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cicd: add publish action #4

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cicd: add publish action #4

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cicd: add publish action
jsstevenson Feb 13, 2025
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jsstevenson Feb 14, 2025
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jsstevenson Feb 14, 2025
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28 changes: 28 additions & 0 deletions .github/workflows/publish.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
name: publish to GHCR
on:
release:
types: [published]
jobs:
publish-image:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4

- name: Login to GHCR
uses: docker/login-action@v3
with:
registry: ghcr.io
username: gks-anvil
password: ${{ secrets.GHCR_TOKEN }}

- name: Set up QEMU
uses: docker/setup-qemu-action@v3

- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3

- name: Build and push
uses: docker/build-push-action@v6
with:
push: true
tags: ghcr.io/gks-anvil/vrsix-workflow:latest
3 changes: 1 addition & 2 deletions containers/base/Dockerfile
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@@ -1,5 +1,4 @@
# TODO python version
from circleci/python:3.12
FROM cimg/python:3.12

RUN pip install vrsix~=0.1.2

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245 changes: 245 additions & 0 deletions test/GIAB_sample_annotated.vcf
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Binary file added test/test_index_input.db
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4 changes: 4 additions & 0 deletions test/test_inputs.json
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{
"vrsix_construct.vcf_path": "test/test_vcf_input.vcf",
"vrsix_construct.index_db_path": "test/test_index_input.db"
}
Empty file added test/test_vcf_input.vcf
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6 changes: 3 additions & 3 deletions vrsix-construct.wdl
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Expand Up @@ -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.",
}
}

Expand Down Expand Up @@ -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.",
}
}

Expand All @@ -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"
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