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ingest-to-phylo: Add inputs for Docker image
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Add individuals inputs per workflow to override the default Docker image
used by `nextstrain build`. Having this input has been extremely helpful
to continue running pathogen workflows when we run into new bugs that
are not present in older nextstrain-base images.

I've made separate image inputs for the two workflows because they use
different tools and may require different versions of images.
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joverlee521 committed Mar 29, 2024
1 parent eb5e76d commit 65a8acc
Showing 1 changed file with 11 additions and 0 deletions.
11 changes: 11 additions & 0 deletions .github/workflows/ingest-to-phylogenetic.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,13 @@ defaults:

on:
workflow_dispatch:
inputs:
ingest_image:
description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")'
required: false
phylogenetic_image:
description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")'
required: false

jobs:
ingest:
Expand All @@ -23,6 +30,8 @@ jobs:
# We can migrate to AWS Batch when/if we need to for more resources or if
# the job runs longer than the GH Action limit of 6 hours.
runtime: docker
env: |
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.ingest_image }}
run: |
nextstrain build \
--env AWS_ACCESS_KEY_ID \
Expand Down Expand Up @@ -91,6 +100,8 @@ jobs:
# We can migrate to AWS Batch when/if we need to for more resources or if
# the job runs longer than the GH Action limit of 6 hours.
runtime: docker
env: |
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.phylogenetic_image }}
run: |
nextstrain build \
--env AWS_ACCESS_KEY_ID \
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