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@@ -16,7 +16,6 @@ jobs: | |
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outputs: | ||
component_matrix: ${{ steps.set_matrix.outputs.components }} | ||
workflow_matrix: ${{ steps.set_matrix.outputs.workflows }} | ||
cache_key: ${{ steps.cache.outputs.cache_key }} | ||
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steps: | ||
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@@ -56,12 +55,6 @@ jobs: | |
src: src | ||
format: json | ||
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- id: ns_list_workflows | ||
uses: viash-io/viash-actions/ns-list@v6 | ||
with: | ||
src: workflows | ||
format: json | ||
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- id: set_matrix | ||
run: | | ||
echo "components=$(jq -c '[ .[] | | ||
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@@ -72,14 +65,6 @@ jobs: | |
} | ||
]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT | ||
echo "workflows=$(jq -c '[ .[] | | ||
{ | ||
"name": (.functionality.namespace + "/" + .functionality.name), | ||
"main_script": (.info.config | capture("^(?<dir>.*\/)").dir + "/" + .functionality.test_resources[].path), | ||
"entry": .functionality.test_resources[].entrypoint | ||
} | ||
]' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT | ||
# phase 2 | ||
build: | ||
needs: list | ||
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@@ -128,56 +113,6 @@ jobs: | |
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###################################3 | ||
# phase 3 | ||
integration_test: | ||
needs: [ build, list ] | ||
if: "${{ needs.list.outputs.workflow_matrix != '[]' }}" | ||
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runs-on: ubuntu-latest | ||
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strategy: | ||
fail-fast: false | ||
matrix: | ||
component: ${{ fromJson(needs.list.outputs.workflow_matrix) }} | ||
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steps: | ||
# Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' | ||
- uses: data-intuitive/reclaim-the-bytes@v2 | ||
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- uses: actions/checkout@v4 | ||
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- uses: viash-io/viash-actions/setup@v6 | ||
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- uses: nf-core/[email protected] | ||
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# build target dir | ||
# use containers from release branch, hopefully these are available | ||
- name: Build target dir | ||
uses: viash-io/viash-actions/ns-build@v6 | ||
with: | ||
config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" | ||
parallel: true | ||
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# use cache | ||
- name: Cache resources data | ||
uses: actions/cache@v4 | ||
timeout-minutes: 5 | ||
with: | ||
path: resources_test | ||
key: ${{ needs.list.outputs.cache_key }} | ||
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- name: Run integration test | ||
timeout-minutes: 45 | ||
run: | | ||
# todo: replace with viash test command | ||
export NXF_VER=22.04.5 | ||
nextflow run . \ | ||
-main-script "${{ matrix.component.main_script }}" \ | ||
-entry ${{ matrix.component.entry }} \ | ||
-profile docker,mount_temp,no_publish \ | ||
-c workflows/utils/labels_ci.config | ||
###################################3 | ||
# phase 4 | ||
component_test: | ||
needs: [ build, list ] | ||
if: ${{ needs.list.outputs.component_matrix != '[]' && needs.list.outputs.component_matrix != '' }} | ||
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@@ -208,4 +143,4 @@ jobs: | |
--config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ | ||
"${{ matrix.component.config }}" \ | ||
--cpus 2 \ | ||
--memory "5gb" | ||
--memory "5gb" |