nextflow-io · JosuaCarl · May 6, 2026 · Mar 25, 2026 · Mar 26, 2026 · Apr 10, 2026
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yaml b/.github/ISSUE_TEMPLATE/bug_report.yaml
@@ -138,7 +138,7 @@ body:
           </details>
         </details>
       placeholder: |
-        - Plugin version: 1.2.1
+        - Plugin version: 1.3.0
         - Nextflow version: 25.8.0-edge
         - Java version: openjdk 17.0.14
         - Groovy version: 4.0.25 JVM: 17.0.11

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,11 +1,44 @@
 # New
 ## Bug Fixes:
+
+## Misc:
+
+## Features:
+
+# 1.3.0
+## Bug Fixes:
+- CPU power model now applied correctly
+- Unintended report value removal
+- Fixed floating point error for numerical conversion division
+- Eliminated `Unrecognized config option` warnings under Nextflow's v2 syntax parser by registering `CO2FootprintConfig` as an extension point and aligning the nested file-config scopes with the v2 `ConfigScope` discovery rules
+- Fixed missing ci plot in post-run feature
+
+## Misc:
+- Improved workflow reporting form extension/CLI by deriving and injecting workflow metadata from the provided trace file
+- Added full integration test
+- Adapted to Nextflow 26
+- Reworked `Bytes`, such that it can take binary and decimal-based values
+
+## Features:
+- Transformation of data file to provenance file with schema.org / bioschemas.org type annotation in JSON-LD data format
+
+# 1.2.1
+## Bug Fixes:
+- Total values from workflow in report
+- Missing newlines in non-ANSI logging
+
+## Misc:
+- Aligned Session tracking with Nextflow's trace tracking
+
+## Features:
+- New CI reporting of failed file comparisons
+
+# 1.2.0
+## Bug Fixes:
 - Plot display of titles and axes names in report
 - Accumulation of dates
 - Never initialized observer called for session emissions on CLI command
 - Included descendant processes into session tracking
-- Total values from workflow in report
-- Missing newlines in non-ANSI logging
 
 ## Misc:
 - Improved the testing of log messages
@@ -14,7 +47,6 @@
 - Added recommendation for market-based CI usage
 - Single values in process summary plot
 - Numbers that are not in Double format are now accepted for config values
-- Aligned Session tracking with Nextflow's trace tracking
 
 ## Features:
 - Updated the config syntax inline with standard Nextflow style
@@ -27,7 +59,6 @@
 - Usage of TDP per logical core, becaus this corresponds best to the `cpus` trace metric
 - Tracking of whole session emissions
 - Precursor of machine-actionable file
-- New CI reporting of failed file comparisons
 
 # Version 1.1.0
 ## Bug Fixes:

diff --git a/CITATION.cff b/CITATION.cff
@@ -24,7 +24,7 @@ authors:
     given-names: Sabrina
     orcid: https://orcid.org/0000-0003-0603-7907
 title: "nf-co2footprint - A nextflow plugin to track CO2e emissions"
-version: 1.2.1
+version: 1.3.0
 identifiers:
   - type: doi
     value: 10.5281/zenodo.14622304

diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ Declare the plugin in your Nextflow pipeline configuration file:
 
 ```groovy title="nextflow.config"
 plugins {
-  id 'nf-co2footprint@1.2.1'
+  id 'nf-co2footprint@1.3.0'
 }
 ```
 
@@ -76,7 +76,7 @@ We additionally thank the following people for their extensive assistance in the
 
 ### How to cite:
 ```text
-J. Carl, N. Volkmann, J. Mir-Pedrol, P. Ewels, S. Nahnsen, S. Krakau nextflow-io/nf-co2footprint v1.2.1. (Mar., 2026). nextflow-io. Available: https://github.com/nextflow-io/nf-co2footprint
+J. Carl, N. Volkmann, J. Mir-Pedrol, P. Ewels, S. Nahnsen, S. Krakau nextflow-io/nf-co2footprint v1.3.0. (Mar., 2026). nextflow-io. Available: https://github.com/nextflow-io/nf-co2footprint
 ```
 ```Bibtex
 @software{nf_co2footprint_plugin,
@@ -90,7 +90,7 @@ J. Carl, N. Volkmann, J. Mir-Pedrol, P. Ewels, S. Nahnsen, S. Krakau nextflow-io
     month   =   {March}
     year    =   {2026}
     publisher = {Nextflow-io}
-    version =   {v1.2.1}
+    version =   {v1.3.0}
     url     =   {https://doi.org/10.5281/zenodo.14622304}
     doi     =   {10.5281/zenodo.14622304}
 }

diff --git a/build.gradle b/build.gradle
@@ -58,7 +58,7 @@ sourceSets {
 
 // Versioning of important packages
 ext {
-    nextflowVersion = '24.10.6'
+    nextflowVersion = '26.04.0'
 }
 String groovyVersion = '4.0.27'
 String pf4jVersion = '3.13.0'
@@ -96,18 +96,19 @@ dependencies {
 }
 
 // Plugin version
-version = '1.2.1'
+version = '1.3.0'
 
 nextflowPlugin {
     // Minimum Nextflow version
-    nextflowVersion = '25.10.0'
+    nextflowVersion = '26.04.0'
 
     // Plugin metadata
     provider = 'nextflow'
     className = 'nextflow.co2footprint.CO2FootprintPlugin'
     extensionPoints = [
             'nextflow.co2footprint.CO2FootprintFactory',
-            'nextflow.co2footprint.CO2FootprintExtension'
+            'nextflow.co2footprint.CO2FootprintExtension',
+            'nextflow.co2footprint.CO2FootprintConfig'
     ]
 
 }

diff --git a/docs/assets/co2footprint_report_sample.html b/docs/assets/co2footprint_report_sample.html
diff --git a/docs/assets/co2footprint_summary_sample.txt b/docs/assets/co2footprint_summary_sample.txt
@@ -24,7 +24,7 @@ nf-co2footprint options:
   powerdrawMem: 0.3725
   pue: 1.3
   customCpuTdpFile: null
-  dataFile: out/pipeline_info/co2footprint_data_2026-03-06_13-25-02.yaml
+  provenanceFile: out/pipeline_info/co2footprint_data_2026-03-06_13-25-02.yaml
   reportFile: out/pipeline_info/co2footprint_report_2026-03-06_13-25-02.html
   summaryFile: out/pipeline_info/co2footprint_summary_2026-03-06_13-25-02.txt
   traceFile: out/pipeline_info/co2footprint_trace_2026-03-06_13-25-02.txt
diff --git a/docs/contributing/setup.md b/docs/contributing/setup.md
@@ -47,7 +47,7 @@ The plugin can be tested without using a local Nextflow build using the followin
 2. Run nextflow with this command, specifying the plugin version:
 
    ```bash
-   nextflow run <script/pipeline name> [pipeline params] -plugins nf-co2footprint@1.2.1
+   nextflow run <script/pipeline name> [pipeline params] -plugins nf-co2footprint@1.3.0
    ```
 
 

diff --git a/docs/usage/FAQ.md b/docs/usage/FAQ.md
@@ -31,4 +31,17 @@
     - Set the TDP via `powerdrawCpuDefault = <TDP per core>` and then ignore the warning with `ignoreCpuModel = true`.
 
     For more information see our documentation on [power draw parameters](./parameters.md#hardware-power-draw). You can additionally
-    report the model with the ["Missing chip" GitHub issue](https://github.com/nextflow-io/nf-co2footprint/issues/new?template=missing_chip.yaml).
+    report the model with the ["Missing chip" GitHub issue](https://github.com/nextflow-io/nf-co2footprint/issues/new?template=missing_chip.yaml).
+
+
+<a id="differing-memory"></a>
+??? faq "Differing memory values"
+
+    The conversion of `Byte`-type units, such as `memory` is done in accordance with [SI standard, decimal-based naming](https://en.wikipedia.org/wiki/Metric_prefix#List_of_SI_prefixes), rather than [Nextflows binary-based system](https://en.wikipedia.org/wiki/Byte#Multiple-byte_units).
+    In essence, we use: 1 GB = 1 000 000 000 bytes (1 * 1000^3), while Nextflow uses: 1 GB = 1 073 741 824 bytes (1 * 1024^3), which should be 1 GiB (Gibibyte).
+
+    Example: <br>
+    &emsp;    -> You request `process.memory = 12 GB` <br>
+    &emsp;    -> Nextflow converts it to 12884901888 bytes and passes the restriction onto the executor <br>
+    &emsp;&emsp;        => 12.88 GB = 12 GiB are allocated for the process <br>
+    &emsp;    -> The plugin uses the the former to proceed with calculations and reporting, while Nextflow (incorrectly) reports using the latter <br>
diff --git a/docs/usage/configuration.md b/docs/usage/configuration.md
@@ -13,7 +13,7 @@ To customize the plugin settings to your computing environment and preferences,
 ???+ example
     ```groovy title="nextflow.config"
     plugins {
-      id 'nf-co2footprint@1.2.1'
+      id 'nf-co2footprint@1.3.0'
     }
 
     // Optional example config settings for CO₂ reporting:
@@ -124,7 +124,7 @@ For more information, see [Parameters](parameters.md).
 ???+ example
     ```groovy title="nextflow_cloud.config"
     plugins {
-      id 'nf-co2footprint@1.2.1'
+      id 'nf-co2footprint@1.3.0'
     }
 
     params {

diff --git a/docs/usage/development.md b/docs/usage/development.md
@@ -0,0 +1,34 @@
+### Development of the nf-co2footprint plugin
+Thank you for your interest in contributing to the development of the nf-co2footprint plugin! We welcome contributions of all kinds, including bug fixes, new features, documentation improvements, and more. Below you will find some guidelines to help you get started.
+
+#### PR Template
+When you create a PR you will be prompted to fill out this short template. Please do so, but you may also drop some point if they are not applicable.
+
+```Markdown
+🎯 Motivation
+Why is this change needed?
+
+📋 Summary of changes
+- Short bullet points describing the changes you have made.
+
+## ✅ Checklist
+- [ ] New functionalities are covered by tests
+- [ ] Class structure in `test` reflects class structure in `main`
+- [ ] Documentation reflects changed behaviour
+- [ ] `README.md` contains information on or reference to new features
+- [ ] `CHANGELOG.md` is updated with a note on your changes
+- [ ] Ensure all tests pass (`.\gradlew check`)
+```
+
+#### Testing
+When you run the tests, either through your IDE or via `make test` / `.\gradlew check`, several tests will be done to ensure the core functionality of the plugin. They are by no means comprehensive, but they will help to catch some common issues.
+
+If you have added new functionality, please consider adding tests for it as well.
+
+##### Snapshot testing
+When a test fails due to a mismatch between the generated output and the expected output, the plugin will automatically generate snapshots of the new output files in the `build/resources/test` directory.
+If your changes affect the output, please review the generated snapshots and update their counterparts in the `src/testResources` folder. This way, we can ensure that future tests will compare against the correct expected output.
+The line-by-line comparison of several IDEs can be very helpful for this task.
+
+After you have updated the output files, you may have to update the expected MD5 checksums, number of lines, and special lines (such as lines with local date-times) in the corresponding `file_checks.json`.
+You can do this by extracting the information from the test output or, if necessary, running the tests again.
diff --git a/docs/usage/extension.md b/docs/usage/extension.md
@@ -14,15 +14,27 @@ The plugin provides some [extension points](https://nextflow.io/docs/latest/plug
     }
     ```
 
+!!! info
+
+    In CLI/extension post-run mode, workflow metadata is reconstructed using the trace file (e.g., start/end time, duration) and synthetic/runtime values (e.g., run name, command line), and may differ from reports generated during an integrated plugin run.
+
+#### Shared arguments
+
+Both modes accept the following arguments:
+
+- **tracePath** *(required)*: Path to the execution trace file.
+- **delimiter**: Column separator used in the trace file. Defaults to `'\t'`.
+
 #### From the command line
-The command line functionality utilizes Nextflow configs, like the regular plugin (see [parameters.md](./pa
-rameters.md)).
+The command line functionality utilizes Nextflow configs, like the regular plugin (see [parameters.md](./parameters.md)).
 It is recommended to set the output paths and a fixed carbon intensity value (`ci`) in the config.
 ```bash
-nextflow plugin nf-co2footprint:postRun --config <path_to_nextflow.config> --tracePath <path_to_execution_trace.txt>
+nextflow plugin nf-co2footprint:postRun --tracePath <path_to_execution_trace.txt> [--config <path_to_nextflow.config>] [--delimiter <delimiter>]
 ```
 
+In addition to the [shared arguments](#shared-arguments):
 
+- **--config**: Path to a Nextflow config file (output paths, carbon intensity, etc.).
 
 #### Within a workflow through functions
 The interaction follows the [Nextflow extension function schema](https://nextflow.io/docs/latest/plugins/developing-plugins.html#functions).
@@ -49,26 +61,16 @@ process calculate_CO2 {
 }
 
 workflow {
-  calculate_CO2('<Path_to_your_execution_trace>')
+  calculate_CO2('<Path_to_your_execution_trace>', <config_modifications>, <delimiter>)
 }
 ```
 
 ##### Functions
 ###### `parseTraceFile`
-Parse the trace file into a list of TraceRecord instances.
-
-- **tracePath**:
-  Path to a trace file
-
-- **delimiter**:
-  Deliming character of the tabular trace file. Defaults to `'\t'`.
+Parse the trace file into a list of TraceRecord instances. Accepts the [shared arguments](#shared-arguments).
 
 ###### `calculateCO2`
-Can be used to calculate the emissions of a trace.
-
-- **tracePath**:
-  Path to the trace file 
+Calculate the emissions of a trace. Accepts the [shared arguments](#shared-arguments), plus:
 
-- **configModifications**:
-  Temporarily overrides parameters in the `co2footprint` block of the current Nextflow configuration for a single extension function call. The provided map is merged with the existing configuration and does not affect the overall workflow run. Can be used to adjust settings such as output paths or carbon intensity for post-run estimations. Defaults to [:].  
+- **configModifications**: Temporarily overrides parameters in the `co2footprint` block of the current Nextflow configuration for this call. The provided map is merged with the existing configuration and does not affect the overall workflow run. Defaults to `[:]`.  
   Example: `[trace: [file: <Path_to_your_output_trace_file>], ci: <Your_carbon_intensity>]`
diff --git a/docs/usage/output.md b/docs/usage/output.md
@@ -16,16 +16,14 @@ The nf-co2footprint plugin creates three output files:
 - **`report`** ([sample](../assets/co2footprint_report_sample.html))  
   The HTML report contains information about the carbon footprint of the whole pipeline run as well as plots showing the distributions of the CO₂ emissions for the different processes. The CO₂ emissions are separated into newly generated (i.e. from non-cached tasks) and total (including cached tasks). Additionally, it contains a table with the metrics for all individual tasks. The table is limited to 10000 entries by default. It finishes up with an overview plot of the carbon intensities during the workflow execution.
 
-- **`dataFile`**
-  The data file contains all trace information in a tree structure with the levels in descending order `session -> workflow -> process -> task`. Example: A workflow consists of multiple processes / has multiple `process` level children.
+- **`provenance`**
+  The provenance file contains all trace information contributing to the emission calculation in a tree structure with the levels in descending order `session -> workflow -> process -> task`. Example: A workflow consists of multiple processes / has multiple `process` level children.
+  The file design adheres to the javascript object notation linked-data (JSON-LD) format with type context definitions from schema.org and bioschemas.org.
   The total session emission estimation includes everything from the point of plugin start to stop in a similar manner to how Nextflow defines a `TraceRecord`, but through the Java-native OSHI library.
 
     !!! note "Comparison session vs. workflow"
         The tracking of resource usage, such as `%cpu` and `memory` differs slightly from the way Nextflow determines trace values. Therefore, it might not be 100% comparable. It is not guaranteed that workflow emissions are bigger than session emissions.
 
-    !!! warning "Preliminary feature"
-        The data file is currently not in its final version. Changes in the near future are very likely.
-
 !!! note
 
     Column headers in tables displaying task-specific metrics use the same field names as Nextflow’s native trace output when representing the same metric. For field definitions, see the Nextflow documentation: [Trace file fields](https://www.nextflow.io/docs/latest/tracing.html#trace-file).

diff --git a/docs/usage/parameters.md b/docs/usage/parameters.md
@@ -32,14 +32,14 @@ The following parameters are currently available:
 
     **Default**: `[enabled: true, file: co2footprint_report_<timestamp>.html, overwrite: true, maxTasks: 10000]`
 
-- **`dataFile`**  
+- **`provenance`**  
   Map containing:
     - `enabled`: Whether to produce this file
     - `file`: Name of the data/machine-actionable file containing all metrics that were used during footprint calculation in a structured way.
     - `overwrite`: Whether to overwrite the file, if it already exists.
     - `emissionMetricsOnly`: Whether to only include emission metrics, such as CO₂ equivalents and electricity consumption.
 
-    **Default**: `[enabled: false, file: co2footprint_report_<timestamp>.html, overwrite: true, emissionMetricsOnly: false]`
+    **Default**: `[enabled: false, file: co2footprint_report_<timestamp>.html, overwrite: true, emissionMetricsOnly: true]`
 
     !!! warning "Preliminary feature"
         The data file is currently not in its final version. Changes in the near future are very likely.
@@ -154,12 +154,12 @@ The following parameters are currently available:
 
     !!! warning "Experimental feature"
         The `cpuPowerModel` parameter is experimental and may change in future releases.
+
+    A power model function that takes the parameter `coreUsage`.
 
-    Polynomial coefficients for a custom CPU power model (highest degree first).
-
-    If specified, this overrides TDP-based power draw estimation for CPU cores. The coefficients define a function that returns the **per-core power draw** (in Watts) as a function of core utilization (0–1).
+    If specified, this overrides TDP-based power draw estimation for CPU cores. The function returns the **per-core power draw** (in Watts) as a function of core utilization (0–1).
 
-    **Example**: `[0.5, 10.0]` defines the model `0.5 × coreUsage + 10`
+    **Example**: `{coreUsage -> 0.5 * coreUsage + 10.0}`
 
     **Example visualization**:
-Original file line number
+Diff line change
@@ Expand Up @@
 . Run nextflow with this command, specifying the plugin version:
        ```bash
-       nextflow run <script/pipeline name> [pipeline params] -plugins nf-co2footprint@1.2.1
+       nextflow run <script/pipeline name> [pipeline params] -plugins nf-co2footprint@1.3.0
        ```
@@ Expand Down @@