From 193468c8c2f1183f6f6ade25ac2861800ab7f3f2 Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Thu, 13 Feb 2025 14:38:45 -0500
Subject: [PATCH 1/3] cicd: add publish action

---
 .github/workflows/publish.yaml | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 .github/workflows/publish.yaml

diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
new file mode 100644
index 0000000..4628e0b
--- /dev/null
+++ b/.github/workflows/publish.yaml
@@ -0,0 +1,34 @@
+name: publish to GHCR
+on:
+  release:
+    types: [published]
+jobs:
+  publish-image:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          push: true
+          tags: |
+            ghcr.io/${{ github.repository_owner }}/vrsix:${{ github.event.release.tag_name }}
+            ghcr.io/${{ github.repository_owner }}/vrsix:latest

From 5a735d0f779cee2a518adcb716f1a897a860cc0b Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Fri, 14 Feb 2025 14:58:37 -0500
Subject: [PATCH 2/3] more

---
 .github/workflows/publish.yaml | 23 ++++++++---------------
 1 file changed, 8 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
index 4628e0b..e580e71 100644
--- a/.github/workflows/publish.yaml
+++ b/.github/workflows/publish.yaml
@@ -8,8 +8,11 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
@@ -17,18 +20,8 @@ jobs:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
-      - name: Log in to GitHub Container Registry
-        uses: docker/login-action@v3
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v4
+      - name: Build and push
+        uses: docker/build-push-action@v6
         with:
-          context: .
           push: true
-          tags: |
-            ghcr.io/${{ github.repository_owner }}/vrsix:${{ github.event.release.tag_name }}
-            ghcr.io/${{ github.repository_owner }}/vrsix:latest
+          tags: user/app:latest

From 437cc8cbca814436a940d7208e5ae6971c309c21 Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Fri, 14 Feb 2025 15:54:32 -0500
Subject: [PATCH 3/3] stashing progress

---
 .github/workflows/publish.yaml |   9 +-
 containers/base/Dockerfile     |   3 +-
 test/GIAB_sample_annotated.vcf | 245 +++++++++++++++++++++++++++++++++
 test/test_index_input.db       | Bin 0 -> 24576 bytes
 test/test_inputs.json          |   4 +
 test/test_vcf_input.vcf        |   0
 vrsix-construct.wdl            |   6 +-
 7 files changed, 258 insertions(+), 9 deletions(-)
 create mode 100644 test/GIAB_sample_annotated.vcf
 create mode 100644 test/test_index_input.db
 create mode 100644 test/test_vcf_input.vcf

diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
index e580e71..f0ac187 100644
--- a/.github/workflows/publish.yaml
+++ b/.github/workflows/publish.yaml
@@ -8,11 +8,12 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Login to Docker Hub
+      - name: Login to GHCR
         uses: docker/login-action@v3
         with:
-          username: ${{ vars.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
+          registry: ghcr.io
+          username: gks-anvil
+          password: ${{ secrets.GHCR_TOKEN }}
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
@@ -24,4 +25,4 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           push: true
-          tags: user/app:latest
+          tags: ghcr.io/gks-anvil/vrsix-workflow:latest
diff --git a/containers/base/Dockerfile b/containers/base/Dockerfile
index c777a9d..cfbf873 100644
--- a/containers/base/Dockerfile
+++ b/containers/base/Dockerfile
@@ -1,5 +1,4 @@
-# TODO python version
-from circleci/python:3.12
+FROM cimg/python:3.12
 
 RUN pip install vrsix~=0.1.2
 
diff --git a/test/GIAB_sample_annotated.vcf b/test/GIAB_sample_annotated.vcf
new file mode 100644
index 0000000..627f6c5
--- /dev/null
+++ b/test/GIAB_sample_annotated.vcf
@@ -0,0 +1,245 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20160824
+##CL=vcffilter -i - -o - --javascript "function record() {HG001.PS=\".\";}"
+##contig=<ID=chr1,length=248956422,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr2,length=242193529,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr3,length=198295559,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr4,length=190214555,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr5,length=181538259,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr6,length=170805979,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr7,length=159345973,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr8,length=145138636,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr9,length=138394717,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr10,length=133797422,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr11,length=135086622,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr12,length=133275309,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr13,length=114364328,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr14,length=107043718,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr15,length=101991189,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr16,length=90338345,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr17,length=83257441,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr18,length=80373285,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr19,length=58617616,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr20,length=64444167,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr21,length=46709983,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22,length=50818468,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrX,length=156040895,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrY,length=57227415,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrM,length=16569,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr1_KI270706v1_random,length=175055,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr1_KI270707v1_random,length=32032,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr1_KI270708v1_random,length=127682,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr1_KI270709v1_random,length=66860,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr1_KI270710v1_random,length=40176,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr1_KI270711v1_random,length=42210,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr1_KI270712v1_random,length=176043,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr1_KI270713v1_random,length=40745,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr1_KI270714v1_random,length=41717,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr2_KI270715v1_random,length=161471,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr2_KI270716v1_random,length=153799,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr3_GL000221v1_random,length=155397,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr4_GL000008v2_random,length=209709,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr5_GL000208v1_random,length=92689,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr9_KI270717v1_random,length=40062,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr9_KI270718v1_random,length=38054,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr9_KI270719v1_random,length=176845,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr9_KI270720v1_random,length=39050,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr11_KI270721v1_random,length=100316,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr14_GL000009v2_random,length=201709,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr14_GL000225v1_random,length=211173,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr14_KI270722v1_random,length=194050,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr14_GL000194v1_random,length=191469,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr14_KI270723v1_random,length=38115,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr14_KI270724v1_random,length=39555,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr14_KI270725v1_random,length=172810,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr14_KI270726v1_random,length=43739,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr15_KI270727v1_random,length=448248,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr16_KI270728v1_random,length=1872759,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr17_GL000205v2_random,length=185591,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr17_KI270729v1_random,length=280839,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr17_KI270730v1_random,length=112551,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22_KI270731v1_random,length=150754,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22_KI270732v1_random,length=41543,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22_KI270733v1_random,length=179772,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22_KI270734v1_random,length=165050,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22_KI270735v1_random,length=42811,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22_KI270736v1_random,length=181920,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22_KI270737v1_random,length=103838,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22_KI270738v1_random,length=99375,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chr22_KI270739v1_random,length=73985,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrY_KI270740v1_random,length=37240,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270302v1,length=2274,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270304v1,length=2165,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270303v1,length=1942,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270305v1,length=1472,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270322v1,length=21476,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270320v1,length=4416,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270310v1,length=1201,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270316v1,length=1444,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270315v1,length=2276,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270312v1,length=998,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270311v1,length=12399,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270317v1,length=37690,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270412v1,length=1179,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270411v1,length=2646,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270414v1,length=2489,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270419v1,length=1029,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270418v1,length=2145,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270420v1,length=2321,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270424v1,length=2140,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270417v1,length=2043,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270422v1,length=1445,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270423v1,length=981,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270425v1,length=1884,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270429v1,length=1361,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270442v1,length=392061,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270466v1,length=1233,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270465v1,length=1774,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270467v1,length=3920,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270435v1,length=92983,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270438v1,length=112505,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270468v1,length=4055,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270510v1,length=2415,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270509v1,length=2318,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270518v1,length=2186,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270508v1,length=1951,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270516v1,length=1300,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270512v1,length=22689,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270519v1,length=138126,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270522v1,length=5674,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270511v1,length=8127,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270515v1,length=6361,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270507v1,length=5353,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270517v1,length=3253,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270529v1,length=1899,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270528v1,length=2983,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270530v1,length=2168,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270539v1,length=993,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270538v1,length=91309,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270544v1,length=1202,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270548v1,length=1599,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270583v1,length=1400,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270587v1,length=2969,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270580v1,length=1553,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270581v1,length=7046,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270579v1,length=31033,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270589v1,length=44474,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270590v1,length=4685,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270584v1,length=4513,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270582v1,length=6504,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270588v1,length=6158,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270593v1,length=3041,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270591v1,length=5796,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270330v1,length=1652,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270329v1,length=1040,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270334v1,length=1368,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270333v1,length=2699,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270335v1,length=1048,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270338v1,length=1428,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270340v1,length=1428,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270336v1,length=1026,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270337v1,length=1121,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270363v1,length=1803,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270364v1,length=2855,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270362v1,length=3530,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270366v1,length=8320,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270378v1,length=1048,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270379v1,length=1045,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270389v1,length=1298,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270390v1,length=2387,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270387v1,length=1537,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270395v1,length=1143,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270396v1,length=1880,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270388v1,length=1216,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270394v1,length=970,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270386v1,length=1788,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270391v1,length=1484,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270383v1,length=1750,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270393v1,length=1308,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270384v1,length=1658,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270392v1,length=971,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270381v1,length=1930,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270385v1,length=990,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270382v1,length=4215,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270376v1,length=1136,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270374v1,length=2656,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270372v1,length=1650,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270373v1,length=1451,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270375v1,length=2378,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270371v1,length=2805,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270448v1,length=7992,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270521v1,length=7642,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_GL000195v1,length=182896,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_GL000219v1,length=179198,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_GL000220v1,length=161802,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_GL000224v1,length=179693,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270741v1,length=157432,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_GL000226v1,length=15008,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_GL000213v1,length=164239,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270743v1,length=210658,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270744v1,length=168472,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270745v1,length=41891,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270746v1,length=66486,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270747v1,length=198735,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270748v1,length=93321,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270749v1,length=158759,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270750v1,length=148850,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270751v1,length=150742,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270752v1,length=27745,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270753v1,length=62944,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270754v1,length=40191,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270755v1,length=36723,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270756v1,length=79590,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270757v1,length=71251,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_GL000214v1,length=137718,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_KI270742v1,length=186739,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_GL000216v2,length=176608,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrUn_GL000218v1,length=161147,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##contig=<ID=chrEBV,length=171823,assembly=human_GRCh38_no_alt_analysis_set.fasta>
+##FILTER=<ID=GQlessthan70,Description="Sum of GQ for datasets with this genotype less than 70">
+##FILTER=<ID=allfilteredanddisagree,Description="All callsets have this call filtered or outside the callable regions and they have discordant genotypes or variant calls">
+##FILTER=<ID=allfilteredbutagree,Description="All callsets have this call filtered or outside the callable regions but they have the same genotype">
+##FILTER=<ID=discordantunfiltered,Description="Callsets with unfiltered calls have discordant genotypes or variant calls">
+##FILTER=<ID=discordanthet,Description="Filtered calls where a passing call is het and a high GQ but filtered call is hom var, since often the het is wrong">
+##FILTER=<ID=questionableindel,Description="Filtered calls where some callsets have a filtered indel larger than 10bp and another dataset has an implied homozygous reference call">
+##FILTER=<ID=cgonly,Description="Filtered calls where only Complete Genomics had this call and it was completely missing from any other callset">
+##FILTER=<ID=alleleimbalance,Description="Filtered calls where the net allele balance for unfiltered datasets is <0.2 or >0.8">
+##FILTER=<ID=overlappingcall,Description="Filtered sites that are within 50bp of another passing call but none of the callsets that support the 2 calls match">
+##INFO=<ID=DPSum,Number=1,Type=Integer,Description="Total read depth summed across all datasets, excluding MQ0 reads">
+##INFO=<ID=platforms,Number=1,Type=Integer,Description="Number of different platforms for which at least one callset called this genotype, whether filtered or not">
+##INFO=<ID=platformnames,Number=.,Type=String,Description="Names of platforms for which at least one callset called this genotype, whether filtered or not">
+##INFO=<ID=platformbias,Number=.,Type=String,Description="Names of platforms that have reads containing a variant at this location, but the high-confidence call is homozygous reference, indicating that there is a potential bias.">
+##INFO=<ID=datasets,Number=1,Type=Integer,Description="Number of different datasets for which at least one callset called this genotype, whether filtered or not">
+##INFO=<ID=datasetnames,Number=.,Type=String,Description="Names of datasets for which at least one callset called this genotype, whether filtered or not">
+##INFO=<ID=datasetsmissingcall,Number=.,Type=String,Description="Names of datasets that are missing a call or have an incorrect call at this location, and the high-confidence call is a variant">
+##INFO=<ID=callsets,Number=1,Type=Integer,Description="Number of different callsets that called this genotype, whether filtered or not">
+##INFO=<ID=callsetnames,Number=.,Type=String,Description="Names of callsets that called this genotype, whether filtered or not">
+##INFO=<ID=varType,Number=1,Type=String,Description="Type of variant">
+##INFO=<ID=filt,Number=.,Type=String,Description="List of callsets that had this call filtered.">
+##INFO=<ID=callable,Number=.,Type=String,Description="List of callsets that had this call in a region with low coverage of high MQ reads.">
+##INFO=<ID=difficultregion,Number=.,Type=String,Description="List of difficult region bed files containing this call.">
+##INFO=<ID=arbitrated,Number=1,Type=String,Description="TRUE if callsets had discordant calls so that arbitration was needed.">
+##INFO=<ID=callsetwiththisuniqgenopassing,Number=.,Type=String,Description="Callset that uniquely calls the PASSing genotype in GT when 2+ PASSing callsets support a different genotype.">
+##INFO=<ID=callsetwithotheruniqgenopassing,Number=.,Type=String,Description="Callset that uniquely calls a PASSing genotype different from GT when 2+ PASSing callsets support the genotype in GT.">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth summed across all datasets, excluding MQ0 reads">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Net Genotype quality across all datasets, calculated from GQ scores of callsets supporting the consensus GT, using only one callset from each dataset">
+##FORMAT=<ID=ADALL,Number=R,Type=Integer,Description="Net allele depths across all datasets">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Net allele depths across all unfiltered datasets with called genotype">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Consensus Genotype across all datasets with called genotype">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase set in which this variant falls">
+##INFO=<ID=VRS_Allele_IDs,Number=R,Type=String,Description="The computed identifiers for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles">
+##INFO=<ID=VRS_Error,Number=.,Type=String,Description="If an error occurred computing a VRS Identifier, the error message">
+##INFO=<ID=VRS_Starts,Number=R,Type=String,Description="Interresidue coordinates used as the location starts for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles">
+##INFO=<ID=VRS_Ends,Number=R,Type=String,Description="Interresidue coordinates used as the location ends for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles">
+##INFO=<ID=VRS_States,Number=R,Type=String,Description="The literal sequence states used for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG001
+chr1	783006	.	A	G	50	PASS	platforms=4;platformnames=PacBio,Illumina,10X,CG;datasets=4;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR,CGnormal;callsets=6;callsetnames=CCS15kb_20kbDV,CCS15kb_20kbGATK4,HiSeqPE300xGATK,10XLRGATK,CGnormal,HiSeqPE300xfreebayes;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable;filt=CS_CGnormal_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged,lowmappabilityall;VRS_Allele_IDs=ga4gh:VA.dwwiZdvVtfAmomu0OBsiHue1O-bw5SpG,ga4gh:VA.MiasxyXMXtOpsZgGelL3c4QgtflCNLHD;VRS_Starts=783005,783005;VRS_Ends=783006,783006;VRS_States=A,G	GT:PS:DP:ADALL:AD:GQ	1/1:.:652:16,234:0,82:312
+chr1	783175	.	T	C	50	PASS	platforms=4;platformnames=PacBio,Illumina,10X,Solid;datasets=4;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR,SolidSE75bp;callsets=6;callsetnames=CCS15kb_20kbDV,CCS15kb_20kbGATK4,HiSeqPE300xGATK,10XLRGATK,HiSeqPE300xfreebayes,SolidSE75GATKHC;datasetsmissingcall=CGnormal,IonExome;callable=CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged;VRS_Allele_IDs=ga4gh:VA.5cY2k53xdW7WeHw2WG1HA7jl50iH-r9p,ga4gh:VA.jHaXepIvlbnapfPtH_62y-Qm81hCrBYn;VRS_Starts=783174,783174;VRS_Ends=783175,783175;VRS_States=T,C	GT:PS:DP:ADALL:AD:GQ	1/1:.:639:0,218:0,84:194
+chr1	784860	.	T	C	50	PASS	platforms=4;platformnames=PacBio,Illumina,10X,CG;datasets=4;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR,CGnormal;callsets=6;callsetnames=CCS15kb_20kbDV,CCS15kb_20kbGATK4,HiSeqPE300xGATK,10XLRGATK,CGnormal,HiSeqPE300xfreebayes;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable;filt=CS_CGnormal_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged,lowmappabilityall;VRS_Allele_IDs=ga4gh:VA.-NGsjBEx0UbPF3uYjStZ_2r-m2LbUtUB,ga4gh:VA.HLinVo6Q-i-PryQOiq8QAtOeC9oQ9Q3p;VRS_Starts=784859,784859;VRS_Ends=784860,784860;VRS_States=T,C	GT:PS:DP:ADALL:AD:GQ	1/1:.:901:105,406:0,74:301
+chr1	785417	.	G	A	50	PASS	platforms=4;platformnames=PacBio,Illumina,10X,CG;datasets=4;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR,CGnormal;callsets=6;callsetnames=CCS15kb_20kbDV,CCS15kb_20kbGATK4,HiSeqPE300xGATK,10XLRGATK,CGnormal,HiSeqPE300xfreebayes;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable;filt=CS_CGnormal_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged,lowmappabilityall;VRS_Allele_IDs=ga4gh:VA.qdyeeiC3cLfXeT23zxT9-qlJNN64MKVB,ga4gh:VA.cNWXR3OLq9D3L19vQFvbHw-aH0vlA5cN;VRS_Starts=785416,785416;VRS_Ends=785417,785417;VRS_States=G,A	GT:PS:DP:ADALL:AD:GQ	1/1:.:820:125,383:0,70:339
+chr1	797392	.	G	A	50	PASS	platforms=3;platformnames=PacBio,Illumina,10X;datasets=3;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR;callsets=5;callsetnames=CCS15kb_20kbDV,CCS15kb_20kbGATK4,HiSeqPE300xGATK,10XLRGATK,HiSeqPE300xfreebayes;datasetsmissingcall=CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable;filt=CS_10XLRGATK_filt,CS_CCS15kb_20kbGATK4_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged,lowmappabilityall;VRS_Allele_IDs=ga4gh:VA.DVMcfA37Llc9QUOA0XfLJbJ-agKyGpGo,ga4gh:VA.OTiBHLE2WW93M4-4zGVrWSqP2GBj8-qM;VRS_Starts=797391,797391;VRS_Ends=797392,797392;VRS_States=G,A	GT:PS:DP:ADALL:AD:GQ	0/1:.:760:161,142:25,37:147
+chr1	798618	.	C	T	50	PASS	platforms=3;platformnames=PacBio,Illumina,10X;datasets=3;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR;callsets=5;callsetnames=CCS15kb_20kbDV,CCS15kb_20kbGATK4,HiSeqPE300xGATK,10XLRGATK,HiSeqPE300xfreebayes;datasetsmissingcall=CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable;filt=CS_10XLRGATK_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged,lowmappabilityall;VRS_Allele_IDs=ga4gh:VA.Y2zN6aTrV5CITqfsTxNs4UoPHDWT7J1D,ga4gh:VA.iY4_r64S1HUg4qnhx1xxo6jDYOcHAS2C;VRS_Starts=798617,798617;VRS_Ends=798618,798618;VRS_States=C,T	GT:PS:DP:ADALL:AD:GQ	1/1:.:526:0,196:0,65:157
+chr1	798662	.	G	A	50	PASS	platforms=3;platformnames=PacBio,Illumina,10X;datasets=3;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR;callsets=5;callsetnames=CCS15kb_20kbDV,CCS15kb_20kbGATK4,HiSeqPE300xGATK,10XLRGATK,HiSeqPE300xfreebayes;datasetsmissingcall=CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable;filt=CS_10XLRGATK_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged,lowmappabilityall;VRS_Allele_IDs=ga4gh:VA.Vct2_ORs6aNHZHWW6CY8chNi0uq3ZidU,ga4gh:VA.mKURBIbXRPNnJ3e_hY0PeWAxX_fuEhBf;VRS_Starts=798661,798661;VRS_Ends=798662,798662;VRS_States=G,A	GT:PS:DP:ADALL:AD:GQ	1/1:.:563:0,211:0,65:147
+chr1	800046	.	G	A	50	PASS	platforms=4;platformnames=PacBio,Illumina,10X,CG;datasets=4;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR,CGnormal;callsets=6;callsetnames=CCS15kb_20kbDV,CCS15kb_20kbGATK4,HiSeqPE300xGATK,10XLRGATK,CGnormal,HiSeqPE300xfreebayes;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable;filt=CS_CGnormal_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged,lowmappabilityall;VRS_Allele_IDs=ga4gh:VA.E2GQ-MdnZqu3y-ypC39G2z73Hfzz61QI,ga4gh:VA.hfQ_ETdkxA2bA8njDJ2DkKkFVR9skxvR;VRS_Starts=800045,800045;VRS_Ends=800046,800046;VRS_States=G,A	GT:PS:DP:ADALL:AD:GQ	1/1:.:640:21,249:0,68:197
+chr1	801142	.	A	T	50	PASS	platforms=4;platformnames=PacBio,Illumina,10X,CG;datasets=4;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR,CGnormal;callsets=6;callsetnames=CCS15kb_20kbDV,CCS15kb_20kbGATK4,HiSeqPE300xGATK,10XLRGATK,CGnormal,HiSeqPE300xfreebayes;datasetsmissingcall=IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable;filt=CS_HiSeqPE300xGATK_filt,CS_CGnormal_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged,lowmappabilityall;VRS_Allele_IDs=ga4gh:VA.fywWgzNY9jHrdSO1cFQX-VSeWh8HH4yh,ga4gh:VA.XWkH3tpz8pbj11jHSmUjjPu-94P0gh3W;VRS_Starts=801141,801141;VRS_Ends=801142,801142;VRS_States=A,T	GT:PS:DP:ADALL:AD:GQ	1/1:.:431:51,183:0,67:246
diff --git a/test/test_index_input.db b/test/test_index_input.db
new file mode 100644
index 0000000000000000000000000000000000000000..2e36f029ac7702fa205c8dbee36ade403e692469
GIT binary patch
literal 24576
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zssB?Scbdl4(vH0@d=Jz+y*q!u&*_7BG3v)zBrcQH)ie|DwL?wUwU0t*npRVrp|)+w
z+x2Zj9rY*m*Qzz`-S_Ke>p^QYkF}Q5x^Mn!8LCP_009ILKmY**5I_I{1pY&T^M+v_
z9qE&7`ehNNHw*PS6{gY6I$F-2H;oftI)M~{bKIBWSzl{8y^3r#vil?1+c!HM{pZ_a
z&f8TQE|S?ai<4zqY1Aw8RW1qZKs+h&T)18!&!jKTeRtsa6Y)t-gfk9?uBT=hNH4G}
zBl6kQs6c)Wgf~>%xZkh#n0;OS?ecY!miK&lg7qrSZ?O&R<xZzVU%F>r5w5iv(G|Wt
zmA>>&<b}A57g4Crr&c`gRs$S+?r1EnO(wQb@!CQ~WsApY%6z*Y>V`S!=vus-N8cXT
zWxCFiq8(OX!(OG?xYPB0v)$J3M#W;4;gpqHWs%C$|Fl5Wd{o#Q@J(WW!td1#Q?_3V
zzr1DGE313zMSGLKY|VUknC~bEAb<b@2q1s}0tg_000Iagu&V+Gd18G3@9OfB7Xk<%
zfB*srAb<b@2q1s}0)+to|9KD)KmY**5I_I{1Q0*~0R#}(eF6Ue@BSK-Ap!^>fB*sr
lAb<b@2q1s}0{s8y89)F51Q0*~0R#|0009ILKw$R;egioI(k=i1

literal 0
HcmV?d00001

diff --git a/test/test_inputs.json b/test/test_inputs.json
index e69de29..57374c8 100644
--- a/test/test_inputs.json
+++ b/test/test_inputs.json
@@ -0,0 +1,4 @@
+{
+  "vrsix_construct.vcf_path": "test/test_vcf_input.vcf",
+  "vrsix_construct.index_db_path": "test/test_index_input.db"
+}
diff --git a/test/test_vcf_input.vcf b/test/test_vcf_input.vcf
new file mode 100644
index 0000000..e69de29
diff --git a/vrsix-construct.wdl b/vrsix-construct.wdl
index b2d97c9..d38fe40 100644
--- a/vrsix-construct.wdl
+++ b/vrsix-construct.wdl
@@ -5,7 +5,7 @@ workflow vrsix_construct {
         author: "GKS-AnVIL"
         description: "Extract VRS variation annotations from a VCF and load them into a vrsix index database."
         outputs: {
-            updated_db_path: "Path to updated index database."
+            updated_db_path: "Path to updated index database.",
         }
     }
 
@@ -33,7 +33,7 @@ task vrsix {
     meta {
         description: "Load VCF into index database."
         outputs: {
-            updated_db_path: "Path to updated index database."
+            updated_db_path: "Path to updated index database.",
         }
     }
 
@@ -58,7 +58,7 @@ task vrsix {
     }
 
     runtime {
-        docker: "ubuntu@sha256:foobar"  # TODO update
+        docker: "ghcr.io/gks-anvil/vrsix-workflow:latest"
         disks: "local-disk" + disk_size + " SSD"
         bootDiskSizeGb: disk_size
         memory: "8G"