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Run Nextclade on all sequences #7

Run Nextclade on all sequences

Run Nextclade on all sequences #7

name: Run Nextclade on all sequences
on:
workflow_dispatch:
inputs:
dockerImage:
description: "Specific container image to use for build (will override the default of `nextstrain build`)"
required: false
type: string
jobs:
run-build:
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
secrets: inherit
with:
runtime: aws-batch
env: |
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.dockerImage }}
run: |
nextstrain build \
--detach \
--cpus 36 \
--memory 72gib \
--env AWS_ACCESS_KEY_ID \
--env AWS_SECRET_ACCESS_KEY \
. \
upload_all_nextclade_files \
-p \
--configfile profiles/nextclade.yaml \
--set-threads run_nextclade=12