Update to topic qualimap

modules/nf-core/qualimap/bamqc/main.nf

@@ -24,37 +24,30 @@ process QUALIMAP_BAMQC {
 
     def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
     def memory = (task.memory.mega*0.8).intValue() + 'M'
-    def regions = gff ? "--gff $gff" : ''
+    def regions = gff ? "--gff ${gff}" : ''
 
-    def strandedness = 'non-strand-specific'
-    if (meta.strandedness == 'forward') {
-        strandedness = 'strand-specific-forward'
-    } else if (meta.strandedness == 'reverse') {
-        strandedness = 'strand-specific-reverse'
-    }
     """
     unset DISPLAY
     mkdir -p tmp
     export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
     qualimap \\
-        --java-mem-size=$memory \\
+        --java-mem-size=${memory} \\
         bamqc \\
-        $args \\
-        -bam $bam \\
-        $regions \\
-        -p $strandedness \\
-        $collect_pairs \\
-        -outdir $prefix \\
-        -nt $task.cpus
+        ${args} \\
+        -bam ${bam} \\
+        ${regions} \\
+        ${collect_pairs} \\
+        -outdir ${prefix} \\
+        -nt ${task.cpus}
     """
 
     stub:
-    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
-    mkdir -p $prefix/css
-    mkdir $prefix/images_qualimapReport
-    mkdir $prefix/raw_data_qualimapReport
-    cd $prefix/css
+    mkdir -p ${prefix}/css
+    mkdir ${prefix}/images_qualimapReport
+    mkdir ${prefix}/raw_data_qualimapReport
+    cd ${prefix}/css
     touch agogo.css
     touch basic.css
     touch bgtop.png

modules/nf-core/qualimap/bamqc/meta.yml

@@ -14,7 +14,8 @@ tools:
       homepage: http://qualimap.bioinfo.cipf.es/
       documentation: http://qualimap.conesalab.org/doc_html/index.html
       doi: 10.1093/bioinformatics/bts503
-      licence: ["GPL-2.0-only"]
+      licence:
+        - "GPL-2.0-only"
       identifier: biotools:qualimap
 input:
   - - meta:

modules/nf-core/qualimap/bamqc/tests/main.nf.test

@@ -12,25 +12,19 @@ nextflow_process {
         when {
             process {
                 """
-                gff = []
-
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
+                input[0] = [
+                    [ id:'test', single_end:false ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                input[1] = gff
+                ]
+                input[1] = []
                 """
             }
         }
 
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                    file("${process.out.results[0][1]}/qualimapReport.html").name,
-                    path("${process.out.results[0][1]}/genome_results.txt"),
-                    process.out.findAll {key, value -> key.startsWith("versions")})
-                    .match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys:["results"])).match() }
             )
         }
     }
@@ -40,21 +34,19 @@ nextflow_process {
         when {
             process {
                 """
-                gff = []
-
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
+                input[0] = [
+                    [ id:'test', single_end:false ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                input[1] = gff
+                ]
+                input[1] = []
                 """
             }
         }
 
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap

@@ -2,79 +2,6 @@
     "homo_sapiens [bam] - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            [
-                                "agogo.css:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "ajax-loader.gif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "basic.css:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "bgfooter.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "bgtop.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "comment-bright.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "comment-close.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "comment.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "doctools.js:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "down-pressed.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "down.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "file.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "jquery.js:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "minus.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "plus.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "pygments.css:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "qualimap_logo_small.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "report.css:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "searchtools.js:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "underscore.js:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "up-pressed.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "up.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "websupport.js:md5,d41d8cd98f00b204e9800998ecf8427e"
-                            ],
-                            "genome_results.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            [
-                                "genome_coverage_0to50_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_coverage_across_reference.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_coverage_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_coverage_quotes.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_gc_content_per_window.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_homopolymer_indels.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_insert_size_across_reference.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_insert_size_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_mapping_quality_across_reference.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_mapping_quality_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_reads_clipping_profile.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_reads_content_per_read_position.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_uniq_read_starts_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e"
-                            ],
-                            "qualimapReport.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            [
-                                "coverage_across_reference.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "coverage_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "duplication_rate_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_fraction_coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "homopolymer_indels.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "insert_size_across_reference.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "insert_size_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapped_reads_clipping_profile.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapped_reads_gc-content_distribution.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapped_reads_nucleotide_content.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapping_quality_across_reference.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapping_quality_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                            ]
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        "QUALIMAP_BAMQC",
-                        "qualimap",
-                        "2.3"
-                    ]
-                ],
                 "results": [
                     [
                         {
@@ -150,17 +77,24 @@
                 ]
             }
         ],
+        "timestamp": "2026-08-10T17:20:29.62252359",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-13T22:03:27.280522"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     },
     "homo_sapiens [bam]": {
         "content": [
-            "qualimapReport.html",
-            "genome_results.txt:md5,45103d63ba82df2b905eb04819c32dd3",
             {
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test"
+                    ]
+                ],
                 "versions_qualimap": [
                     [
                         "QUALIMAP_BAMQC",
@@ -170,10 +104,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-08-10T17:20:21.098222842",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-13T22:12:46.38879"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }

modules/nf-core/qualimap/bamqccram/main.nf

@@ -15,7 +15,8 @@ process QUALIMAP_BAMQCCRAM {
 
     output:
     tuple val(meta), path("${prefix}"), emit: results
-    path  "versions.yml"              , emit: versions
+    tuple val("${task.process}"), val('qualimap'), eval("qualimap -h | sed -n 's/^QualiMap v.//p'"), topic: versions, emit: versions_qualimap
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,47 +27,28 @@ process QUALIMAP_BAMQCCRAM {
 
     def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
     def memory = (task.memory.mega*0.8).intValue() + 'M'
-    def regions = gff ? "--gff $gff" : ''
+    def regions = gff ? "--gff ${gff}" : ''
 
-    def strandedness = 'non-strand-specific'
-    if (meta.strandedness == 'forward') {
-        strandedness = 'strand-specific-forward'
-    } else if (meta.strandedness == 'reverse') {
-        strandedness = 'strand-specific-reverse'
-    }
     """
     unset DISPLAY
     mkdir -p tmp
     export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
 
     samtools view -hb -T ${fasta} ${cram} |
     qualimap \\
-        --java-mem-size=$memory \\
+        --java-mem-size=${memory} \\
         bamqc \\
-        $args \\
+        ${args} \\
         -bam /dev/stdin \\
-        $regions \\
-        -p $strandedness \\
-        $collect_pairs \\
-        -outdir $prefix \\
-        -nt $task.cpus
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
+        ${regions} \\
+        ${collect_pairs} \\
+        -outdir ${prefix} \\
+        -nt ${task.cpus}
     """
 
     stub:
-    prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir ${prefix}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }

modules/nf-core/qualimap/bamqccram/meta.yml

@@ -14,7 +14,8 @@ tools:
       homepage: http://qualimap.bioinfo.cipf.es/
       documentation: http://qualimap.conesalab.org/doc_html/index.html
       doi: 10.1093/bioinformatics/bts503
-      licence: ["GPL-2.0-only"]
+      licence:
+        - "GPL-2.0-only"
       identifier: biotools:qualimap
 input:
   - - meta:
@@ -58,13 +59,50 @@ output:
           type: directory
           description: Qualimap results dir
           pattern: "*/*"
+  versions_qualimap:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - qualimap:
+          type: string
+          description: The name of the tool
+      - qualimap -h | sed -n 's/^QualiMap v.//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          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
+      - qualimap:
+          type: string
+          description: The name of the tool
+      - qualimap -h | sed -n 's/^QualiMap v.//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@FriederikeHanssen"
 maintainers: