nf-core · delfiterradas · Feb 19, 2026 · Feb 24, 2026 · Feb 26, 2026 · Feb 27, 2026
diff --git a/modules/nf-core/bcl2fastq/main.nf b/modules/nf-core/bcl2fastq/main.nf
@@ -75,6 +75,8 @@ process BCL2FASTQ {
 
     mkdir -p InterOp
     echo "fake interop file" > InterOp/IndexMetricsOut.bin
+    mkdir -p flowcell
+    echo "fake runinfo file" > flowcell/RunInfo.xml
     mkdir -p output/Reports
     echo "fake report" > output/Reports/index.html
     mkdir -p output/Stats

diff --git a/modules/nf-core/bcl2fastq/tests/main.nf.test.snap b/modules/nf-core/bcl2fastq/tests/main.nf.test.snap
@@ -63,7 +63,10 @@
                             "id": "test",
                             "lane": 1
                         },
-                        "RunInfo.xml:md5,38623309618e3aee6b10365b49348b87"
+                        [
+                            "RunInfo.xml:md5,ec995517c9f57a734c620b701522147f",
+                            "RunInfo.xml:md5,38623309618e3aee6b10365b49348b87"
+                        ]
                     ]
                 ],
                 "8": [
@@ -141,16 +144,19 @@
                             "id": "test",
                             "lane": 1
                         },
-                        "RunInfo.xml:md5,38623309618e3aee6b10365b49348b87"
+                        [
+                            "RunInfo.xml:md5,ec995517c9f57a734c620b701522147f",
+                            "RunInfo.xml:md5,38623309618e3aee6b10365b49348b87"
+                        ]
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-02-26T21:17:54.287768"
+        "timestamp": "2026-02-27T22:07:52.116693092"
     },
     "homo sapiens illumina [bcl]": {
         "content": [
@@ -403,8 +409,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-02-26T21:14:22.182282"
+        "timestamp": "2026-02-27T22:07:40.249895733"
     }
 }
diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf
@@ -15,6 +15,7 @@ process BCLCONVERT {
     tuple val(meta), path("output/Reports/*.{csv,xml,bin}"), emit: reports
     tuple val(meta), path("output/Logs/*.{log,txt}"), emit: logs
     tuple val(meta), path("output/InterOp/*.bin"), emit: interop, optional: true
+    tuple val(meta), path("output/Reports/RunInfo.xml"), emit: runinfo
     tuple val("${task.process}"), val('bclconvert'), eval("bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //'"), topic: versions, emit: versions_bclconvert
 
     when:

diff --git a/modules/nf-core/bclconvert/meta.yml b/modules/nf-core/bclconvert/meta.yml
@@ -103,6 +103,16 @@ output:
           pattern: "InterOp/*.bin"
           ontologies:
             - edam: http://edamontology.org/format_2333 #BINARY
+  runinfo:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - output/Reports/RunInfo.xml:
+          type: file
+          description: RunInfo.xml file
+          pattern: "*.{xml}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2332" # XML
   versions_bclconvert:
     - - ${task.process}:
           type: string

diff --git a/modules/nf-core/bclconvert/tests/main.nf.test.snap b/modules/nf-core/bclconvert/tests/main.nf.test.snap
@@ -160,6 +160,15 @@
                     ]
                 ],
                 "7": [
+                    [
+                        {
+                            "id": "test",
+                            "lane": 1
+                        },
+                        "RunInfo.xml:md5,f6efb28f2f9dcd1d0cb85b78f33aa656"
+                    ]
+                ],
+                "8": [
                     [
                         "BCLCONVERT",
                         "bclconvert",
@@ -231,6 +240,15 @@
                         ]
                     ]
                 ],
+                "runinfo": [
+                    [
+                        {
+                            "id": "test",
+                            "lane": 1
+                        },
+                        "RunInfo.xml:md5,f6efb28f2f9dcd1d0cb85b78f33aa656"
+                    ]
+                ],
                 "undetermined": [
                     [
                         {
@@ -254,9 +272,9 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-02-17T14:13:11.717962"
+        "timestamp": "2026-02-19T16:46:51.349435535"
     },
     "homo_sapiens illumina [bcl]": {
         "content": [

diff --git a/modules/nf-core/multiqcsav/environment.yml b/modules/nf-core/multiqcsav/environment.yml
@@ -10,4 +10,4 @@ dependencies:
   - bioconda::multiqc_sav=0.2.0
   - pip=25.3
   - pip:
-      - interop==1.9.0
+      - interop==1.9.0
diff --git a/modules/nf-core/multiqcsav/main.nf b/modules/nf-core/multiqcsav/main.nf
@@ -3,9 +3,9 @@ process MULTIQCSAV {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/36/3634362a0bf5a0530a6459bdba392622262d6de6cc0062e9a293bacc3098b323/data'
-        : 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:b142653b3920c82b'}"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/36/3634362a0bf5a0530a6459bdba392622262d6de6cc0062e9a293bacc3098b323/data' :
+        'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:b142653b3920c82b' }"
 
     input:
     tuple  val(meta), path(xml), path(interop_bin, stageAs: "InterOp/*"), path(extra_multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
@@ -50,4 +50,4 @@ process MULTIQCSAV {
     touch multiqc_plots/.stub
     touch multiqc_report.html
     """
-}
+}
diff --git a/modules/nf-core/multiqcsav/meta.yml b/modules/nf-core/multiqcsav/meta.yml
@@ -136,4 +136,4 @@ authors:
   - "@matthdsm"
   - "@delfiterradas"
 maintainers:
-  - "@matthdsm"
+  - "@matthdsm"
diff --git a/modules/nf-core/multiqcsav/tests/main.nf.test.snap b/modules/nf-core/multiqcsav/tests/main.nf.test.snap
@@ -28,10 +28,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-02-26T15:17:26.065765698"
+        "timestamp": "2026-03-02T19:39:58.798414069"
     },
     "NovaSeq6000 - stub": {
         "content": [
@@ -88,9 +88,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-02-26T15:18:42.648653899"
+        "timestamp": "2026-03-02T19:40:11.70643624"
     }
 }
diff --git a/subworkflows/nf-core/bcl_demultiplex/main.nf b/subworkflows/nf-core/bcl_demultiplex/main.nf
@@ -4,8 +4,9 @@
 // Demultiplex Illumina BCL data using bcl-convert or bcl2fastq
 //
 
-include { BCLCONVERT } from "../../../modules/nf-core/bclconvert/main"
-include { BCL2FASTQ  } from "../../../modules/nf-core/bcl2fastq/main"
+include { BCLCONVERT                                       } from "../../../modules/nf-core/bclconvert/main"
+include { BCL2FASTQ                                        } from "../../../modules/nf-core/bcl2fastq/main"
+include { MULTIQCSAV                                       } from "../../../modules/nf-core/multiqcsav/main"
 
 workflow BCL_DEMULTIPLEX {
     take:
@@ -18,6 +19,10 @@ workflow BCL_DEMULTIPLEX {
     ch_stats = channel.empty()
     ch_interop = channel.empty()
     ch_logs = channel.empty()
+    ch_runinfo = channel.empty()
+    ch_multiqc_report = channel.empty()
+    ch_multiqc_data = channel.empty()
+    ch_multiqc_plots = channel.empty()
 
     // Split flowcells into separate channels containing run as tar and run as path
     // https://nextflow.slack.com/archives/C02T98A23U7/p1650963988498929
@@ -49,12 +54,18 @@ workflow BCL_DEMULTIPLEX {
         ch_interop = ch_interop.mix(BCLCONVERT.out.interop)
         ch_reports = ch_reports.mix(BCLCONVERT.out.reports)
         ch_logs = ch_logs.mix(BCLCONVERT.out.logs)
+        ch_runinfo = ch_runinfo.mix(BCLCONVERT.out.runinfo)
         ch_fastq_with_meta = ch_fastq_with_meta.mix(
             generateReadgroupBCLCONVERT(
-                BCLCONVERT.out.reports.map { meta, reports ->
-                    return [meta, reports.find { report -> report.name == "fastq_list.csv" }]
+                BCLCONVERT.out.reports
+                    .map { meta, reports_dir ->
+                        def csvFile = reports_dir.find { report -> report.name == "fastq_list.csv"} ?:
+                            reports_dir.eachFileRecurse { report_file ->
+                                report_file.name == "fastq_list.csv"
+                            }
+                    return [meta, csvFile]
                 },
-                BCLCONVERT.out.fastq,
+                BCLCONVERT.out.fastq
             )
         )
     }
@@ -66,7 +77,7 @@ workflow BCL_DEMULTIPLEX {
         ch_interop = ch_interop.mix(BCL2FASTQ.out.interop)
         ch_reports = ch_reports.mix(BCL2FASTQ.out.reports)
         ch_stats = ch_stats.mix(BCL2FASTQ.out.stats)
-
+        ch_runinfo = ch_runinfo.mix(BCL2FASTQ.out.xml)
         ch_fastq_with_meta = ch_fastq_with_meta.mix(
             generateReadgroupBCL2FASTQ(
                 BCL2FASTQ.out.fastq
@@ -82,13 +93,29 @@ workflow BCL_DEMULTIPLEX {
         return [meta, fastq]
     }
 
+    // MODULE: multiqcsav
+    // Generate MultiQC report for demultiplexing step
+    ch_sav_input = ch_runinfo.join(ch_interop)
+    ch_mqc_input = ch_reports.mix(ch_stats).map { meta, files -> [meta, files.flatten()] }
+    ch_multiqcsav_input = ch_sav_input.join(ch_mqc_input).map{ meta, xml, bin, files -> [meta, xml, bin, files, [], [], [], []]}
+    MULTIQCSAV(
+        ch_multiqcsav_input
+    )
+
+    ch_multiqc_report  = MULTIQCSAV.out.report
+    ch_multiqc_data    = MULTIQCSAV.out.data
+    ch_multiqc_plots   = MULTIQCSAV.out.plots
+
     emit:
-    fastq       = ch_fastq.fastq
-    empty_fastq = ch_fastq.empty
-    reports     = ch_reports
-    stats       = ch_stats
-    interop     = ch_interop
-    logs        = ch_logs
+    fastq           = ch_fastq.fastq
+    empty_fastq     = ch_fastq.empty
+    reports         = ch_reports
+    stats           = ch_stats
+    interop         = ch_interop
+    logs            = ch_logs
+    multiqc_report  = ch_multiqc_report
+    multiqc_data    = ch_multiqc_data
+    multiqc_plots   = ch_multiqc_plots
 }
 
 def generateReadgroupBCLCONVERT(ch_fastq_list_csv, ch_fastq) {

diff --git a/subworkflows/nf-core/bcl_demultiplex/meta.yml b/subworkflows/nf-core/bcl_demultiplex/meta.yml
@@ -7,9 +7,11 @@ keywords:
   - bcl2fastq
   - demultiplex
   - fastq
+  - multiqcsav
 components:
   - bcl2fastq
   - bclconvert
+  - multiqcsav
 input:
   - meta:
       type: map
@@ -52,6 +54,18 @@ output:
       type: file
       description: Demultiplexing logs (bclconvert only)
       pattern: "Logs/*"
+  - multiqc_report:
+      type: file
+      description: Multiqc report
+      pattern: "*.html"
+  - multiqc_data:
+      type: file
+      description: Multiqc data
+      pattern: "*_data"
+  - multiqc_plots:
+      type: file
+      description: Multiqc plots
+      pattern: "*_plots"
   - versions:
       type: file
       description: File containing software versions

diff --git a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test
@@ -11,6 +11,7 @@ nextflow_workflow {
     tag "subworkflows/bcl_demultiplex"
     tag "bclconvert"
     tag "bcl2fastq"
+    tag "multiqcsav"
 
     test("bclconvert") {
 
@@ -32,7 +33,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs"]).collectEntries { key, val ->
+                    sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "multiqc_data", "multiqc_report"]).collectEntries { key, val ->
                         if (key == "interop") {
                             return [ key, val.collect { meta, files ->
                                 [
@@ -75,7 +76,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    sanitizeOutput(workflow.out).collectEntries { key, val ->
+                    sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "multiqc_data", "multiqc_report"]).collectEntries { key, val ->
                         if (key == "fastq")
                         if (key == "interop") {
                             return [ key, val.collect { meta, files ->