Merge pull request #164 from Aratz/feature/pna-1351_publish_samplesheet

Publish samplesheet to output directory

Author: Aratz

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 - Improve test suite by @Aratz [#163](https://github.com/nf-core/pixelator/pull/163)
+- Publish samplesheet to output directory by @Aratz [#164](https://github.com/nf-core/pixelator/pull/164)
 
 ## [[2.2.0](https://github.com/nf-core/pixelator/releases/tag/2.2.0)] - 2025-11-02
 

docs/output.md

@@ -243,6 +243,7 @@ The output from this step will be placed in the output folder root.
   - 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.
   - Metadata file with software versions, environment information and pipeline configuration for debugging: `metadata.json`
   - Parameters used by the pipeline run: `params.json`.
+  - Samplesheet used for the run
 
 </details>
 

tests/mpx.nf.test.snap

@@ -5,6 +5,7 @@
             [
                 "pipeline_info",
                 "pipeline_info/nf_core_pixelator_software_mqc_versions.yml",
+                "pipeline_info/samplesheet_mpx_scsp_v1_immunology1.csv",
                 "pixelator",
                 "pixelator/adapterqc",
                 "pixelator/adapterqc/sample01.meta.json",
@@ -83,7 +84,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T13:59:04.912661216"
+        "timestamp": "2025-11-10T10:30:44.484792758"
     },
     "Params: default": {
         "content": [
@@ -123,6 +124,7 @@
             [
                 "pipeline_info",
                 "pipeline_info/nf_core_pixelator_software_mqc_versions.yml",
+                "pipeline_info/samplesheet_mpx_scsp_v1_immunology1.csv",
                 "pixelator",
                 "pixelator/adapterqc",
                 "pixelator/adapterqc/sample01.failed.fastq.gz",
@@ -263,6 +265,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:15:16.036689873"
+        "timestamp": "2025-11-10T10:29:02.843097439"
     }
 }

tests/pna.nf.test.snap

@@ -5,6 +5,7 @@
             [
                 "pipeline_info",
                 "pipeline_info/nf_core_pixelator_software_mqc_versions.yml",
+                "pipeline_info/samplesheet_pna.csv",
                 "pixelator",
                 "pixelator/PNA055_Sample07_filtered_S7.pxl",
                 "pixelator/PNA055_Sample07_unfiltered_S7.pxl",
@@ -121,7 +122,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:20:51.001644946"
+        "timestamp": "2025-11-10T10:34:15.536242041"
     },
     "Params: all": {
         "content": [
@@ -164,6 +165,7 @@
             [
                 "pipeline_info",
                 "pipeline_info/nf_core_pixelator_software_mqc_versions.yml",
+                "pipeline_info/samplesheet_pna.csv",
                 "pixelator",
                 "pixelator/PNA055_Sample07_filtered_S7.layout.pxl",
                 "pixelator/PNA055_Sample07_unfiltered_S7.layout.pxl",
@@ -261,6 +263,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:19:44.285870175"
+        "timestamp": "2025-11-10T10:33:13.546967296"
     }
 }

workflows/pixelator.nf

@@ -60,6 +60,8 @@ workflow PIXELATOR {
 
     main:
 
+    file(params.input).copyTo("${params.outdir}/pipeline_info")
+
     ch_versions = Channel.empty()
 
     //