update bclconvert with topic

modules/nf-core/bclconvert/Dockerfile

@@ -2,6 +2,24 @@
 # Dockerfile to create container with bcl-convert
 # Push to nfcore/bclconvert:<VER>
 
+# Build stage: unpack the RPM file
+FROM debian:bullseye-slim AS build
+ARG BCLCONVERT_VERSION="4.4.6"
+
+# Install tools needed to extract RPM
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+    rpm2cpio \
+    cpio \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Extract bcl-convert from RPM
+COPY bcl-convert-4.4.6-2.el8.x86_64.rpm bcl-convert.rpm
+RUN rpm2cpio bcl-convert.rpm | cpio -idmv \
+    && rm bcl-convert.rpm
+
+# Final stage: minimal image with only necessary components
 FROM debian:bullseye-slim
 ARG BCLCONVERT_VERSION="4.4.6"
 LABEL org.opencontainers.image.description="Docker image containing bcl-convert"
@@ -12,20 +30,16 @@ LABEL org.opencontainers.image.vendor="nf-core"
 LABEL org.opencontainers.image.license="https://github.com/nf-core/modules/blob/master/modules/nf-core/bclconvert/LICENSE"
 
 # Disclaimer: this container is not provided nor supported by Illumina
-# 'ps' command is need by some nextflow executions to collect system stats
-# Install procps and clean apt cache
+# Install procps (for 'ps' command needed by Nextflow) and rclone (for parallel file transfers)
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
     procps \
-    rpm2cpio \
-    cpio \
+    rclone \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
+
 # Link hostname cmd to fix hardcoded path
 RUN ln -s /bin/hostname /usr/bin/hostname
-# Install bcl-convert
-COPY bcl-convert-4.4.6-2.el8.x86_64.rpm bcl-convert.rpm
-SHELL ["/bin/bash", "-o", "pipefail", "-c"]
-RUN rpm2cpio bcl-convert.rpm | cpio -idmv \
-    && rm bcl-convert.rpm
-RUN rm -rf /var/log/bcl-convert && ln -sfT /tmp /var/log/bcl-convert
+
+# Copy bcl-convert executable from build stage
+COPY --from=build /usr/bin/bcl-convert /usr/bin/bcl-convert

modules/nf-core/bclconvert/main.nf

@@ -2,7 +2,7 @@ process BCLCONVERT {
     tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" }
     label 'process_high'
 
-    container "nf-core/bclconvert:4.4.6"
+    container "nf-core/bclconvert:4.4.6_1"
 
     input:
     tuple val(meta), path(samplesheet), path(run_dir)
@@ -12,10 +12,10 @@ process BCLCONVERT {
     tuple val(meta), path("output/**_S[1-9]*_I?_00?.fastq.gz")        , emit: fastq_idx       , optional:true
     tuple val(meta), path("output/**Undetermined_S0*_R?_00?.fastq.gz"), emit: undetermined    , optional:true
     tuple val(meta), path("output/**Undetermined_S0*_I?_00?.fastq.gz"), emit: undetermined_idx, optional:true
-    tuple val(meta), path("output/Reports")                           , emit: reports
-    tuple val(meta), path("output/Logs")                              , emit: logs
-    tuple val(meta), path("output/InterOp/*.bin")                     , emit: interop         , optional:true
-    path("versions.yml")                                              , emit: versions
+    tuple val(meta), path("output/Reports/*")                         , emit: reports
+    tuple val(meta), path("output/Logs/*")                            , emit: logs
+    tuple val(meta), path("output/InterOp/*.bin")                     , emit: interop
+    tuple val("${task.process}"), val('bclconvert'), eval("bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //'"), topic: versions, emit: versions_bclconvert
 
     when:
     task.ext.when == null || task.ext.when
@@ -65,11 +65,6 @@ process BCLCONVERT {
     # copy the InterOp folder contents to ensure it gets picked up when using fusion
     mkdir -p output/InterOp/
     cp -n **/InterOp/*.bin output/InterOp/
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
-    END_VERSIONS
     """
 
     stub:
@@ -102,10 +97,6 @@ process BCLCONVERT {
     touch output/InterOp/IndexMetricsOut.bin
     touch output/InterOp/QMetricsOut.bin
     touch output/InterOp/TileMetricsOut.bin
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
-    END_VERSIONS
     """
 
 }

modules/nf-core/bclconvert/meta.yml

@@ -99,13 +99,18 @@ output:
           description: Interop files
           pattern: "*.{bin}"
           ontologies: []
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - bclconvert:
+          type: string
+          description: The tool name
+      - "bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //'":
+          type: string
+          description: The command used to generate the version of the tool
+
 authors:
   - "@matthdsm"
 maintainers:

modules/nf-core/bclconvert/tests/main.nf.test

@@ -34,12 +34,11 @@ nextflow_process {
                     process.out.undetermined.collect { meta, fastq -> file(fastq).name },
                     process.out.undetermined_idx,
                     process.out.reports,
-                    process.out.logs.collect { meta, logs -> file(logs).list().sort() },
+                    process.out.logs.collect { meta, logs -> logs.sort() },
                     process.out.interop.collect { meta, interop ->
                                                 interop.findAll { interopfile ->
                                                 file(interopfile).name != "IndexMetricsOut.bin" } },
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match() }
             )
         }
@@ -76,13 +75,12 @@ nextflow_process {
                     process.out.undetermined.collect { meta, fastq -> file(fastq).name },
                     process.out.undetermined_idx,
                     process.out.reports,
-                    process.out.logs.collect { meta, logs -> file(logs).list().sort() },
+                    process.out.logs.collect { meta, logs -> logs.sort() },
                     process.out.interop,
                     process.out.interop.collect { meta, interop ->
                                                 interop.findAll { interopfile ->
                                                 file(interopfile).name != "IndexMetricsOut.bin" } },
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match() }
             )
         }

modules/nf-core/bclconvert/tests/main.nf.test.snap

@@ -42,10 +42,10 @@
             ],
             [
                 [
-                    "Errors.log",
-                    "FastqComplete.txt",
-                    "Info.log",
-                    "Warnings.log"
+                    "Errors.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "FastqComplete.txt:md5,081aedbb6928d0f348031f9ca49ac468",
+                    "Info.log:md5,bec9273b64edca95b3b53c929dd8fdfc",
+                    "Warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ],
             [
@@ -92,20 +92,21 @@
                     "TileMetricsOut.bin:md5,21388348d81fa9be326d30ef6d348464"
                 ]
             ],
-            [
-                "versions.yml:md5,a7ddd79ad04a69cb254185a11296f1b6"
-            ],
             {
-                "BCLCONVERT": {
-                    "bclconvert": "4.4.6"
-                }
+                "versions_bclconvert": [
+                    [
+                        "BCLCONVERT",
+                        "bclconvert",
+                        "4.4.6"
+                    ]
+                ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-09-23T10:12:42.943671245"
+        "timestamp": "2025-12-02T14:58:16.031029"
     },
     "homo_sapiens illumina [bcl] - stub": {
         "content": [
@@ -188,7 +189,11 @@
                     ]
                 ],
                 "7": [
-                    "versions.yml:md5,a7ddd79ad04a69cb254185a11296f1b6"
+                    [
+                        "BCLCONVERT",
+                        "bclconvert",
+                        "4.4.6"
+                    ]
                 ],
                 "fastq": [
                     [
@@ -267,16 +272,20 @@
                 "undetermined_idx": [
 
                 ],
-                "versions": [
-                    "versions.yml:md5,a7ddd79ad04a69cb254185a11296f1b6"
+                "versions_bclconvert": [
+                    [
+                        "BCLCONVERT",
+                        "bclconvert",
+                        "4.4.6"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-09-23T10:12:55.362214653"
+        "timestamp": "2025-12-02T14:30:30.75002"
     },
     "homo_sapiens illumina [bcl]": {
         "content": [
@@ -323,10 +332,10 @@
             ],
             [
                 [
-                    "Errors.log",
-                    "FastqComplete.txt",
-                    "Info.log",
-                    "Warnings.log"
+                    "Errors.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "FastqComplete.txt:md5,388544f10d63d386a8d20865abf22557",
+                    "Info.log:md5,2f3fa352080124ed5ee62afbdbc999d4",
+                    "Warnings.log:md5,a7ec94ec82336a0e81409fe13b922f4a"
                 ]
             ],
             [
@@ -339,19 +348,20 @@
                     "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c"
                 ]
             ],
-            [
-                "versions.yml:md5,a7ddd79ad04a69cb254185a11296f1b6"
-            ],
             {
-                "BCLCONVERT": {
-                    "bclconvert": "4.4.6"
-                }
+                "versions_bclconvert": [
+                    [
+                        "BCLCONVERT",
+                        "bclconvert",
+                        "4.4.6"
+                    ]
+                ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-09-23T10:12:18.369689549"
+        "timestamp": "2025-12-02T14:57:47.218447"
     }
 }

subworkflows/nf-core/bcl_demultiplex/main.nf

@@ -51,7 +51,6 @@ 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_versions = ch_versions.mix(BCLCONVERT.out.versions.first())
         }
 
         // MODULE: bcl2fastq

subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap

@@ -130,7 +130,12 @@
                             "id": "HMTFYDRXX",
                             "lane": 1
                         },
-                        "Logs"
+                        [
+                            "Errors.log",
+                            "FastqComplete.txt",
+                            "Info.log",
+                            "Warnings.log"
+                        ]
                     ]
                 ],
                 "reports": [
@@ -160,15 +165,15 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,b1427a2b3abad63b04f1dd62c8f40e2e"
+
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-04T16:13:41.469897018"
+        "timestamp": "2025-12-02T14:30:56.578335"
     },
     "bcl2fastq": {
         "content": [