Update to topic pints

modules/nf-core/pints/caller/environment.yml

@@ -4,11 +4,13 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bedtools=2.31.1
-  - htslib=1.22.1
-  - pip=25.2
-  - pybedtools=0.12.0
-  - python=3.12.6
+  - bioconda::bedtools=2.31.1
+  - bioconda::htslib=1.22.1
+  - bioconda::pybedtools=0.12.0
+  - conda-forge::python=3.12.6
+  - conda-forge::numpy=2.1.1
+  - conda-forge::pandas=2.2.3
+  - conda-forge::pip=25.2
   - pip:
       # NOTE PINTS isn't adding conda builds and is a few versions behind.
       # renovate: datasource=pypi depName=pypints

modules/nf-core/pints/caller/main.nf

@@ -13,11 +13,12 @@ process PINTS_CALLER {
     val assay_type
 
     output:
-    tuple val(meta), path("*_divergent_peaks.bed")     , optional:true, emit: divergent_TREs
-    tuple val(meta), path("*_bidirectional_peaks.bed") , optional:true, emit: bidirectional_TREs
-    tuple val(meta), path("*_unidirectional_peaks.bed"), optional:true, emit: unidirectional_TREs
-    tuple val(meta), path("peakcalling_*.log")                        , emit: peakcalling_log
-    path  "versions.yml"                                              , emit: versions
+    tuple val(meta), path("*_divergent_peaks.bed")     , emit: divergent_TREs     , optional:true
+    tuple val(meta), path("*_bidirectional_peaks.bed") , emit: bidirectional_TREs , optional:true
+    tuple val(meta), path("*_unidirectional_peaks.bed"), emit: unidirectional_TREs, optional:true
+    tuple val(meta), path("peakcalling_*.log")         , emit: peakcalling_log
+    tuple val("${task.process}"), val('pints') , eval("pints_caller --version")               , emit: versions_pints , topic: versions
+    tuple val("${task.process}"), val('python'), eval("python --version | sed 's/Python //g'"), emit: versions_python, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,18 +32,22 @@ process PINTS_CALLER {
     //                    error "Please use bam or BigWig files"
     """
     pints_caller \\
-        --bam-file $bams \\
+        --bam-file ${bams} \\
         --save-to . \\
-        --file-prefix $prefix \\
-        --thread $task.cpus \\
+        --file-prefix ${prefix} \\
+        --thread ${task.cpus} \\
         --dont-check-updates \\
-        --exp-type $assay_type \\
-        $args
+        --exp-type ${assay_type} \\
+        ${args}
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-        pints: \$(pints_caller --version)
-    END_VERSIONS
+    """
+    touch ${prefix}_divergent_peaks.bed
+    touch ${prefix}_bidirectional_peaks.bed
+    touch ${prefix}_unidirectional_peaks.bed
+    touch peakcalling_2026_08_05_14_20_53_41.log
     """
 }

modules/nf-core/pints/caller/meta.yml

@@ -19,7 +19,8 @@ tools:
       documentation: "https://github.com/hyulab/PINTS/blob/main/README.md"
       tool_dev_url: "https://github.com/hyulab/PINTS"
       doi: "10.1038/s41587-022-01211-7"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:pyPINTS
 input:
   - - meta:
@@ -73,8 +74,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*_unidirectional_peaks.bed":
           type: file
-          description: Unidirectional TREs, maybe lncRNAs transcribed from enhancers
-            (e-lncRNAs)
+          description: Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs)
           pattern: "*_unidirectional_peaks.bed"
           optional: true
           ontologies: []
@@ -89,13 +89,50 @@ output:
           description: Peakcalling log for debugging purposes
           pattern: "peakcalling_*.log"
           ontologies: []
+  versions_pints:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pints:
+          type: string
+          description: The name of the tool
+      - pints_caller --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+
+  versions_python:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - python:
+          type: string
+          description: The name of the tool
+      - python --version | sed 's/Python //g':
+          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
+      - pints:
+          type: string
+          description: The name of the tool
+      - pints_caller --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - python:
+          type: string
+          description: The name of the tool
+      - python --version | sed 's/Python //g':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@edmundmiller"
 maintainers:

modules/nf-core/pints/caller/tests/main.nf.test

@@ -31,25 +31,24 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
+                { assert snapshot( // Ignore peakcalling_log as file name has time stamp
                     process.out.divergent_TREs,
                     process.out.bidirectional_TREs,
-                    file(process.out.unidirectional_TREs.get(0).get(1).get(0)).name,
-                    path(process.out.versions.get(0)).yaml,
-                ).match("bams")
-                },
+                    process.out.unidirectional_TREs.collect{meta, beds -> [meta, beds.collect{bed -> file(bed).name}]},
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
             )
         }
-
     }
 
     test("groHMM data - [bam], fasta") {
+        tag "test"
 
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ],
                     file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S0mR1.bam", checkIfExists: true),
                     [],
                 ]
@@ -61,14 +60,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
+                { assert snapshot( // Ignore peakcalling_log as file name has time stamp
                     process.out.divergent_TREs,
                     process.out.bidirectional_TREs,
-                    file(process.out.unidirectional_TREs[0][1]).name,
-                    path(process.out.versions.get(0)).yaml,
-                ).match("single_bam")
-                },
-                { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") },
+                    process.out.unidirectional_TREs.collect{meta, bed -> [meta, file(bed).name]},
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
             )
         }
     }
@@ -79,7 +76,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ],
+                    [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
                     [],
                 ]
@@ -96,6 +93,32 @@ nextflow_process {
         }
     }
 
+    test("groHMM data - [bam, bam], fasta -- stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S0mR1.bam", checkIfExists: true),
+                        file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S40mR1.bam", checkIfExists: true)
+                    ],
+                    [],
+                ]
+                input[1] = "GROseq"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
     // TODO Test single bigwig input
     // TODO Test multiple bigwig input
 }