Pass software versions to experiment summary

CHANGELOG.md

@@ -5,6 +5,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [[5.1.0dev]($tag_url)] - $date
 
+### Patches
+
+#### Enhancements & fixes
+
+- Pass the collated software versions to the experiment summary report. By @Aratz [#248](https://github.com/nf-core/pixelator/pull/248)
+
 ## [[5.0.1](https://github.com/nf-core/pixelator/releases/tag/5.0.1)] - 2026-08-17
 
 ### Patches

modules/local/experiment_summary/main.nf

@@ -10,10 +10,15 @@ process EXPERIMENT_SUMMARY {
     input:
     path samplesheet_path
     tuple val(meta), val(result_stages), path(results_data, arity: "1..*", stageAs: "results_raw/?/*")
+    path versions_yml, stageAs: 'software_versions.yml'
 
     output:
     tuple val(meta), path("*experiment-summary.html")  , emit: html
-    tuple val("${task.process}"), val('experiment-summary'), eval("Rscript -e 'cat(as.character(packageVersion(\"pixelatorES\")), \"\\n\")'"), emit: versions_experiment_summary, topic: versions
+    // This process must not push its version to the `versions` topic. It consumes a file
+    // collated from that topic, and a topic only closes once all of its publishers have
+    // finished, so publishing to it would hang the pipeline forever.
+    // This mimics how MultiQC handles version reporting.
+    tuple val("${task.process}"), val('experiment-summary'), eval("Rscript -e 'cat(as.character(packageVersion(\"pixelatorES\")), \"\\n\")'"), emit: versions_experiment_summary
 
     script:
     def args = task.ext.args ?: ''
@@ -28,6 +33,8 @@ process EXPERIMENT_SUMMARY {
     cp -r /workspace/inst/quarto/ ./quarto/
     mkdir -p results
 
+    cp software_versions.yml results/software_versions.yml
+
     # Stage each result file into results/<stage>/. Files are staged into
     # results_raw/1, results_raw/2, ... in the same order as the stage names.
     stages=(${stageArray})

modules/local/experiment_summary/meta.yml

@@ -31,6 +31,11 @@ input:
         type: file
         description: Result files to organize under stage folders in the report input.
         ontologies: []
+  - - versions_yml:
+        type: file
+        description: Collated software versions, copied into the report data folder.
+        pattern: "*.{yml,yaml}"
+        ontologies: []
 output:
   html:
     - - meta:
@@ -51,17 +56,6 @@ output:
       - Rscript -e 'cat(as.character(packageVersion("pixelatorES")), "\n")':
           type: eval
           description: The expression used to obtain the tool version.
-topics:
-  versions:
-    - - ${task.process}:
-          type: string
-          description: The process the versions were collected from.
-      - experiment-summary:
-          type: string
-          description: The tool name.
-      - Rscript -e 'cat(as.character(packageVersion("pixelatorES")), "\n")':
-          type: eval
-          description: The expression used to obtain the tool version.
 authors:
   - "@Aratz"
   - "@johandahlberg"

modules/local/experiment_summary/tests/main.nf.test

@@ -29,6 +29,13 @@ nextflow_process {
                         file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/amplicon/pool1.report.json', checkIfExists: true),
                     ]
                 ]
+                input[2] = channel.of(
+                    'PIXELATOR_AMPLICON:',
+                    '  pixelator: 0.30.0',
+                    'Workflow:',
+                    '    nf-core/pixelator: 5.1.0dev',
+                    '    Nextflow: 25.10.4',
+                ).collectFile(name: 'software_versions.yml', newLine: true)
                 """
             }
         }
@@ -130,6 +137,13 @@ nextflow_process {
                         file(params.pipelines_testdata_base_path + 'new-test-data/pna/modules/sample_calling/sample4.report.json', checkIfExists: true),
                     ]
                 ]
+                input[2] = channel.of(
+                    'PIXELATOR_AMPLICON:',
+                    '  pixelator: 0.30.0',
+                    'Workflow:',
+                    '    nf-core/pixelator: 5.1.0dev',
+                    '    Nextflow: 25.10.4',
+                ).collectFile(name: 'software_versions.yml', newLine: true)
                 """
             }
         }

subworkflows/local/pna/v1/main.nf

@@ -24,7 +24,8 @@ include { PIXELATOR_DENOISE          } from '../../../../modules/local/pixelator
 include { PIXELATOR_ANALYSIS         } from '../../../../modules/local/pixelator/analysis/main'
 include { PIXELATOR_COMBINE_COLLAPSE } from '../../../../modules/local/pixelator/combine_collapse/main'
 include { PIXELATOR_LAYOUT           } from '../../../../modules/local/pixelator/layout/main'
-include { EXPERIMENT_SUMMARY             } from '../../../../modules/local/experiment_summary/main'
+include { EXPERIMENT_SUMMARY         } from '../../../../modules/local/experiment_summary/main'
+include { collateVersionsFromTopic   } from '../../utils_nfcore_pixelator_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -193,26 +194,31 @@ workflow PIXELATOR_PNA_V1 {
     PIXELATOR_LAYOUT(ch_analysis)
 
     // Prepare all data needed by reporting for each pixelator step
-    ch_input = channel.fromPath(params.input)
-    ch_experiment_summary_input = channel
-        .topic('all_results_for_reports')
-        .map { stage, files ->
-            def values = files instanceof List ? files : [files]
-            values.collect { f -> tuple(stage, f) }
-        }
-        .flatMap { it }
-        .collect(flat: false)
-        .map { stageFilePairs ->
-            def meta = [id: 'all']
-            def stages = stageFilePairs.collect { it[0] }
-            def files = stageFilePairs.collect { it[1] }
-            tuple(meta, stages, files)
-        }
-
     if (!params.skip_experiment_summary) {
+        ch_input = channel.fromPath(params.input)
+        ch_experiment_summary_input = channel
+            .topic('all_results_for_reports')
+            .map { stage, files ->
+                def values = files instanceof List ? files : [files]
+                values.collect { f -> tuple(stage, f) }
+            }
+            .flatMap { it }
+            .collect(flat: false)
+            .map { stageFilePairs ->
+                def meta = [id: 'all']
+                def stages = stageFilePairs.collect { it[0] }
+                def files = stageFilePairs.collect { it[1] }
+                tuple(meta, stages, files)
+            }
+
+        ch_versions_yml = collateVersionsFromTopic()
+            .collectFile(name: 'software_versions.yml', sort: true, newLine: true)
+            .first()
+
         EXPERIMENT_SUMMARY(
             ch_input,
             ch_experiment_summary_input,
+            ch_versions_yml,
         )
     }
 

subworkflows/local/pna/v1/meta.yml

@@ -17,7 +17,7 @@ components:
   - pixelator/analysis
   - pixelator/layout
   - experiment/summary
-  - pna_generate_reports
+  - collateversionsfromtopic
 input:
   - fastq:
       type: file

subworkflows/local/pna/v2/main.nf

@@ -27,8 +27,9 @@ include { PIXELATOR_COMBINE_COLLAPSE } from '../../../../modules/local/pixelator
 include { PIXELATOR_LAYOUT           } from '../../../../modules/local/pixelator/layout'
 
 
-include { EXPERIMENT_SUMMARY } from '../../../../modules/local/experiment_summary/main'
-include { CAT_FASTQ                     } from '../../../../modules/nf-core/cat/fastq/main'
+include { EXPERIMENT_SUMMARY         } from '../../../../modules/local/experiment_summary/main'
+include { CAT_FASTQ                  } from '../../../../modules/nf-core/cat/fastq/main'
+include { collateVersionsFromTopic   } from '../../utils_nfcore_pixelator_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -57,9 +58,6 @@ workflow PIXELATOR_PNA_V2 {
     ch_panel_files         // channel: [ meta, path(panel_file) |  ]
 
     main:
-    ch_versions = Channel.empty()
-
-
     ch_fastq_grouped_by_pool = ch_fastq
         .map { meta, fq -> tuple(meta.pool, [meta, fq]) }
         .groupTuple()
@@ -239,26 +237,31 @@ workflow PIXELATOR_PNA_V2 {
     PIXELATOR_LAYOUT( ch_analysis )
 
     // Prepare all data needed by reporting for each pixelator step
-    ch_input = channel.fromPath(params.input)
-    ch_experiment_summary_input = channel
-        .topic('all_results_for_reports')
-        .map { stage, files ->
-            def values = files instanceof List ? files : [files]
-            values.collect { f -> tuple(stage, f) }
-        }
-        .flatMap { it }
-        .collect(flat: false)
-        .map { stageFilePairs ->
-            def meta = [id: 'all']
-            def stages = stageFilePairs.collect { it[0] }
-            def files = stageFilePairs.collect { it[1] }
-            tuple(meta, stages, files)
-        }
-
     if (!params.skip_experiment_summary) {
+        ch_input = channel.fromPath(params.input)
+        ch_experiment_summary_input = channel
+            .topic('all_results_for_reports')
+            .map { stage, files ->
+                def values = files instanceof List ? files : [files]
+                values.collect { f -> tuple(stage, f) }
+            }
+            .flatMap { it }
+            .collect(flat: false)
+            .map { stageFilePairs ->
+                def meta = [id: 'all']
+                def stages = stageFilePairs.collect { it[0] }
+                def files = stageFilePairs.collect { it[1] }
+                tuple(meta, stages, files)
+            }
+
+        ch_versions_yml = collateVersionsFromTopic()
+            .collectFile(name: 'software_versions.yml', sort: true, newLine: true)
+            .first()
+
         EXPERIMENT_SUMMARY(
             ch_input,
             ch_experiment_summary_input,
+            ch_versions_yml,
         )
     }
 

subworkflows/local/pna/v2/meta.yml

@@ -18,7 +18,7 @@ components:
   - pixelator/analysis
   - pixelator/layout
   - experiment/summary
-  - pna_generate_reports
+  - collateversionsfromtopic
 input:
   - fastq:
       type: file

subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf

@@ -13,6 +13,7 @@ include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { samplesheetToList         } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML    } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
@@ -106,11 +107,6 @@ workflow PIPELINE_INITIALISATION {
         nextflow_cli_args
     )
 
-    //
-    // Create channel from input file provided through params.input
-    //
-    ch_versions = channel.empty()
-
     //
     // Resolve relative paths and validate fastq files existence
     //
@@ -239,6 +235,33 @@ def getGenomeAttribute(attribute) {
     return null
 }
 
+//
+// Collate the `versions` topic into a channel of YAML fragments
+//
+// Any process consuming the result must not emit to the `versions` topic itself,
+// as the topic only closes once all of its publishers have finished.
+//
+def collateVersionsFromTopic() {
+    def topic_versions = channel.topic("versions")
+        .distinct()
+        .branch { entry ->
+            versions_file: entry instanceof Path
+            versions_tuple: true
+        }
+
+    def topic_versions_string = topic_versions.versions_tuple
+        .map { process, tool, version ->
+            [ process[process.lastIndexOf(':')+1..-1], "  ${tool}: ${version}" ]
+        }
+        .groupTuple(by:0)
+        .map { process, tool_versions ->
+            tool_versions.unique().sort()
+            "${process}:\n${tool_versions.join('\n')}"
+        }
+
+    return softwareVersionsToYAML(topic_versions.versions_file).mix(topic_versions_string)
+}
+
 //
 // Generate methods description for MultiQC
 //

subworkflows/local/utils_nfcore_pixelator_pipeline/meta.yml

@@ -13,6 +13,7 @@ components:
   - pixelator/list/options
   - completionemail
   - completionsummary
+  - softwareversionstoyaml
 input:
   - version:
       type: boolean

tests/proxiome_v1.nf.test.snap

@@ -102,9 +102,6 @@
                 "CAT_FASTQ": {
                     "cat": 9.5
                 },
-                "EXPERIMENT_SUMMARY": {
-                    "experiment-summary": "0.12.0"
-                },
                 "PIXELATOR_AMPLICON": {
                     "pixelator": "0.30.0"
                 },
@@ -137,7 +134,7 @@
                 }
             }
         ],
-        "timestamp": "2026-08-11T08:23:21.795999696",
+        "timestamp": "2026-08-17T11:09:58.197955852",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.2"
@@ -150,9 +147,6 @@
                 "CAT_FASTQ": {
                     "cat": 9.5
                 },
-                "EXPERIMENT_SUMMARY": {
-                    "experiment-summary": "0.12.0"
-                },
                 "PIXELATOR_AMPLICON": {
                     "pixelator": "0.30.0"
                 },
@@ -279,7 +273,7 @@
 
             ]
         ],
-        "timestamp": "2026-08-11T08:22:39.094080602",
+        "timestamp": "2026-08-17T11:09:13.418847968",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.2"

tests/proxiome_v2.nf.test.snap

@@ -133,9 +133,6 @@
                 "CAT_FASTQ": {
                     "cat": 9.5
                 },
-                "EXPERIMENT_SUMMARY": {
-                    "experiment-summary": "0.12.0"
-                },
                 "PIXELATOR_AMPLICON": {
                     "pixelator": "0.30.0"
                 },
@@ -171,7 +168,7 @@
                 }
             }
         ],
-        "timestamp": "2026-08-11T08:27:56.30759346",
+        "timestamp": "2026-08-17T11:14:37.297215197",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.2"
@@ -184,9 +181,6 @@
                 "CAT_FASTQ": {
                     "cat": 9.5
                 },
-                "EXPERIMENT_SUMMARY": {
-                    "experiment-summary": "0.12.0"
-                },
                 "PIXELATOR_AMPLICON": {
                     "pixelator": "0.30.0"
                 },
@@ -357,7 +351,7 @@
 
             ]
         ],
-        "timestamp": "2026-08-11T08:27:04.705573587",
+        "timestamp": "2026-08-17T11:13:43.166533768",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.2"