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

@@ -9,7 +9,8 @@ tools:
       description: "Demultiplex Illumina BCL files"
       homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
       documentation: "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm"
-      licence: ["ILLUMINA"]
+      licence:
+        - "ILLUMINA"
       identifier: ""
 input:
   - - meta:
@@ -22,7 +23,7 @@ input:
         description: "Input samplesheet"
         pattern: "*.{csv}"
         ontologies:
-          - edam: http://edamontology.org/format_3752 # CSV
+          - edam: http://edamontology.org/format_3752
     - run_dir:
         type: file
         description: |
@@ -33,79 +34,101 @@ output:
   fastq:
     - - meta:
           type: map
-          description: Groovy Map containing sample information
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - output/**_S[1-9]*_R?_00?.fastq.gz:
           type: file
           description: Demultiplexed sample FASTQ files
           pattern: "**_S*_L00?_R?_00?.fastq.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: http://edamontology.org/format_3989
   fastq_idx:
     - - meta:
           type: map
-          description: Groovy Map containing sample information
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - output/**_S[1-9]*_I?_00?.fastq.gz:
           type: file
           description: Optional demultiplexed index FASTQ files
           pattern: "**_S*_L00?_I?_00?.fastq.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: http://edamontology.org/format_3989
   undetermined:
     - - meta:
           type: map
-          description: Groovy Map containing sample information
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - output/**Undetermined_S0*_R?_00?.fastq.gz:
           type: file
           description: Optional undetermined sample FASTQ files
           pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: http://edamontology.org/format_3989
   undetermined_idx:
     - - meta:
           type: map
-          description: Groovy Map containing sample information
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - output/**Undetermined_S0*_I?_00?.fastq.gz:
           type: file
           description: Optional undetermined index FASTQ files
           pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: http://edamontology.org/format_3989
   reports:
     - - meta:
           type: map
-          description: Groovy Map containing sample information
-      - output/Reports:
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - output/Reports/*:
           type: file
-          description: Demultiplexing Reports
-          pattern: "Reports/*.{csv,xml}"
-          ontologies:
-            - edam: http://edamontology.org/format_3752 # CSV
-            - edam: http://edamontology.org/format_2332 # XML
+          description: Demultiplexing reports
+          pattern: "*.{html,txt}"
+          ontologies: []
   logs:
     - - meta:
           type: map
           description: Groovy Map containing sample information
-      - output/Logs:
+      - output/Logs/*:
           type: file
           description: Log files
-          pattern: "Logs/*.{log,txt}"
+          pattern: "*.{log,txt}"
           ontologies: []
   interop:
     - - meta:
           type: map
           description: Groovy Map containing sample information
-      - "output/InterOp/*.bin":
+      - output/InterOp/*.bin:
           type: file
           description: Interop files
           pattern: "*.{bin}"
           ontologies: []
+  versions_bclconvert:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bclconvert:
+          type: string
+          description: The name of the tool
+      - bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+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 name of the process
+      - bclconvert:
+          type: string
+          description: The name of the tool
+      - bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@matthdsm"
 maintainers:

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

@@ -33,13 +33,12 @@ nextflow_process {
                     process.out.fastq_idx,
                     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.reports.collect { meta, reports -> reports.findAll {report -> file(report).name }},
+                    process.out.logs.collect { meta, logs -> logs.sort().findAll { log -> file(log).name} },
                     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() }
             )
         }
@@ -75,14 +74,13 @@ nextflow_process {
                     process.out.fastq_idx,
                     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.reports.collect { meta, reports -> reports.findAll {report -> file(report).name }},
+                    process.out.logs.collect { meta, logs -> logs.sort().findAll { log -> file(log).name} },
                     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() }
             )
         }