fetch co2 report and initial rendering on pipeline pages

bin/pipelines.json.js

@@ -1,5 +1,6 @@
 #! /usr/bin/env node
 import { octokit, getDocFiles, getGitHubFile, githubFolderExists } from "../sites/main-site/src/components/octokit.js";
+import { fetchCO2FootprintFiles } from "./s3Utils.js";
 
 import { promises as fs, writeFileSync, existsSync } from "fs";
 import yaml from "js-yaml";
@@ -491,6 +492,17 @@ export const writePipelinesJson = async () => {
           nf_core_version = extractNfCoreVersion(nfCoreYml);
         }
 
+        // Check if this release has plugins already stored either as dev or as "main"/"master"
+        let plugins = data[`main_nextflow_config_plugins`] || data[`master_nextflow_config_plugins`] || [];
+
+        // Fetch CO2 footprint files if nf-co2footprint plugin is used and we are not in the dev tree
+        console.log(plugins);
+        let co2footprint_files = null;
+        if (plugins.join(" ").includes("nf-co2footprint") && tag_name !== "dev") {
+          console.log(`Fetching CO2 footprint files for ${name} ${tag_name}`);
+          co2footprint_files = await fetchCO2FootprintFiles(name, tag_sha);
+        }
+
         let components = await octokit
           .request("GET /repos/{owner}/{repo}/contents/{path}?ref={ref}", {
             owner: "nf-core",
@@ -556,6 +568,8 @@ export const writePipelinesJson = async () => {
           components,
           nextflow_version,
           nf_core_version,
+          plugins,
+          co2footprint_files,
         };
       }),
     );

bin/s3Utils.js

@@ -0,0 +1,122 @@
+import { S3Client, ListObjectsV2Command, GetObjectCommand } from "@aws-sdk/client-s3";
+
+/**
+ * Creates an anonymous S3 client for public bucket access
+ */
+export function createS3Client() {
+  return new S3Client({
+    region: "eu-west-1",
+    signer: { sign: async (request) => request },
+    credentials: {
+      accessKeyId: "",
+      secretAccessKey: "",
+    },
+  });
+}
+
+/**
+ * Fetches all objects with a given prefix from S3
+ * @param {string} bucketName - S3 bucket name
+ * @param {string} prefix - Object key prefix
+ * @param {string} [delimiter] - Optional delimiter for folder-like structure
+ * @returns {Promise<{bucketContents: Array, commonPrefixes: Array}>} Object containing Contents and CommonPrefixes arrays
+ */
+export async function fetchS3Objects(bucketName, prefix, delimiter) {
+  const client = createS3Client();
+
+  let bucketContents = [];
+  let commonPrefixes = [];
+  let isTruncated = true;
+  let continuationToken;
+
+  try {
+    while (isTruncated) {
+      const response = await client.send(
+        new ListObjectsV2Command({
+          Bucket: bucketName,
+          Prefix: prefix,
+          Delimiter: delimiter,
+          ContinuationToken: continuationToken,
+        }),
+      );
+
+      if (response.KeyCount === 0) {
+        break;
+      }
+
+      if (response.Contents) {
+        bucketContents.push(...response.Contents);
+      }
+
+      if (response.CommonPrefixes) {
+        commonPrefixes.push(...response.CommonPrefixes);
+      }
+
+      isTruncated = response.IsTruncated ?? false;
+      continuationToken = response.NextContinuationToken;
+    }
+
+    return { bucketContents, commonPrefixes };
+  } catch (error) {
+    console.warn(`Failed to fetch S3 objects for prefix ${prefix}:`, error);
+    return { bucketContents: [], commonPrefixes: [] };
+  }
+}
+
+/**
+ * Fetches and parses CO2 footprint summary file from S3 for a given pipeline and commit SHA
+ * @param {string} pipelineName - Name of the pipeline (e.g., 'rnaseq')
+ * @param {string} commitSha - Git commit SHA for the release
+ * @returns {Promise<{filename: string, co2e_emissions: number|null, energy_consumption: number|null}|null>} CO2 footprint data object with filename, co2e_emissions, and energy_consumption, or null if not found
+ */
+export async function fetchCO2FootprintFiles(pipelineName, commitSha) {
+  console.log(`Fetching CO2 footprint files for ${pipelineName} ${commitSha}`);
+  const bucketName = "nf-core-awsmegatests";
+  const prefix = `${pipelineName}/results-${commitSha}/`;
+
+  const { bucketContents } = await fetchS3Objects(bucketName, prefix);
+
+  // Filter for CO2 footprint summary file matching the pattern
+  const co2FootprintFile = bucketContents.find((file) => {
+    const fileName = file.Key?.split("/").pop() || "";
+    return /co2footprint_summary_.*\.txt$/.test(fileName);
+  });
+  console.log(`CO2 footprint file found: ${co2FootprintFile?.Key}`);
+
+  if (!co2FootprintFile) {
+    return null;
+  }
+
+  const client = createS3Client();
+
+  try {
+    const response = await client.send(
+      new GetObjectCommand({
+        Bucket: bucketName,
+        Key: co2FootprintFile.Key,
+      }),
+    );
+
+    // Read the stream and convert to string
+    const bodyContents = await response.Body?.transformToString();
+
+    if (!bodyContents) {
+      return null;
+    }
+
+    // Parse CO2e emissions and energy consumption
+    const co2Match = bodyContents.match(/CO2e emissions:\s*([\d.]+)\s*g/);
+    const energyMatch = bodyContents.match(/Energy consumption:\s*([\d.]+)\s*Wh/);
+
+    const fileName = co2FootprintFile.Key?.split("/").pop() || "";
+
+    return {
+      filename: fileName,
+      co2e_emissions: co2Match ? parseFloat(co2Match[1]) : null,
+      energy_consumption: energyMatch ? parseFloat(energyMatch[1]) : null,
+    };
+  } catch (error) {
+    console.warn(`Failed to fetch CO2 footprint file ${co2FootprintFile.Key}:`, error);
+    return null;
+  }
+}

public/pipelines.json

@@ -26081,7 +26081,7 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/multiplesequencealign",
             "created_at": "2023-07-24T14:30:12Z",
-            "updated_at": "2025-10-02T01:27:27Z",
+            "updated_at": "2025-10-02T11:57:09Z",
             "pushed_at": "2025-07-09T08:24:51Z",
             "homepage": "https://nf-co.re/multiplesequencealign",
             "size": 20538,
@@ -26290,7 +26290,17 @@
                         ]
                     },
                     "nextflow_version": "!>=25.04.2",
-                    "nf_core_version": "3.2.1"
+                    "nf_core_version": "3.2.1",
+                    "plugins": [
+                        "nf-schema@2.2.0",
+                        "nf-co2footprint@1.0.0-beta",
+                        "nf-prov@1.2.2"
+                    ],
+                    "co2footprint_files": {
+                        "filename": "co2footprint_summary_2025-05-28_13-38-21.txt",
+                        "co2e_emissions": 169.72,
+                        "energy_consumption": 357.36
+                    }
                 },
                 {
                     "tag_name": "1.1.0",
@@ -26446,7 +26456,13 @@
                         ]
                     },
                     "nextflow_version": "!>=25.04.2",
-                    "nf_core_version": "3.2.1"
+                    "nf_core_version": "3.2.1",
+                    "plugins": [
+                        "nf-schema@2.2.0",
+                        "nf-co2footprint@1.0.0-beta",
+                        "nf-prov@1.2.2"
+                    ],
+                    "co2footprint_files": null
                 }
             ]
         },

sites/main-site/src/components/pipeline/PipelineSidebar.astro

@@ -23,6 +23,10 @@ export interface Props {
                 modules?: string[];
                 subworkflows?: string[];
             };
+            co2footprint_files: {
+                co2e_emissions: number;
+                energy_consumption: number;
+            };
         }[];
         stargazers_count: number;
         subscribers_count: number;
@@ -178,6 +182,15 @@ const subworkflows: string[] = meta.releases[0].components?.subworkflows || [];
             },
         ]}
     />
+    <SidebarStatsRow
+        content={[
+            {
+                title: "CO<sub>2</sub>e emissions <i class='fas fa-info-circle' title='calculated using the nf-co2footprint plugin and a realistic dataset.'></i>",
+                value: meta.releases[0].co2footprint_files.co2e_emissions + " g",
+            },
+            { title: "energy consumption", value: meta.releases[0].co2footprint_files.energy_consumption + " Wh" },
+        ]}
+    />
     {
         modules.length > 0 && (
             <SidebarStatsRow content={[{ title: "included modules" }]}>

sites/main-site/src/components/sidebar/SidebarStatsRow.astro

@@ -17,9 +17,8 @@ export interface Props {
             if (entry.title && entry.value) {
                 return (
                     <div class="col mb-1">
-                        <h6 class="text-body-secondary my-1">
+                        <h6 class="text-body-secondary my-1" set:html={entry.title}>
                             {entry.icon && <i class={entry.icon + " fa-fw me-1"} />}
-                            {entry.title}
                         </h6>
                         <div class="overflow-x-auto" set:html={entry.value}>
                             <slot />

sites/main-site/src/layouts/ResultsLayout.astro

@@ -1,7 +1,7 @@
 ---
 import PipelinePageLayout from "@layouts/PipelinePageLayout.astro";
 import pipelines_json from "@public/pipelines.json";
-import { S3Client, ListObjectsV2Command } from "@aws-sdk/client-s3";
+import { fetchS3Objects } from "../../../../bin/s3Utils";
 import AWSFile from "@components/pipeline/AWSFile.astro";
 import AWSFilePreview from "@components/pipeline/AWSFilePreview.astro";
 
@@ -34,41 +34,13 @@ const pathParts = path.split("/");
 let filename = Astro.url.searchParams.get("file");
 const description = meta?.description;
 const depth = pathParts.length;
-let awsResponse;
 let isTruncated = commonPrefixes.length === 0;
 
 if (bucketContents.length === 0 && commonPrefixes.length === 0) {
-    let client = new S3Client({
-        region: "eu-west-1",
-        signer: { sign: async (request) => request },
-        credentials: {
-            accessKeyId: "",
-            secretAccessKey: "",
-        },
-    });
-
-    while (isTruncated) {
-        awsResponse = await client.send(
-            new ListObjectsV2Command({
-                Bucket: bucketName,
-                ContinuationToken: awsResponse?.NextContinuationToken,
-                Prefix: path + "/",
-                Delimiter: "/",
-            }),
-        );
-
-        if (awsResponse.KeyCount === 0) {
-            break;
-        }
-        if (awsResponse.Contents) {
-            bucketContents.push(...awsResponse.Contents);
-        }
-        if (awsResponse.CommonPrefixes) {
-            commonPrefixes.push(...awsResponse.CommonPrefixes);
-        }
-
-        isTruncated = awsResponse.IsTruncated;
-    }
+    const result = await fetchS3Objects(bucketName, path + "/", "/");
+    bucketContents = result.bucketContents;
+    commonPrefixes = result.commonPrefixes;
+    isTruncated = false;
 }
 let directories: { name: string | undefined; path: string; depth: number; size: number; lastModified: Date }[] = [];
 let files: { name: string | undefined; path: string; depth: number; size: number; lastModified: Date }[] = [];