Add nf-co2footprint plugin for emissions tracking

Track CO2 emissions during nf-test runs and upload reports to S3
for analysis with DuckDB.

Refs: #9291

test: Trigger CI to test CO2 footprint tracking

Author: edmundmiller

.github/workflows/nf-test.yml

@@ -171,6 +171,31 @@ jobs:
           total_shards: ${{ env.TOTAL_SHARDS }}
           paths: "${{ join(fromJson(steps.filter.outputs.filtered_paths), ' ') }}"
 
+      - name: Upload CO2 footprint reports to S3
+        if: always() && steps.filter.outputs.filtered_paths != '[]'
+        shell: bash
+        run: |
+          # Find all CO2 footprint trace files
+          CO2_FILES=$(find . -name "co2footprint_trace*.txt" -type f)
+
+          if [ -n "$CO2_FILES" ]; then
+            # Get current date and sanitize branch name
+            DATE=$(date +%Y-%m-%d)
+            BRANCH_NAME=$(echo "${{ github.head_ref || github.ref_name }}" | sed 's/[^a-zA-Z0-9._-]/_/g')
+
+            # S3 destination path
+            S3_BASE="s3://nf-core-resource-optimization/co2reports/modules/${DATE}/${BRANCH_NAME}/${{ matrix.profile }}/${{ matrix.shard }}"
+
+            # Upload each CO2 trace file
+            for file in $CO2_FILES; do
+              filename=$(basename "$file")
+              aws s3 cp "$file" "${S3_BASE}/${filename}" --no-progress
+              echo "Uploaded: $file -> ${S3_BASE}/${filename}"
+            done
+          else
+            echo "No CO2 footprint trace files found"
+          fi
+
   confirm-pass-nf-test:
     runs-on:
       - runs-on=${{ github.run_id }}-confirm-pass-nf-test

modules/nf-core/shasta/tests/main.nf.test

@@ -1,4 +1,4 @@
-
+// Trigger CI to test CO2 footprint tracking
 nextflow_process {
 
     name "Test Process SHASTA"

tests/config/nf-test.config

@@ -1,3 +1,7 @@
+plugins {
+    id '[email protected]'
+}
+
 params {
     publish_dir_mode                  = "copy"
     singularity_pull_docker_container = false