.0/docs/GERMLINE_SNV_ANNOT_README.md).
 
   ## Pathogenicity Preprocessing Workflow
   This workflow uses the prerequisite input to run the InterVar workflow and autoPVS1 tool.
   The major pieces of software being used are:
-   - ANNOVAR latest: The software has no versioning, but references do. See `annovar_db` section in [Recommended inputs](#recommended-inputs)
-   - InterVar v2.2.1
-   - AutoPVS1 v2.0.0: Modified from AutoPVS1 v2.0 to fit annotated KF vcf output. See [README for autoPVS1](https://github.com/d3b-center/D3b-autoPVS1/tree/v2.0.0#readme) for details
+  - ANNOVAR latest: The software has no versioning, but references do. See `annovar_db` section in [Recommended inputs](#recommended-inputs)
+  - InterVar v2.2.1
+  - AutoPVS1 v2.0.0: Modified from AutoPVS1 v2.0 to fit annotated KF vcf output. See [README for autoPVS1](https://github.com/d3b-center/D3b-autoPVS1/tree/v2.0.0#readme) for details
 
-  Optionally, if you which to add (and in needed, overwrite) another annotation from a vcf file (likely ClinVar), a bcftools strip and annotate steps are provided. The input vcf will be processed and its result will appear as an additional output in the workflow. 
+  Optionally, if you wish to add and, if needed, overwrite another annotation from a VCF file (likely ClinVar), a BCFtools strip and annotate steps are provided. The input VCF will be processed, and its result will appear as an additional output in the workflow. 
   ### Recommended inputs:
-   - `annovar_db`: ANNOVAR Database with at minimum required resources to InterVar. Need to use [ANNOVAR download commands](https://annovar.openbioinformatics.org/en/latest/user-guide/download/) to get the following:
-       ```
+  - `annovar_db`: ANNOVAR Database with at minimum required resources to InterVar. Need to use [ANNOVAR download commands](https://annovar.openbioinformatics.org/en/latest/user-guide/download/) to get the following:
+      ```
           annovar_humandb_hg38_intervar/
           ├── hg38_AFR.sites.2015_08.txt
           ├── hg38_AFR.sites.2015_08.txt.idx
@@ -62,8 +62,8 @@ doc: |-
               ├── annovar_downdb.log
               └── hg38.fa
       ```
-   - `intervar_db`: InterVar Database from git repo + mim_genes.txt
-   - `autopvs1_db`: git repo files plus a user-provided fasta reference. For hg38, recommend:
+  - `intervar_db`: InterVar Database from git repo + mim_genes.txt
+  - `autopvs1_db`: git repo files plus a user-provided fasta reference. For hg38, recommend:
       ```
       data/
           ├── Homo_sapiens_assembly38.fasta
@@ -78,9 +78,9 @@ doc: |-
           ├── mutational_hotspots_hg38.bed
           └── ncbiRefSeq_hg38.gpe
       ```
-   - `annovar_db_str`: Name of dir created when `annovar_db` tar ball in decompressed. Default: `annovar_humandb_hg38_intervar`
-   - `autopvs1_db_str`: Name of dir created when `autopvs1_db` tar ball in decompressed. Default: `data`
-   - `intervar_db_str`: Name of dir created when `intervar_db_str` tar ball in decompressed. Default: `intervardb`
+  - `annovar_db_str`: Name of dir created when `annovar_db` tar ball in decompressed. Default: `annovar_humandb_hg38_intervar`
+  - `autopvs1_db_str`: Name of dir created when `autopvs1_db` tar ball in decompressed. Default: `data`
+  - `intervar_db_str`: Name of dir created when `intervar_db_str` tar ball in decompressed. Default: `intervardb`
   #### **Note:** We used a gene symbol liftover tool to allow gene symbols searches from different gene models to be found, `PVS1.level` was augmented with additional entries in which a gene symbols from the original file has changed.
   The [update_gene_symbols.py](https://github.com/d3b-center/D3b-DGD-Collaboration/blob/v0.2.0/scripts/update_gene_symbols.py) tool was used to achieve this, with liftover source obtained from [here](https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/hgnc_complete_set_2021-06-01.txt) to match gene symbols from default/recommended VEP annotation. Example command:
   ```sh
@@ -97,12 +97,12 @@ doc: |-
 
   ### Optional Inputs
   As mentioned above, the preprocessing workflow can add an additional annotation
-   - `annotation_vcf`: hg38 chromosome-formatted vcf file with multi-allelics split. If provided bcftools will add annotation from the specified columns for each variant that matches
-   - `bcftools_annot_columns`: A csv string of from annotation to port into the input vcf. Must provide if `annotation_vcf` given. See [bcftools annotate](https://samtools.github.io/bcftools/bcftools.html#annotate) documentation on how to properly reference
-   - `bcftools_strip_for_vep`: If re-annotating certain `INFO` fields, it's best to strip the old annotation first to avoid conflicts. Use the same format as `bcftools_annot_columns` to reference fields being stripped
-   - `bcftools_strip_for_annovar`: More of a convenience to strip the ANNOVAR VCF of annotations that maybe have been used initially in the workflow, but will likely not be used downstream 
-   #### A note on ClinVar annotation
-   For the publication, [ClinVar release 20231028](https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2023/clinvar_20231028.vcf.gz) was used. In order to be compatible with our hg38-aligned vcfs, we additionally downloaded the [variant suammry](https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz) file, ran a [custom script](scripts/cleanup_clinvar.py) that:
+  - `annotation_vcf`: hg38 chromosome-formatted VCF. If provided BCFtools will add annotation from the specified columns for each variant that matches
+  - `bcftools_annot_columns`: A CSV string of from annotation to port into the input vcf. Must provide if `annotation_vcf` given. See [BCFtools annotate](https://samtools.github.io/bcftools/bcftools.html#annotate) documentation on how to properly reference
+  - `bcftools_strip_for_vep`: If re-annotating certain `INFO` fields, it's best to strip the old annotation first to avoid conflicts. Use the same format as `bcftools_annot_columns` to reference fields being stripped
+  - `bcftools_strip_for_annovar`: More of a convenience to strip the ANNOVAR VCF of annotations that maybe have been used initially in the workflow, but will likely not be used downstream 
+  #### A note on ClinVar annotation
+  For the publication, [ClinVar release 20231028](https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2023/clinvar_20231028.vcf.gz) was used. In order to be compatible with our hg38-aligned VCFs, we additionally downloaded the [variant summary](https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz) file, ran a [custom script](scripts/cleanup_clinvar.py) that:
     - Converted contigs to `chr` format
     - Dropped contigs not in hg38
     - Use the variant summary table to replace `N` alleles and split into canonical `ACGT` alleles as those `N` were actually representing extended IUPAC nucleotides
@@ -222,7 +222,7 @@ hints:
 - class: sbg:maxNumberOfParallelInstances
   value: 2
 "sbg:links":
-- id: 'https://github.com/d3b-center/D3b-Pathogenicity-Preprocessing/releases/tag/v1.1.0'
+- id: 'https://github.com/childrens-bti/D3b-Pathogenicity-Preprocessing-CNH/releases/tag/v1.0.0'
   label: github-release
 sbg:license: Apache License 2.0
 sbg:publisher: KFDRC

From 72ae280670111cef2a1916f3644dcf8245b91f86 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Tue, 6 Jan 2026 14:51:33 -0500
Subject: [PATCH 03/28] :whale: update docker to newest version

---
 tools/autogvp_annotate_cavatica.cwl | 2 +-
 tools/autogvp_annotate_custom.cwl   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/autogvp_annotate_cavatica.cwl b/tools/autogvp_annotate_cavatica.cwl
index b24f078..9266b16 100644
--- a/tools/autogvp_annotate_cavatica.cwl
+++ b/tools/autogvp_annotate_cavatica.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.4'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
 
 baseCommand: []
 arguments:
diff --git a/tools/autogvp_annotate_custom.cwl b/tools/autogvp_annotate_custom.cwl
index 06a1bf6..2bdf563 100644
--- a/tools/autogvp_annotate_custom.cwl
+++ b/tools/autogvp_annotate_custom.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.4'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
 
 baseCommand: []
 arguments:

From 66a4425c564a8b186abc5ef13822ebbcfea356e8 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Tue, 6 Jan 2026 14:56:59 -0500
Subject: [PATCH 04/28] use new file ids

---
 workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
index d93ad77..1a4104d 100644
--- a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
+++ b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
@@ -121,7 +121,7 @@ inputs:
   output_basename: {type: string, doc: "String that will be used in the output filenames. Be sure to be consistent with this as InterVar
       will use this too"}
   annovar_db: {type: File, doc: "Annovar Database with at minimum required resources to InterVar", "sbg:suggestedValue": {class: File,
-      path: 648b2bf575423d2473af6ed8, name: annovar_humandb_hg38_intervar.tgz}}
+      path: 695d3c4c5ddfaa35efd4d025, name: annovar_humandb_hg38_intervar.tgz}}
   annovar_db_str: {type: 'string?', doc: "Name of dir created when annovar db is un-tarred", default: "annovar_humandb_hg38_intervar"}
   annovar_protocol: {type: 'string?', doc: "csv string of databases within `annovar_db` cache to run", default: "refGene,esp6500siv2_all,1000g2015aug_all,avsnp147,dbnsfp42a,clinvar_20210501,gnomad_genome,dbscsnv11,rmsk,ensGene,knownGene"}
   annovar_operation: {type: 'string?', doc: "csv string of how to treat each listed protocol", default: "g,f,f,f,f,f,f,f,r,g,g"}
@@ -139,11 +139,11 @@ inputs:
   # bcftools annotate if more to do
   bcftools_annot_columns: {type: 'string?', doc: "csv string of columns from annotation to port into the input vcf", default: "INFO/ALLELEID,INFO/CLNDN,INFO/CLNDNINCL,INFO/CLNDISDB,INFO/CLNDISDBINCL,INFO/CLNHGVS,INFO/CLNREVSTAT,INFO/CLNSIG,INFO/CLNSIGCONF,INFO/CLNSIGINCL,INFO/CLNVC,INFO/CLNVCSO,INFO/CLNVI"}
   annotation_vcf: {type: 'File?', secondaryFiles: ['.tbi'], doc: "additional bgzipped annotation vcf file"}
-  intervar_db: {type: File, doc: "InterVar Database from git repo + mim_genes.txt", "sbg:suggestedValue": {class: File, path: 648b2bf575423d2473af6ed6,
+  intervar_db: {type: File, doc: "InterVar Database from git repo + mim_genes.txt", "sbg:suggestedValue": {class: File, path: 695d3c4c5ddfaa35efd4d023,
       name: intervardb_2021-08.tar.gz}}
   intervar_db_str: {type: 'string?', doc: "Name of dir created when intervar db is un-tarred", default: "intervardb"}
   intervar_ram: {type: 'int?', doc: "Min ram needed for task in GB", default: 32}
-  autopvs1_db: {type: File, doc: "git repo files plus a user-provided fasta reference", "sbg:suggestedValue": {class: File, path: 648b2bf575423d2473af6ed7,
+  autopvs1_db: {type: File, doc: "git repo files plus a user-provided fasta reference", "sbg:suggestedValue": {class: File, path: 695d3c4c5ddfaa35efd4d02d,
       name: autoPVS1_references_sym_updated.tar.gz}}
   autopvs1_db_str: {type: 'string?', doc: "Name of dir created when annovar db is un-tarred", default: "data"}
 outputs:

From 72ffc6662af5090bbf6f2f677d835792ce898129 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Wed, 4 Feb 2026 10:42:36 -0500
Subject: [PATCH 05/28] add item action

---
 .github/workflows/add-issues-to-project.yml | 23 +++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 .github/workflows/add-issues-to-project.yml

diff --git a/.github/workflows/add-issues-to-project.yml b/.github/workflows/add-issues-to-project.yml
new file mode 100644
index 0000000..ccb77d7
--- /dev/null
+++ b/.github/workflows/add-issues-to-project.yml
@@ -0,0 +1,23 @@
+name: Add issues to project
+
+on:
+  issues:
+    types:
+      - opened
+  pull_request:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add issue to project
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/add-to-project@244f685bbc3b7adfa8466e08b698b5577571133e
+        with:
+          # You can target a project in a different organization or user account
+          # to the issue.
+          # For organization projects: https://github.com/orgs/ORG_NAME/projects/PROJECT_NUMBER
+          # For user projects: https://github.com/users/USER_NAME/projects/PROJECT_NUMBER
+          project-url: https://github.com/orgs/childrens-bti/projects/1
+          github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}

From 25744e2716088a9f241f550914ae106a6ec3b894 Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Mon, 20 Apr 2026 21:27:21 -0400
Subject: [PATCH 06/28] update autoGVP

---
 tools/autogvp_annotate_cavatica.cwl | 11 +++++----
 workflows/autogvp.cwl               | 35 +++--------------------------
 2 files changed, 8 insertions(+), 38 deletions(-)

diff --git a/tools/autogvp_annotate_cavatica.cwl b/tools/autogvp_annotate_cavatica.cwl
index 9266b16..6b6d881 100644
--- a/tools/autogvp_annotate_cavatica.cwl
+++ b/tools/autogvp_annotate_cavatica.cwl
@@ -1,8 +1,8 @@
 cwlVersion: v1.2
 class: CommandLineTool
-id: autogvp_annotate_cavatica
+id: autogvp_annotate
 doc: |
-  Tool for the 02-annotate_variants_CAVATICA_input.R script from AutoGVP
+  Tool for the 02-annotate_variants.R script from AutoGVP
 requirements:
   - class: ShellCommandRequirement
   - class: InlineJavascriptRequirement
@@ -17,18 +17,17 @@ arguments:
   - position: 0
     shellQuote: false
     valueFrom: >-
-      Rscript /rocker-build/AutoGVP/scripts/02-annotate_variants_CAVATICA_input.R --outdir .
+      Rscript /rocker-build/AutoGVP/scripts/02-annotate_variants.R --outdir .
 
 inputs:
   vcf_file: { type: 'File', inputBinding: { position: 2, prefix: "--vcf" }, doc: "Input vcf file with VEP annotations" }
-  clinvar_file: { type: 'File?', inputBinding: { position: 2, prefix: "--clinvar" }, doc: "specific clinVar file (format: clinvar_20211225.vcf.gz)" }
+  clinvar_file: { type: 'File', inputBinding: { position: 2, prefix: "--clinvar" }, doc: "ClinVar resolved clinical significance file (format: resolved-clinvar-interpretations.tsv)" }
   multianno_file: { type: 'File', inputBinding: { position: 2, prefix: "--multianno" }, doc: "input multianno file" }
   autopvs1_file: { type: 'File', inputBinding: { position: 2, prefix: "--autopvs1" }, doc: "input autopvs1 file" }
   intervar_file: { type: 'File', inputBinding: { position: 2, prefix: "--intervar" }, doc: "input intervar file" }
-  variant_summary: { type: 'File', inputBinding: { position: 2, prefix: "--variant_summary" }, doc: "variant_summary file (format: variant_summary_2023-02.txt)" }
   output_basename: { type: 'string?', default: "test", inputBinding: { position: 2, prefix: "--output" }, doc: "String to use as base for output filenames" }
   sample_id: {type: 'string', inputBinding: { position: 2, prefix: "--sample_id" }, doc: "Input sample bioassay id."}
   cpu: { type: 'int?', default: 1, doc: "CPUs to allocate to this task" }
   ram: { type: 'int?', default: 2, doc: "GB of RAM to allocate to this task" }
 outputs:
-  annotation_report: { type: 'File', outputBinding: { glob: '*.cavatica_input.annotations_report.abridged.tsv' }}
+  annotation_report: { type: 'File', outputBinding: { glob: '*.annotations_report.abridged.tsv' }}
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index ff1184f..9b5ff63 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -22,10 +22,8 @@ doc: |
   ## Inputs
 
   ```yaml
-  workflow: Indicate whether the input VCF is from a cavatica or custom workflow
   vcf_file: Input VCF file. Can be either VEP-annotated VCF file or or VEP- and ClinVar-annotated VCF file
   filter_criteria: Any additional VCF filtering criteria
-  clinvar_file: ClinVar file. Required for inputs from a custom workflow!
   intevar_file: InterVar results file
   autopsv1_file: AutoPVS1 results file
   multianno_file: ANNOVAR multianno file
@@ -46,7 +44,6 @@ doc: |
   - `output_colnames`
 
   Additionally, AutoGVP provides [a bash script](https://github.com/diskin-lab-chop/AutoGVP/blob/main/scripts/download_db_files.sh) to obtain:
-  - `clinvar_file`
   - `submission_summary_file`
   - `variant_summary_file`
 
@@ -67,11 +64,8 @@ requirements:
 - class: StepInputExpressionRequirement
 - class: MultipleInputFeatureRequirement
 inputs:
-  workflow: {type: {type: enum, symbols: ["cavatica", "custom"], name: "workflow"}, doc: "Indicate whether the input VCF is from a
-      cavatica or custom workflow"}
   vcf_file: {type: 'File', doc: "Input VCF file. Can be either VEP-annotated VCF file or or VEP- and ClinVar-annotated VCF file"}
   filter_criteria: {type: 'string[]?', doc: "Any additional VCF filtering criteria"}
-  clinvar_file: {type: 'File?', doc: "ClinVar file. Required for inputs from a custom workflow!"}
   intevar_file: {type: 'File', doc: "InterVar results file"}
   autopsv1_file: {type: 'File', doc: "AutoPVS1 results file"}
   multianno_file: {type: 'File', doc: "ANNOVAR multianno file"}
@@ -114,37 +108,16 @@ steps:
       output_basename: output_basename
       filter_criteria: filter_criteria
     out: [filtered_vcf, filtered_multianno, filtered_autopsv, filtered_intervar]
-  annotate_cavatica:
+  annotate:
     run: ../tools/autogvp_annotate_cavatica.cwl
-    when: $(inputs.workflow == "cavatica")
     in:
-      workflow: workflow
       vcf_file: filter_vcf/filtered_vcf
-      clinvar_file: clinvar_file
-      multianno_file: filter_vcf/filtered_multianno
-      autopvs1_file: filter_vcf/filtered_autopsv
-      intervar_file: filter_vcf/filtered_intervar
-      variant_summary:
+      clinvar_file:
         source: [selected_clinvar_submissions, select_clinvar_subs/clinvar_submissions]
         pickValue: first_non_null
-      output_basename: output_basename
-      sample_id: sample_id
-      cpu: annotate_cpu
-      ram: annotate_ram
-    out: [annotation_report]
-  annotate_custom:
-    run: ../tools/autogvp_annotate_custom.cwl
-    when: $(inputs.workflow == "custom")
-    in:
-      workflow: workflow
-      vcf_file: filter_vcf/filtered_vcf
-      clinvar_file: clinvar_file
       multianno_file: filter_vcf/filtered_multianno
       autopvs1_file: filter_vcf/filtered_autopsv
       intervar_file: filter_vcf/filtered_intervar
-      variant_summary:
-        source: [selected_clinvar_submissions, select_clinvar_subs/clinvar_submissions]
-        pickValue: first_non_null
       output_basename: output_basename
       sample_id: sample_id
       cpu: annotate_cpu
@@ -159,9 +132,7 @@ steps:
     run: ../tools/autogvp_filter_annotations.cwl
     in:
       vcf_file: parse_vcf/parsed_tsv
-      autogvp_file:
-        source: [annotate_cavatica/annotation_report, annotate_custom/annotation_report]
-        pickValue: the_only_non_null
+      autogvp_file: annotate/annotation_report
       colnames_file: output_colnames
       csq_subfields: parse_vcf/csq_subfields_tsv
       output_basename: output_basename

From 7750d38e0274659043fc995b96520da3ca566300 Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Mon, 27 Apr 2026 11:35:11 -0400
Subject: [PATCH 07/28] update autogvp docker to 1.0.5

---
 tools/autogvp_filter_annotations.cwl  | 2 +-
 tools/autogvp_filter_vcf.cwl          | 2 +-
 tools/autogvp_parse_vcf.cwl           | 2 +-
 tools/autogvp_select_clinvar_subs.cwl | 2 +-
 workflows/autogvp.cwl                 | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/autogvp_filter_annotations.cwl b/tools/autogvp_filter_annotations.cwl
index 8c23781..bdc7320 100644
--- a/tools/autogvp_filter_annotations.cwl
+++ b/tools/autogvp_filter_annotations.cwl
@@ -15,7 +15,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.3'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.csq_subfields)
diff --git a/tools/autogvp_filter_vcf.cwl b/tools/autogvp_filter_vcf.cwl
index a271ffe..0495461 100644
--- a/tools/autogvp_filter_vcf.cwl
+++ b/tools/autogvp_filter_vcf.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.3'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
 
 baseCommand: []
 arguments:
diff --git a/tools/autogvp_parse_vcf.cwl b/tools/autogvp_parse_vcf.cwl
index 2616812..1085497 100644
--- a/tools/autogvp_parse_vcf.cwl
+++ b/tools/autogvp_parse_vcf.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.3'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.vcf_file)
diff --git a/tools/autogvp_select_clinvar_subs.cwl b/tools/autogvp_select_clinvar_subs.cwl
index cb857f5..30a71ac 100644
--- a/tools/autogvp_select_clinvar_subs.cwl
+++ b/tools/autogvp_select_clinvar_subs.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.3'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
 
 baseCommand: []
 arguments:
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 9b5ff63..c92981e 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -56,7 +56,7 @@ doc: |
 
   ## Resources
 
-  Dockerfile: pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.3
+  Dockerfile: pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5
   AutoGVP Paper: https://doi.org/10.1093/bioinformatics/btae114
   AutoGVP GitHub: https://github.com/diskin-lab-chop/AutoGVP
 requirements:

From cfccb275428c7767ae5519d61ab3f5d7b603bce0 Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Mon, 27 Apr 2026 11:37:22 -0400
Subject: [PATCH 08/28] remove custom anno tool

---
 tools/autogvp_annotate_custom.cwl | 34 -------------------------------
 1 file changed, 34 deletions(-)
 delete mode 100644 tools/autogvp_annotate_custom.cwl

diff --git a/tools/autogvp_annotate_custom.cwl b/tools/autogvp_annotate_custom.cwl
deleted file mode 100644
index 2bdf563..0000000
--- a/tools/autogvp_annotate_custom.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.2
-class: CommandLineTool
-id: autogvp_annotate_custom
-doc: |
-  Tool for the 02-annotate_variants_custom_input.R script from AutoGVP
-requirements:
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: ResourceRequirement
-    ramMin: $(inputs.ram * 1000)
-    coresMin: $(inputs.cpu)
-  - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
-
-baseCommand: []
-arguments:
-  - position: 0
-    shellQuote: false
-    valueFrom: >-
-      Rscript /rocker-build/AutoGVP/scripts/02-annotate_variants_custom_input.R --outdir .
-
-inputs:
-  vcf_file: { type: 'File', inputBinding: { position: 2, prefix: "--vcf" }, doc: "Input vcf file with VEP annotations" }
-  clinvar_file: { type: 'File', inputBinding: { position: 2, prefix: "--clinvar" }, doc: "specific clinVar file (format: clinvar_20211225.vcf.gz)" }
-  multianno_file: { type: 'File', inputBinding: { position: 2, prefix: "--multianno" }, doc: "input multianno file" }
-  autopvs1_file: { type: 'File', inputBinding: { position: 2, prefix: "--autopvs1" }, doc: "input autopvs1 file" }
-  intervar_file: { type: 'File', inputBinding: { position: 2, prefix: "--intervar" }, doc: "input intervar file" }
-  variant_summary: { type: 'File', inputBinding: { position: 2, prefix: "--variant_summary" }, doc: "variant_summary file (format: variant_summary_2023-02.txt)" }
-  output_basename: { type: 'string?', default: "test", inputBinding: { position: 2, prefix: "--output" }, doc: "String to use as base for output filenames" }
-  sample_id: {type: 'string', inputBinding: { position: 2, prefix: "--sample_id" }, doc: "Input sample bioassay id."}
-  cpu: { type: 'int?', default: 1, doc: "CPUs to allocate to this task" }
-  ram: { type: 'int?', default: 2, doc: "GB of RAM to allocate to this task" }
-outputs:
-  annotation_report: { type: 'File', outputBinding: { glob: '*.custom_input.annotations_report.abridged.tsv' }}

From 382d5e3e36c32a10981807224393facf4d6b57cc Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Wed, 20 May 2026 12:41:48 -0400
Subject: [PATCH 09/28] CI: Add/Update workflow 'add-issues-to-project.yml' to
 manage project issues

---
 .github/workflows/add-issues-to-project.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/add-issues-to-project.yml b/.github/workflows/add-issues-to-project.yml
index ccb77d7..a2dd579 100644
--- a/.github/workflows/add-issues-to-project.yml
+++ b/.github/workflows/add-issues-to-project.yml
@@ -13,11 +13,10 @@ jobs:
     name: Add issue to project
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/add-to-project@244f685bbc3b7adfa8466e08b698b5577571133e
+      - uses: actions/add-to-project@5afcf98fcd03f1c2f92c3c83f58ae24323cc57fd #v2.0.0
         with:
           # You can target a project in a different organization or user account
           # to the issue.
           # For organization projects: https://github.com/orgs/ORG_NAME/projects/PROJECT_NUMBER
-          # For user projects: https://github.com/users/USER_NAME/projects/PROJECT_NUMBER
           project-url: https://github.com/orgs/childrens-bti/projects/1
           github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}

From a309c4a5ae9845f270efa1695cacf51050f46a7a Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Wed, 27 May 2026 15:58:17 -0400
Subject: [PATCH 10/28] update autogvp docker to 1.0.6

---
 tools/autogvp_filter_annotations.cwl  | 2 +-
 tools/autogvp_filter_vcf.cwl          | 2 +-
 tools/autogvp_parse_vcf.cwl           | 2 +-
 tools/autogvp_select_clinvar_subs.cwl | 2 +-
 workflows/autogvp.cwl                 | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/autogvp_filter_annotations.cwl b/tools/autogvp_filter_annotations.cwl
index bdc7320..ae3fef6 100644
--- a/tools/autogvp_filter_annotations.cwl
+++ b/tools/autogvp_filter_annotations.cwl
@@ -15,7 +15,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.csq_subfields)
diff --git a/tools/autogvp_filter_vcf.cwl b/tools/autogvp_filter_vcf.cwl
index 0495461..8b161d9 100644
--- a/tools/autogvp_filter_vcf.cwl
+++ b/tools/autogvp_filter_vcf.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
 
 baseCommand: []
 arguments:
diff --git a/tools/autogvp_parse_vcf.cwl b/tools/autogvp_parse_vcf.cwl
index 1085497..55f9aab 100644
--- a/tools/autogvp_parse_vcf.cwl
+++ b/tools/autogvp_parse_vcf.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.vcf_file)
diff --git a/tools/autogvp_select_clinvar_subs.cwl b/tools/autogvp_select_clinvar_subs.cwl
index 30a71ac..93d6dd7 100644
--- a/tools/autogvp_select_clinvar_subs.cwl
+++ b/tools/autogvp_select_clinvar_subs.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
 
 baseCommand: []
 arguments:
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index c92981e..c920899 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -56,7 +56,7 @@ doc: |
 
   ## Resources
 
-  Dockerfile: pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5
+  Dockerfile: pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6
   AutoGVP Paper: https://doi.org/10.1093/bioinformatics/btae114
   AutoGVP GitHub: https://github.com/diskin-lab-chop/AutoGVP
 requirements:

From 8a795fd3ee9bdec61c58961b4f876920c930f8ca Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Thu, 28 May 2026 13:10:28 -0400
Subject: [PATCH 11/28] update varname typos

---
 tools/autogvp_annotate_cavatica.cwl |  2 +-
 workflows/autogvp.cwl               | 20 ++++++++++----------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/tools/autogvp_annotate_cavatica.cwl b/tools/autogvp_annotate_cavatica.cwl
index 6b6d881..379f67f 100644
--- a/tools/autogvp_annotate_cavatica.cwl
+++ b/tools/autogvp_annotate_cavatica.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.5'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
 
 baseCommand: []
 arguments:
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index c920899..1713d09 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -24,8 +24,8 @@ doc: |
   ```yaml
   vcf_file: Input VCF file. Can be either VEP-annotated VCF file or or VEP- and ClinVar-annotated VCF file
   filter_criteria: Any additional VCF filtering criteria
-  intevar_file: InterVar results file
-  autopsv1_file: AutoPVS1 results file
+  intervar_file: InterVar results file
+  autopvs1_file: AutoPVS1 results file
   multianno_file: ANNOVAR multianno file
   output_colnames: File with column name information
   output_basename: String to use as the basename for stored outputs
@@ -37,9 +37,9 @@ doc: |
   ```
 
   The following files can be obtained from the [AutoGVP GitHub data directory](https://github.com/diskin-lab-chop/AutoGVP/tree/main/data):
-  - `autopsv1_file`
+  - `autopvs1_file`
   - `concept_ids`
-  - `intevar_file`
+  - `intervar_file`
   - `multianno_file`
   - `output_colnames`
 
@@ -66,8 +66,8 @@ requirements:
 inputs:
   vcf_file: {type: 'File', doc: "Input VCF file. Can be either VEP-annotated VCF file or or VEP- and ClinVar-annotated VCF file"}
   filter_criteria: {type: 'string[]?', doc: "Any additional VCF filtering criteria"}
-  intevar_file: {type: 'File', doc: "InterVar results file"}
-  autopsv1_file: {type: 'File', doc: "AutoPVS1 results file"}
+  intervar_file: {type: 'File', doc: "InterVar results file"}
+  autopvs1_file: {type: 'File', doc: "AutoPVS1 results file"}
   multianno_file: {type: 'File', doc: "ANNOVAR multianno file"}
   output_colnames: {type: 'File', doc: "File with column name information."}
   output_basename: {type: 'string?', default: "out", doc: "String to use as the basename for stored outputs."}
@@ -103,11 +103,11 @@ steps:
     in:
       vcf_file: vcf_file
       multianno_file: multianno_file
-      autopvs1_file: autopsv1_file
-      intervar_file: intevar_file
+      autopvs1_file: autopvs1_file
+      intervar_file: intervar_file
       output_basename: output_basename
       filter_criteria: filter_criteria
-    out: [filtered_vcf, filtered_multianno, filtered_autopsv, filtered_intervar]
+    out: [filtered_vcf, filtered_multianno, filtered_autopvs1, filtered_intervar]
   annotate:
     run: ../tools/autogvp_annotate_cavatica.cwl
     in:
@@ -116,7 +116,7 @@ steps:
         source: [selected_clinvar_submissions, select_clinvar_subs/clinvar_submissions]
         pickValue: first_non_null
       multianno_file: filter_vcf/filtered_multianno
-      autopvs1_file: filter_vcf/filtered_autopsv
+      autopvs1_file: filter_vcf/filtered_autopvs1
       intervar_file: filter_vcf/filtered_intervar
       output_basename: output_basename
       sample_id: sample_id

From 308b19e2b398788a77965f1923c3dd6be7375390 Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Thu, 28 May 2026 13:15:03 -0400
Subject: [PATCH 12/28] update filtered autopvs1 output file name

---
 tools/autogvp_filter_vcf.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/autogvp_filter_vcf.cwl b/tools/autogvp_filter_vcf.cwl
index 8b161d9..50bc719 100644
--- a/tools/autogvp_filter_vcf.cwl
+++ b/tools/autogvp_filter_vcf.cwl
@@ -34,5 +34,5 @@ inputs:
 outputs:
   filtered_vcf: { type: File, outputBinding: { glob: '*.filtered.vcf' }}
   filtered_multianno: { type: File, outputBinding: { glob: '*_multianno_filtered.txt' }}
-  filtered_autopsv: { type: File, outputBinding: { glob: '*_autopvs1_filtered.tsv' }}
+  filtered_autopvs1: { type: File, outputBinding: { glob: '*_autopvs1_filtered.tsv' }}
   filtered_intervar: { type: File, outputBinding: { glob: '*_intervar_filtered.txt' }}

From cf039af18a9e5f7c592c175f8dda82f1ab2d31f7 Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Thu, 28 May 2026 17:01:41 -0400
Subject: [PATCH 13/28] custom/default autogvp colnames input

---
 tools/autogvp_filter_annotations.cwl | 3 ++-
 workflows/autogvp.cwl                | 9 ++++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/tools/autogvp_filter_annotations.cwl b/tools/autogvp_filter_annotations.cwl
index ae3fef6..cbf929a 100644
--- a/tools/autogvp_filter_annotations.cwl
+++ b/tools/autogvp_filter_annotations.cwl
@@ -30,7 +30,8 @@ arguments:
 inputs:
   vcf_file: { type: 'File', inputBinding: { position: 2, prefix: "--vcf" }, doc: "Input filtered and parsed VEP VCF file" }
   autogvp_file: { type: 'File', inputBinding: { position: 2, prefix: "--autogvp" }, doc: "input AutoGVP annotated file" }
-  colnames_file: { type: 'File', inputBinding: { position: 2, prefix: "--colnames" }, doc: "file listing output colnames" }
+  default_colnames_file: { type: 'File', inputBinding: { position: 2, prefix: "--default_colnames" }, doc: "file listing output colnames" }
+  custom_colnames_file: { type: 'File?', inputBinding: { position: 2, prefix: "--custom_colnames" }, doc: "file listing custom output colnames" }  
   csq_subfields: { type: 'File', doc: "VCF file CSQ field names" }
   output_basename: { type: 'string?', default: "test", inputBinding: { position: 2, prefix: "--output" }, doc: "String to use as base for output filenames" }
   cpu: { type: 'int?', default: 1, doc: "CPUs to allocate to this task" }
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 1713d09..fd64df2 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -27,7 +27,8 @@ doc: |
   intervar_file: InterVar results file
   autopvs1_file: AutoPVS1 results file
   multianno_file: ANNOVAR multianno file
-  output_colnames: File with column name information
+  output_colnames: File with default column name information
+  output_custom_colnames: File with custom column name information
   output_basename: String to use as the basename for stored outputs
   selected_clinvar_submissions: ClinVar variant file with conflicts resolved. If not provided, this file will be generated in the workflow
   variant_summary_file: ClinVar variant summary file
@@ -69,7 +70,8 @@ inputs:
   intervar_file: {type: 'File', doc: "InterVar results file"}
   autopvs1_file: {type: 'File', doc: "AutoPVS1 results file"}
   multianno_file: {type: 'File', doc: "ANNOVAR multianno file"}
-  output_colnames: {type: 'File', doc: "File with column name information."}
+  output_colnames: {type: 'File', doc: "File with default column name information."}
+  output_custom_colnames: {type: 'File?', doc: "File with custom column name information."}
   output_basename: {type: 'string?', default: "out", doc: "String to use as the basename for stored outputs."}
   sample_id: {type: 'string', doc: "Input sample bioassay id."}
   selected_clinvar_submissions: {type: 'File?', doc: "ClinVar variant file with conflicts resolved. If not provided, this file will
@@ -133,7 +135,8 @@ steps:
     in:
       vcf_file: parse_vcf/parsed_tsv
       autogvp_file: annotate/annotation_report
-      colnames_file: output_colnames
+      default_colnames_file: output_colnames
+      custom_colnames_file: output_custom_colnames
       csq_subfields: parse_vcf/csq_subfields_tsv
       output_basename: output_basename
       cpu: filter_annot_cpu

From 4e6c91393beb744a2a391ae41cbcbb05ff31a976 Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Thu, 4 Jun 2026 13:24:20 -0400
Subject: [PATCH 14/28] reflect autogvp new script and file name in resolve
 clinvar submission tool

---
 tools/autogvp_select_clinvar_subs.cwl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/autogvp_select_clinvar_subs.cwl b/tools/autogvp_select_clinvar_subs.cwl
index 93d6dd7..34009dc 100644
--- a/tools/autogvp_select_clinvar_subs.cwl
+++ b/tools/autogvp_select_clinvar_subs.cwl
@@ -1,8 +1,8 @@
 cwlVersion: v1.2
 class: CommandLineTool
-id: antogvp_select_clinvar_subs
+id: autogvp_select_clinvar_subs
 doc: |
-  Tool for the select-clinVar-submissions.R script from AutoGVP
+  Tool for the resolve-clinvar-intepretations.R script from AutoGVP
 requirements:
   - class: ShellCommandRequirement
   - class: InlineJavascriptRequirement
@@ -17,7 +17,7 @@ arguments:
   - position: 0
     shellQuote: false
     valueFrom: >-
-      Rscript /rocker-build/AutoGVP/scripts/select-clinVar-submissions.R --outdir .
+      Rscript /rocker-build/AutoGVP/scripts/resolve-clinvar-intepretations.R --outdir .
 
 inputs:
   variant_summary: { type: 'File', inputBinding: { prefix: "--variant_summary", position: 2 }, doc: "ClinVar variant summary file." }
@@ -27,4 +27,4 @@ inputs:
   cpu: { type: 'int?', default: 1, doc: "CPUs to allocate to this task." }
   ram: { type: 'int?', default: 2, doc: "GB of RAM to allocate to this task." }
 outputs:
-  clinvar_submissions: { type: File, outputBinding: { glob: 'ClinVar-selected-submissions.tsv'} }
+  clinvar_submissions: { type: File, outputBinding: { glob: "resolved-clinvar-*.tsv"} }

From aeca3cc7f0382a66ee210286feadc4f8efd010f2 Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Mon, 6 Jul 2026 13:41:38 +1000
Subject: [PATCH 15/28] autogvp docker v2

---
 tools/autogvp_annotate_cavatica.cwl   | 2 +-
 tools/autogvp_filter_annotations.cwl  | 2 +-
 tools/autogvp_filter_vcf.cwl          | 2 +-
 tools/autogvp_parse_vcf.cwl           | 2 +-
 tools/autogvp_select_clinvar_subs.cwl | 2 +-
 workflows/autogvp.cwl                 | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/autogvp_annotate_cavatica.cwl b/tools/autogvp_annotate_cavatica.cwl
index 379f67f..d09d86b 100644
--- a/tools/autogvp_annotate_cavatica.cwl
+++ b/tools/autogvp_annotate_cavatica.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
 
 baseCommand: []
 arguments:
diff --git a/tools/autogvp_filter_annotations.cwl b/tools/autogvp_filter_annotations.cwl
index cbf929a..7851275 100644
--- a/tools/autogvp_filter_annotations.cwl
+++ b/tools/autogvp_filter_annotations.cwl
@@ -15,7 +15,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.csq_subfields)
diff --git a/tools/autogvp_filter_vcf.cwl b/tools/autogvp_filter_vcf.cwl
index 50bc719..17d4ee8 100644
--- a/tools/autogvp_filter_vcf.cwl
+++ b/tools/autogvp_filter_vcf.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
 
 baseCommand: []
 arguments:
diff --git a/tools/autogvp_parse_vcf.cwl b/tools/autogvp_parse_vcf.cwl
index 55f9aab..1ecabcd 100644
--- a/tools/autogvp_parse_vcf.cwl
+++ b/tools/autogvp_parse_vcf.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.vcf_file)
diff --git a/tools/autogvp_select_clinvar_subs.cwl b/tools/autogvp_select_clinvar_subs.cwl
index 34009dc..cf6fea0 100644
--- a/tools/autogvp_select_clinvar_subs.cwl
+++ b/tools/autogvp_select_clinvar_subs.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
 
 baseCommand: []
 arguments:
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index fd64df2..510caae 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -57,7 +57,7 @@ doc: |
 
   ## Resources
 
-  Dockerfile: pgc-images.sbgenomics.com/diskin-lab/autogvp:v1.0.6
+  Dockerfile: pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0
   AutoGVP Paper: https://doi.org/10.1093/bioinformatics/btae114
   AutoGVP GitHub: https://github.com/diskin-lab-chop/AutoGVP
 requirements:

From 5898fe14676f86848506e5634ea4693a1969b977 Mon Sep 17 00:00:00 2001
From: pj-sullivan <patricia.sullivan199@gmail.com>
Date: Thu, 9 Jul 2026 10:49:41 +1000
Subject: [PATCH 16/28] Suggested file inputs

---
 workflows/autogvp.cwl | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 510caae..3d40522 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -75,10 +75,14 @@ inputs:
   output_basename: {type: 'string?', default: "out", doc: "String to use as the basename for stored outputs."}
   sample_id: {type: 'string', doc: "Input sample bioassay id."}
   selected_clinvar_submissions: {type: 'File?', doc: "ClinVar variant file with conflicts resolved. If not provided, this file will
-      be generated in the workflow"}
-  variant_summary_file: {type: 'File?', doc: "ClinVar variant summary file"}
-  submission_summary_file: {type: 'File?', doc: "ClinVar submission summary file"}
-  concept_ids: {type: 'File?', doc: "File containing list of conceptIDs to prioritize submissions for ClinVar variant conflict resolution"}
+      be generated in the workflow", "sbg:suggestedValue": {class: File,
+      path: 6a29cc70b729272b1d16e328, name: resolved-clinvar-2026-06-cancer-latest.tsv}}
+  variant_summary_file: {type: 'File?', doc: "ClinVar variant summary file", "sbg:suggestedValue": {class: File,
+      path: 6a21b0c945eadc53bf786cf3, name: variant_summary_2026-06.txt.gz}}
+  submission_summary_file: {type: 'File?', doc: "ClinVar submission summary file", "sbg:suggestedValue": {class: File,
+      path: 6a21b0c945eadc53bf786cf4, name: submission_summary_2026-06.txt.gz}}
+  concept_ids: {type: 'File?', doc: "File containing list of conceptIDs to prioritize submissions for ClinVar variant conflict resolution",
+      "sbg:suggestedValue": {class: File, path: 6a21b0c945eadc53bf786cf5, name: clinvar_cancer_concept_ids_20260130.txt}}
   conflict_res: {type: ['null', {type: enum, symbols: ["latest", "most_severe"], name: "conflict_resolution"}], doc: "How to resolve
       conflicts associated with conceptIDs: latest or most_severe"}
   annotate_cpu: { type: 'int?', default: 1, doc: "CPUs to allocate to AutoGVP annotation" }

From 853221ca7b432183a68b6d223799db890f349ca8 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Wed, 15 Jul 2026 13:53:18 -0400
Subject: [PATCH 17/28] update links with v2.0.0 release

---
 workflows/autogvp.cwl                                | 2 +-
 workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 3d40522..300f8a3 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -153,7 +153,7 @@ hints:
 - class: sbg:maxNumberOfParallelInstances
   value: 2
 "sbg:links":
-- id: 'https://github.com/childrens-bti/D3b-Pathogenicity-Preprocessing-CNH/releases/tag/v1.0.0'
+- id: 'https://github.com/d3b-center/D3b-Pathogenicity-Assessment/releases/tag/v2.0.0'
   label: github-release
 sbg:license: Apache License 2.0
 sbg:publisher: KFDRC
diff --git a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
index 1a4104d..4788173 100644
--- a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
+++ b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
@@ -222,7 +222,7 @@ hints:
 - class: sbg:maxNumberOfParallelInstances
   value: 2
 "sbg:links":
-- id: 'https://github.com/childrens-bti/D3b-Pathogenicity-Preprocessing-CNH/releases/tag/v1.0.0'
+- id: 'https://github.com/d3b-center/D3b-Pathogenicity-Assessment/releases/tag/v2.0.0'
   label: github-release
 sbg:license: Apache License 2.0
 sbg:publisher: KFDRC

From 2471ea830ace5b4abc5a24edfb655a1b67a7e64b Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Tue, 21 Jul 2026 16:00:31 -0400
Subject: [PATCH 18/28] :fire: remove default col names from cwl

---
 tools/autogvp_filter_annotations.cwl | 1 -
 workflows/autogvp.cwl                | 1 -
 2 files changed, 2 deletions(-)

diff --git a/tools/autogvp_filter_annotations.cwl b/tools/autogvp_filter_annotations.cwl
index 7851275..0d7bca4 100644
--- a/tools/autogvp_filter_annotations.cwl
+++ b/tools/autogvp_filter_annotations.cwl
@@ -30,7 +30,6 @@ arguments:
 inputs:
   vcf_file: { type: 'File', inputBinding: { position: 2, prefix: "--vcf" }, doc: "Input filtered and parsed VEP VCF file" }
   autogvp_file: { type: 'File', inputBinding: { position: 2, prefix: "--autogvp" }, doc: "input AutoGVP annotated file" }
-  default_colnames_file: { type: 'File', inputBinding: { position: 2, prefix: "--default_colnames" }, doc: "file listing output colnames" }
   custom_colnames_file: { type: 'File?', inputBinding: { position: 2, prefix: "--custom_colnames" }, doc: "file listing custom output colnames" }  
   csq_subfields: { type: 'File', doc: "VCF file CSQ field names" }
   output_basename: { type: 'string?', default: "test", inputBinding: { position: 2, prefix: "--output" }, doc: "String to use as base for output filenames" }
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 3d40522..5e51dc2 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -70,7 +70,6 @@ inputs:
   intervar_file: {type: 'File', doc: "InterVar results file"}
   autopvs1_file: {type: 'File', doc: "AutoPVS1 results file"}
   multianno_file: {type: 'File', doc: "ANNOVAR multianno file"}
-  output_colnames: {type: 'File', doc: "File with default column name information."}
   output_custom_colnames: {type: 'File?', doc: "File with custom column name information."}
   output_basename: {type: 'string?', default: "out", doc: "String to use as the basename for stored outputs."}
   sample_id: {type: 'string', doc: "Input sample bioassay id."}

From 3a25dfb9df738f787be970e3fddd2c804658f3a6 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Tue, 21 Jul 2026 16:35:42 -0400
Subject: [PATCH 19/28] :fire: remove more default colnames

---
 workflows/autogvp.cwl | 2 --
 1 file changed, 2 deletions(-)

diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 5e51dc2..70eb71f 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -27,7 +27,6 @@ doc: |
   intervar_file: InterVar results file
   autopvs1_file: AutoPVS1 results file
   multianno_file: ANNOVAR multianno file
-  output_colnames: File with default column name information
   output_custom_colnames: File with custom column name information
   output_basename: String to use as the basename for stored outputs
   selected_clinvar_submissions: ClinVar variant file with conflicts resolved. If not provided, this file will be generated in the workflow
@@ -138,7 +137,6 @@ steps:
     in:
       vcf_file: parse_vcf/parsed_tsv
       autogvp_file: annotate/annotation_report
-      default_colnames_file: output_colnames
       custom_colnames_file: output_custom_colnames
       csq_subfields: parse_vcf/csq_subfields_tsv
       output_basename: output_basename

From 4c37bb5ad37e54a495e6753a8351d0b131e4b15f Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Fri, 24 Jul 2026 10:50:26 -0400
Subject: [PATCH 20/28] :whale: update autopvs1 and autogvp dockers to latest
 versions

---
 tools/autogvp_annotate_cavatica.cwl   | 2 +-
 tools/autogvp_filter_annotations.cwl  | 2 +-
 tools/autogvp_filter_vcf.cwl          | 2 +-
 tools/autogvp_parse_vcf.cwl           | 2 +-
 tools/autogvp_select_clinvar_subs.cwl | 2 +-
 tools/compress_annovar_output.cwl     | 2 +-
 workflows/autogvp.cwl                 | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/tools/autogvp_annotate_cavatica.cwl b/tools/autogvp_annotate_cavatica.cwl
index d09d86b..a61e47a 100644
--- a/tools/autogvp_annotate_cavatica.cwl
+++ b/tools/autogvp_annotate_cavatica.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.1'
 
 baseCommand: []
 arguments:
diff --git a/tools/autogvp_filter_annotations.cwl b/tools/autogvp_filter_annotations.cwl
index 0d7bca4..1d75ca9 100644
--- a/tools/autogvp_filter_annotations.cwl
+++ b/tools/autogvp_filter_annotations.cwl
@@ -15,7 +15,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.1'
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.csq_subfields)
diff --git a/tools/autogvp_filter_vcf.cwl b/tools/autogvp_filter_vcf.cwl
index 17d4ee8..a9e56ab 100644
--- a/tools/autogvp_filter_vcf.cwl
+++ b/tools/autogvp_filter_vcf.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.1'
 
 baseCommand: []
 arguments:
diff --git a/tools/autogvp_parse_vcf.cwl b/tools/autogvp_parse_vcf.cwl
index 1ecabcd..dbdb7a9 100644
--- a/tools/autogvp_parse_vcf.cwl
+++ b/tools/autogvp_parse_vcf.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.1'
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.vcf_file)
diff --git a/tools/autogvp_select_clinvar_subs.cwl b/tools/autogvp_select_clinvar_subs.cwl
index cf6fea0..58f8c74 100644
--- a/tools/autogvp_select_clinvar_subs.cwl
+++ b/tools/autogvp_select_clinvar_subs.cwl
@@ -10,7 +10,7 @@ requirements:
     ramMin: $(inputs.ram * 1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0'
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.1'
 
 baseCommand: []
 arguments:
diff --git a/tools/compress_annovar_output.cwl b/tools/compress_annovar_output.cwl
index 4e1a7ad..3527204 100644
--- a/tools/compress_annovar_output.cwl
+++ b/tools/compress_annovar_output.cwl
@@ -9,7 +9,7 @@ requirements:
     ramMin: 16000
     coresMin: 8
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/autopvs1:v1.0.1'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/autopvs1:v2.0.0'
 
 baseCommand: [pigz, -c, -p 8]
 arguments:
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 70eb71f..4aa6ec4 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -56,7 +56,7 @@ doc: |
 
   ## Resources
 
-  Dockerfile: pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.0
+  Dockerfile: pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.1
   AutoGVP Paper: https://doi.org/10.1093/bioinformatics/btae114
   AutoGVP GitHub: https://github.com/diskin-lab-chop/AutoGVP
 requirements:

From 03331d124a25256a771403c3ad7ae75861522f81 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Fri, 24 Jul 2026 14:03:48 -0400
Subject: [PATCH 21/28] rename output colnames input again

---
 tools/autogvp_filter_annotations.cwl | 2 +-
 workflows/autogvp.cwl                | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/autogvp_filter_annotations.cwl b/tools/autogvp_filter_annotations.cwl
index 1d75ca9..6c1c9ba 100644
--- a/tools/autogvp_filter_annotations.cwl
+++ b/tools/autogvp_filter_annotations.cwl
@@ -30,7 +30,7 @@ arguments:
 inputs:
   vcf_file: { type: 'File', inputBinding: { position: 2, prefix: "--vcf" }, doc: "Input filtered and parsed VEP VCF file" }
   autogvp_file: { type: 'File', inputBinding: { position: 2, prefix: "--autogvp" }, doc: "input AutoGVP annotated file" }
-  custom_colnames_file: { type: 'File?', inputBinding: { position: 2, prefix: "--custom_colnames" }, doc: "file listing custom output colnames" }  
+  output_colnames_file: { type: 'File?', inputBinding: { position: 2, prefix: "--output_colnames" }, doc: "file listing custom output colnames" }
   csq_subfields: { type: 'File', doc: "VCF file CSQ field names" }
   output_basename: { type: 'string?', default: "test", inputBinding: { position: 2, prefix: "--output" }, doc: "String to use as base for output filenames" }
   cpu: { type: 'int?', default: 1, doc: "CPUs to allocate to this task" }
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 4aa6ec4..7d32fff 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -27,7 +27,7 @@ doc: |
   intervar_file: InterVar results file
   autopvs1_file: AutoPVS1 results file
   multianno_file: ANNOVAR multianno file
-  output_custom_colnames: File with custom column name information
+  output_colnames: File with custom column name information
   output_basename: String to use as the basename for stored outputs
   selected_clinvar_submissions: ClinVar variant file with conflicts resolved. If not provided, this file will be generated in the workflow
   variant_summary_file: ClinVar variant summary file
@@ -69,7 +69,7 @@ inputs:
   intervar_file: {type: 'File', doc: "InterVar results file"}
   autopvs1_file: {type: 'File', doc: "AutoPVS1 results file"}
   multianno_file: {type: 'File', doc: "ANNOVAR multianno file"}
-  output_custom_colnames: {type: 'File?', doc: "File with custom column name information."}
+  output_colnames: {type: 'File?', doc: "File with custom column name information."}
   output_basename: {type: 'string?', default: "out", doc: "String to use as the basename for stored outputs."}
   sample_id: {type: 'string', doc: "Input sample bioassay id."}
   selected_clinvar_submissions: {type: 'File?', doc: "ClinVar variant file with conflicts resolved. If not provided, this file will
@@ -137,7 +137,7 @@ steps:
     in:
       vcf_file: parse_vcf/parsed_tsv
       autogvp_file: annotate/annotation_report
-      custom_colnames_file: output_custom_colnames
+      output_colnames_file: output_colnames
       csq_subfields: parse_vcf/csq_subfields_tsv
       output_basename: output_basename
       cpu: filter_annot_cpu

From ef1c2034a6c9ccb74969a81cae2cde2b1290a6a0 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Tue, 28 Jul 2026 15:15:43 -0400
Subject: [PATCH 22/28] update reference file ids and add update_intervar step

---
 tools/autogvp_update_intervar.cwl | 28 ++++++++++++++++++++++++++++
 workflows/autogvp.cwl             | 21 ++++++++++++++++-----
 2 files changed, 44 insertions(+), 5 deletions(-)
 create mode 100644 tools/autogvp_update_intervar.cwl

diff --git a/tools/autogvp_update_intervar.cwl b/tools/autogvp_update_intervar.cwl
new file mode 100644
index 0000000..e75568a
--- /dev/null
+++ b/tools/autogvp_update_intervar.cwl
@@ -0,0 +1,28 @@
+cwlVersion: v1.2
+class: CommandLineTool
+id: autogvp_filter_vcf
+doc: |
+  Tool for the 01-filter_vcf script from AutoGVP
+requirements:
+  - class: ShellCommandRequirement
+  - class: InlineJavascriptRequirement
+  - class: ResourceRequirement
+    ramMin: $(inputs.ram * 1000)
+    coresMin: $(inputs.cpu)
+  - class: DockerRequirement
+    dockerPull: 'pgc-images.sbgenomics.com/diskin-lab/autogvp:v2.0.1'
+
+baseCommand: []
+arguments:
+  - position: 0
+    shellQuote: false
+    valueFrom: >-
+      bash /rocker-build/AutoGVP/scripts/update_intervar.R
+
+inputs:
+  vcf_file: { type: 'File', inputBinding: { position: 3 }, doc: "VCF file to filter" }
+  multianno_file: { type: 'File', inputBinding: { position: 4 }, doc: "multianno file" }
+  autopvs1_file: { type: 'File', inputBinding: { position: 5 }, doc: "autopvs1 results file" }
+  intervar_file: { type: 'File', inputBinding: { position: 6 }, doc: "intervar results file" }
+outputs:
+  updated_intervar: { type: File, outputBinding: { glob: '*updated*' }}
diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 7d32fff..5a23b68 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -74,13 +74,15 @@ inputs:
   sample_id: {type: 'string', doc: "Input sample bioassay id."}
   selected_clinvar_submissions: {type: 'File?', doc: "ClinVar variant file with conflicts resolved. If not provided, this file will
       be generated in the workflow", "sbg:suggestedValue": {class: File,
-      path: 6a29cc70b729272b1d16e328, name: resolved-clinvar-2026-06-cancer-latest.tsv}}
+      path: 6a322ff1b729272b1d1bbea4, name: resolved-clinvar-2026-06-cancer-latest.tsv}}
   variant_summary_file: {type: 'File?', doc: "ClinVar variant summary file", "sbg:suggestedValue": {class: File,
-      path: 6a21b0c945eadc53bf786cf3, name: variant_summary_2026-06.txt.gz}}
+      path: 6a322ff1b729272b1d1bbe9b, name: variant_summary_2026-06.txt.gz}}
+  clinvar_hgvs4_file: {type: 'File?', doc: "ClinVar hgvs4 file with amino acid changes", "sbg:suggestedValue": {class: File,
+      path: 6a68726f08505474f85a109b, name: hgvs4variation-2026-07.txt.gz}}
   submission_summary_file: {type: 'File?', doc: "ClinVar submission summary file", "sbg:suggestedValue": {class: File,
-      path: 6a21b0c945eadc53bf786cf4, name: submission_summary_2026-06.txt.gz}}
+      path: 6a322ff1b729272b1d1bbea2, name: submission_summary_2026-06.txt.gz}}
   concept_ids: {type: 'File?', doc: "File containing list of conceptIDs to prioritize submissions for ClinVar variant conflict resolution",
-      "sbg:suggestedValue": {class: File, path: 6a21b0c945eadc53bf786cf5, name: clinvar_cancer_concept_ids_20260130.txt}}
+      "sbg:suggestedValue": {class: File, path: 6a322ff1b729272b1d1bbe93, name: clinvar_cancer_concept_ids_20260130.txt}}
   conflict_res: {type: ['null', {type: enum, symbols: ["latest", "most_severe"], name: "conflict_resolution"}], doc: "How to resolve
       conflicts associated with conceptIDs: latest or most_severe"}
   annotate_cpu: { type: 'int?', default: 1, doc: "CPUs to allocate to AutoGVP annotation" }
@@ -112,6 +114,15 @@ steps:
       output_basename: output_basename
       filter_criteria: filter_criteria
     out: [filtered_vcf, filtered_multianno, filtered_autopvs1, filtered_intervar]
+  update_intervar:
+    run: ../tools/update_intervar.cwl
+    in:
+      intervar_file: filter_vcf/filtered_intervar
+      clinvar_file:
+        source: [selected_clinvar_submissions, select_clinvar_subs/clinvar_submissions]
+        pickValue: first_non_null
+      clinvar_hgvs4_file: clinvar_hgvs4_file
+    out: [updated_intervar]
   annotate:
     run: ../tools/autogvp_annotate_cavatica.cwl
     in:
@@ -121,7 +132,7 @@ steps:
         pickValue: first_non_null
       multianno_file: filter_vcf/filtered_multianno
       autopvs1_file: filter_vcf/filtered_autopvs1
-      intervar_file: filter_vcf/filtered_intervar
+      intervar_file: update_intervar/updated_intervar
       output_basename: output_basename
       sample_id: sample_id
       cpu: annotate_cpu

From 4a1d0afa963485efca20d57fb7d28392cf962328 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Tue, 28 Jul 2026 15:18:00 -0400
Subject: [PATCH 23/28] use correct tool name

---
 workflows/autogvp.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index 5a23b68..d7bd231 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -115,7 +115,7 @@ steps:
       filter_criteria: filter_criteria
     out: [filtered_vcf, filtered_multianno, filtered_autopvs1, filtered_intervar]
   update_intervar:
-    run: ../tools/update_intervar.cwl
+    run: ../tools/autogvp_update_intervar.cwl
     in:
       intervar_file: filter_vcf/filtered_intervar
       clinvar_file:

From 925ed0c3a7c2fb2a702c40d40ca3a3bdecd91e90 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Tue, 28 Jul 2026 15:47:35 -0400
Subject: [PATCH 24/28] fix inputs

---
 tools/autogvp_update_intervar.cwl | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tools/autogvp_update_intervar.cwl b/tools/autogvp_update_intervar.cwl
index e75568a..2ba2b5c 100644
--- a/tools/autogvp_update_intervar.cwl
+++ b/tools/autogvp_update_intervar.cwl
@@ -20,9 +20,8 @@ arguments:
       bash /rocker-build/AutoGVP/scripts/update_intervar.R
 
 inputs:
-  vcf_file: { type: 'File', inputBinding: { position: 3 }, doc: "VCF file to filter" }
-  multianno_file: { type: 'File', inputBinding: { position: 4 }, doc: "multianno file" }
-  autopvs1_file: { type: 'File', inputBinding: { position: 5 }, doc: "autopvs1 results file" }
-  intervar_file: { type: 'File', inputBinding: { position: 6 }, doc: "intervar results file" }
+  intervar_file: { type: 'File', inputBinding: { position: 2, prefix: "--intervar_file" }, doc: "intervar results file" }
+  clinvar_file: { type: 'File', inputBinding: { position: 2, prefix: "--clinvar_file" }, doc: "ClinVar resolved clinical significance file (format: resolved-clinvar-interpretations.tsv)" }
+  clinvar_hgvs4_file: { type: 'File', inputBinding: { position: 2, prefix: "--clinvar_hgvs4_file" }, doc: "ClinVar hgvs4 file with amino acid changes" }
 outputs:
   updated_intervar: { type: File, outputBinding: { glob: '*updated*' }}

From e58e24f858ce3c920c3e3f8f66df0d55abba12da Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Tue, 28 Jul 2026 16:40:16 -0400
Subject: [PATCH 25/28] run the rscript as an Rscript

---
 tools/autogvp_update_intervar.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/autogvp_update_intervar.cwl b/tools/autogvp_update_intervar.cwl
index 2ba2b5c..97b00ff 100644
--- a/tools/autogvp_update_intervar.cwl
+++ b/tools/autogvp_update_intervar.cwl
@@ -17,7 +17,7 @@ arguments:
   - position: 0
     shellQuote: false
     valueFrom: >-
-      bash /rocker-build/AutoGVP/scripts/update_intervar.R
+      Rscript /rocker-build/AutoGVP/scripts/update_intervar.R
 
 inputs:
   intervar_file: { type: 'File', inputBinding: { position: 2, prefix: "--intervar_file" }, doc: "intervar results file" }

From d022f16f10ab07a1690fbec2301b4d839a753271 Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Tue, 28 Jul 2026 16:50:52 -0400
Subject: [PATCH 26/28] update result dir

---
 tools/autogvp_update_intervar.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/autogvp_update_intervar.cwl b/tools/autogvp_update_intervar.cwl
index 97b00ff..16e9d85 100644
--- a/tools/autogvp_update_intervar.cwl
+++ b/tools/autogvp_update_intervar.cwl
@@ -17,7 +17,7 @@ arguments:
   - position: 0
     shellQuote: false
     valueFrom: >-
-      Rscript /rocker-build/AutoGVP/scripts/update_intervar.R
+      Rscript /rocker-build/AutoGVP/scripts/update_intervar.R --outdir .
 
 inputs:
   intervar_file: { type: 'File', inputBinding: { position: 2, prefix: "--intervar_file" }, doc: "intervar results file" }

From 973e75fb214828fd78994aa50c2eec5def38708d Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Wed, 15 Jul 2026 13:53:18 -0400
Subject: [PATCH 27/28] update links with v2.0.0 release

---
 workflows/autogvp.cwl                                | 2 +-
 workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/autogvp.cwl b/workflows/autogvp.cwl
index d7bd231..d5f4dc7 100644
--- a/workflows/autogvp.cwl
+++ b/workflows/autogvp.cwl
@@ -161,7 +161,7 @@ hints:
 - class: sbg:maxNumberOfParallelInstances
   value: 2
 "sbg:links":
-- id: 'https://github.com/childrens-bti/D3b-Pathogenicity-Preprocessing-CNH/releases/tag/v1.0.0'
+- id: 'https://github.com/d3b-center/D3b-Pathogenicity-Assessment/releases/tag/v2.0.0'
   label: github-release
 sbg:license: Apache License 2.0
 sbg:publisher: KFDRC
diff --git a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
index 1a4104d..4788173 100644
--- a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
+++ b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl
@@ -222,7 +222,7 @@ hints:
 - class: sbg:maxNumberOfParallelInstances
   value: 2
 "sbg:links":
-- id: 'https://github.com/childrens-bti/D3b-Pathogenicity-Preprocessing-CNH/releases/tag/v1.0.0'
+- id: 'https://github.com/d3b-center/D3b-Pathogenicity-Assessment/releases/tag/v2.0.0'
   label: github-release
 sbg:license: Apache License 2.0
 sbg:publisher: KFDRC

From e1937aaad0cca4388d70668337ea97a68773b60e Mon Sep 17 00:00:00 2001
From: Alex Sickler <sickler.alex@gmail.com>
Date: Thu, 30 Jul 2026 12:00:13 -0400
Subject: [PATCH 28/28] update readme to point to d3b repo

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 97a1059..c1c1dbf 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Pathogenicity Preprocessing Workflow
 This repo makes use of the git submodule feature for ease of code maintenance. To properly retrieve all relevant code:
 ```sh
-git clone  https://github.com/childrens-bti/D3b-Pathogenicity-Preprocessing-CNH
+git clone https://github.com/d3b-center/D3b-Pathogenicity-Preprocessing
 git submodule init
 git submodule update
 ```