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feat: Integrate wave_singularity.py script for Singularity container HTTPS SIF URL reporting #9079

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feat: Integrate wave_singularity.py script for Singularity container HTTPS SIF URL reporting #9079

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Copilot Sep 16, 2025
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Update wave.yml workflow to integrate wave_singularity.py script for …
Copilot Sep 16, 2025
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43 changes: 42 additions & 1 deletion .github/workflows/wave.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,47 @@ jobs:
--tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
--tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}

# Only for singularity matrix runs:
# - Install uv (uses script-declared deps)
# - Extract ORAS ref from wave output
# - Run script to resolve HTTPS SIF URL
# - Paste only the HTTPS SIF URL to the workflow summary
- name: Install uv
if: ${{ matrix.profile == 'singularity' && success() }}
uses: astral-sh/setup-uv@v6

- name: Get ORAS image reference for Singularity
if: ${{ matrix.profile == 'singularity' && success() }}
id: oras-ref
env:
TOWER_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
TOWER_WORKSPACE_ID: ${{ secrets.TOWER_WORKSPACE_ID }}
run: |
set -euo pipefail
REF="$(wave --conda-file "${{ matrix.files }}" \
--singularity \
--freeze \
--platform "${{ matrix.platform }}" \
--tower-token "${TOWER_TOKEN}" \
--tower-workspace-id "${TOWER_WORKSPACE_ID}" \
2>&1 | grep -Eo 'oras://[^[:space:]]+' | head -n1 || true)"
if [ -z "${REF}" ]; then
echo "Failed to extract ORAS image reference from wave output" >&2
exit 1
fi
echo "ref=${REF}" >> "${GITHUB_OUTPUT}"

- name: Report HTTPS SIF URL
if: ${{ matrix.profile == 'singularity' && success() }}
env:
# Script reads SEQERA_ACCESS_TOKEN when provided
SEQERA_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
run: |
set -euo pipefail
SIF_URL="$(uv run .github/scripts/wave_singularity.py "${{ steps.oras-ref.outputs.ref }}")"
echo "${SIF_URL}" >> "${GITHUB_STEP_SUMMARY}"
echo "HTTPS SIF URL: ${SIF_URL}"

dockerfile-wave:
# NOTE This should get skipped because generate-matrix won't run
# if: github.repository == 'nf-core/modules'
Expand Down Expand Up @@ -183,4 +224,4 @@ jobs:
# git add .
# git status
# git commit -m "[automated] Bump versions snapshot"
# git push
# git push