Merge branch 'dev' into csi

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.
 - [#184](https://github.com/nf-core/phaseimpute/pull/184) - Add support `.csi` index for `.bam` files.
 
 ### `Changed`
@@ -21,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#166](https://github.com/nf-core/phaseimpute/pull/166) - Fix depth type to `number` to enable float.
 - [#179](https://github.com/nf-core/phaseimpute/pull/179) - Fix VCF usage in `GLIMPSE2`.
+- [#183](https://github.com/nf-core/phaseimpute/pull/183) - Remove wrongfully added files in `BAM_EXTRACT_REGION_SAMTOOLS`.
 
 ## v1.0.0 - Black Labrador [2024-12-09]
 

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 {