Merge pull request #181 from LouisLeNezet/co2_footprint

Add nf-co2 plugin and configuration

Author: LouisLeNezet

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#175](https://github.com/nf-core/phaseimpute/pull/175) - Add support for all input files in `.json` or `.yaml` format.
+- [#181](https://github.com/nf-core/phaseimpute/pull/181) - Add nf-co2footprint plugin to the config file.
 
 ### `Changed`
 

docs/output.md

@@ -210,8 +210,8 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 - `pipeline_info/`
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
-  - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
   - Parameters used by the pipeline run: `params.json`.
+  - Report generated by [`nf-co2footprint`](https://nextflow-io.github.io/nf-co2footprint/): `co2footprint_trace.txt`, `co2footprint_summary.txt` and `co2footprint_report`.html.
 
 </details>
 

nextflow.config

@@ -339,6 +339,14 @@ manifest {
 // Nextflow plugins
 plugins {
     id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id '[email protected]' // Calculate the carbon footprint of a Nextflow pipeline
+}
+
+// CO2 footprint calculation
+co2footprint {
+    traceFile   = "${params.outdir}/pipeline_info/co2footprint_trace_${params.trace_report_suffix}.txt"
+    reportFile  = "${params.outdir}/pipeline_info/co2footprint_report_${params.trace_report_suffix}.html"
+    summaryFile = "${params.outdir}/pipeline_info/co2footprint_summary_${params.trace_report_suffix}.txt"
 }
 
 validation {

workflows/phaseimpute/tests/main.nf.test

@@ -25,7 +25,12 @@ nextflow_pipeline {
                         .collect { getRecursiveFileNames(it, outputDir) }
                         .flatten(),
                     path("$outputDir/imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""),
-                    path("$outputDir/imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz").vcf.header.getGenotypeSamples().sort()
+                    path("$outputDir/imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz").vcf.header.getGenotypeSamples().sort(),
+                    path("${outputDir}/pipeline_info/")
+                        .list()
+                        .collect { getRecursiveFileNames(it, outputDir) }
+                        .flatten()
+                        .collect { removeTimestamp(it) }
                 ).match()
                 }
             )
@@ -299,3 +304,7 @@ def getRecursiveFileNames(fileOrDir, outputDir) {
     }
     return fileOrDir.toString().replace("${outputDir}/", "")
 }
+
+def removeTimestamp(filename) {
+    filename.replaceAll(/_\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}/, "")
+}

workflows/phaseimpute/tests/main.nf.test.snap

@@ -408,13 +408,23 @@
                 "NA12878",
                 "NA19401",
                 "NA20359"
+            ],
+            [
+                "pipeline_info/co2footprint_report.html",
+                "pipeline_info/co2footprint_summary.txt",
+                "pipeline_info/co2footprint_trace.txt",
+                "pipeline_info/execution_report.html",
+                "pipeline_info/execution_timeline.html",
+                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/params.json",
+                "pipeline_info/pipeline_dag.html"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.1",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-27T18:11:44.567996758"
+        "timestamp": "2025-02-20T09:18:56.431336345"
     },
     "Check test_dog": {
         "content": [