From 2b727520ca9ed47913082beedc776f7e5096f0ed Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund@nf-co.re>
Date: Wed, 29 Oct 2025 11:03:36 +0100
Subject: [PATCH 1/4] Add nf-co2footprint plugin for emissions tracking

---
 .github/workflows/nf-test.yml             | 25 +++++++++++++++++++++++
 modules/nf-core/shasta/tests/main.nf.test |  2 +-
 tests/config/nf-test.config               |  4 ++++
 3 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 97e55ba5c666..0cdd4f8a486c 100644
--- a/.github/workflows/nf-test.yml
+++ b/.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
diff --git a/modules/nf-core/shasta/tests/main.nf.test b/modules/nf-core/shasta/tests/main.nf.test
index ee6654930a7e..1d5c8760bb1a 100644
--- a/modules/nf-core/shasta/tests/main.nf.test
+++ b/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"
diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index 336f2e178917..2e5af5e2c499 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -1,3 +1,7 @@
+plugins {
+    id 'nf-co2footprint@1.0.0'
+}
+
 params {
     publish_dir_mode                  = "copy"
     singularity_pull_docker_container = false

From c0a83d81ce93b89e3621206bbaeebc78e57dd47c Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund@nf-co.re>
Date: Wed, 29 Oct 2025 17:07:27 +0100
Subject: [PATCH 2/4] chore: update CO2 reports to use nf-core-co2-reports
 bucket

---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 0cdd4f8a486c..230e1cc25a3a 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -184,7 +184,7 @@ jobs:
             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 }}"
+            S3_BASE="s3://nf-core-co2-reports/modules/${DATE}/${BRANCH_NAME}/${{ matrix.profile }}/${{ matrix.shard }}"
 
             # Upload each CO2 trace file
             for file in $CO2_FILES; do

From 64587e772f8d7d25ee7e44084c5c6f1989a9bb2a Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund@nf-co.re>
Date: Sun, 2 Nov 2025 11:36:14 +0100
Subject: [PATCH 3/4] ci: add AWS credentials for CO2 reports S3 upload

---
 .github/workflows/nf-test.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 230e1cc25a3a..020464b475a7 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -171,6 +171,14 @@ jobs:
           total_shards: ${{ env.TOTAL_SHARDS }}
           paths: "${{ join(fromJson(steps.filter.outputs.filtered_paths), ' ') }}"
 
+      - name: Configure AWS credentials for CO2 reports
+        if: always() && steps.filter.outputs.filtered_paths != '[]'
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-access-key-id: ${{ secrets.CO2_REPORTS_AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.CO2_REPORTS_AWS_SECRET_ACCESS_KEY }}
+          aws-region: ${{ secrets.CO2_REPORTS_AWS_REGION }}
+
       - name: Upload CO2 footprint reports to S3
         if: always() && steps.filter.outputs.filtered_paths != '[]'
         shell: bash

From 73f1087d6a5965e755f0f539bcda066f52d9c8d3 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund@nf-co.re>
Date: Sun, 2 Nov 2025 12:54:27 +0100
Subject: [PATCH 4/4] ci: fail CO2 upload step when no trace files found

---
 .github/workflows/nf-test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 020464b475a7..2726a47ebf37 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -201,7 +201,8 @@ jobs:
               echo "Uploaded: $file -> ${S3_BASE}/${filename}"
             done
           else
-            echo "No CO2 footprint trace files found"
+            echo "ERROR: No CO2 footprint trace files found"
+            exit 1
           fi
 
   confirm-pass-nf-test: