Rseqc add bam index - topics-based versions - version bump

modules/nf-core/rseqc/bamstat/environment.yml

@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::rseqc=5.0.3
+  - bioconda::rseqc=5.0.4
   - conda-forge::r-base=3.5

modules/nf-core/rseqc/bamstat/main.nf

@@ -4,15 +4,15 @@ process RSEQC_BAMSTAT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.4--pyhdfd78af_1' :
+        'biocontainers/rseqc:5.0.4--pyhdfd78af_1' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai)
 
     output:
     tuple val(meta), path("*.bam_stat.txt"), emit: txt
-    path  "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('rseqc'), eval('bam_stat.py --version | sed "s/bam_stat.py //"'), emit: versions_rseqc, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,21 +25,11 @@ process RSEQC_BAMSTAT {
         -i $bam \\
         $args \\
         > ${prefix}.bam_stat.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(bam_stat.py --version | sed -e "s/bam_stat.py //g")
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam_stat.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(bam_stat.py --version | sed -e "s/bam_stat.py //g")
-    END_VERSIONS
     """
 }

modules/nf-core/rseqc/bamstat/meta.yml

@@ -25,6 +25,11 @@ input:
         description: the bam file to calculate statistics of
         pattern: "*.{bam}"
         ontologies: []
+    - bai:
+        type: file
+        description: BAM index file
+        pattern: "*.{bai}"
+        ontologies: []
 output:
   txt:
     - - meta:
@@ -37,16 +42,32 @@ output:
           description: bam statistics report
           pattern: "*.bam_stat.txt"
           ontologies: []
+  versions_rseqc:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - rseqc:
+          type: string
+          description: The tool name
+      - bam_stat.py --version | sed "s/bam_stat.py //":
+          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 process the versions were collected from
+      - rseqc:
+          type: string
+          description: The tool name
+      - bam_stat.py --version | sed "s/bam_stat.py //":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+  - "@rhassaine"
 maintainers:
   - "@drpatelh"
   - "@kevinmenden"
+  - "@rhassaine"

modules/nf-core/rseqc/bamstat/tests/main.nf.test

@@ -16,38 +16,44 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [
+                input[0] = channel.of([
                     [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam')
-                ]
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
                 """
             }
         }
 
         then {
-            assert process.success
-            assert snapshot(process.out).match()
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
         }
     }
 
     test("sarscov2 - [meta] - bam - stub") {
 
-    options "-stub"
+        options "-stub"
 
         when {
             process {
                 """
-                input[0] = [
+                input[0] = channel.of([
                     [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam')
-                ]
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
                 """
             }
         }
 
         then {
-            assert process.success
-            assert snapshot(process.out).match()
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
         }
     }
 }

modules/nf-core/rseqc/bamstat/tests/main.nf.test.snap

@@ -11,7 +11,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,58f74a7ff9d2966142c81a4a4735dbf3"
+                    [
+                        "RSEQC_BAMSTAT",
+                        "rseqc",
+                        "5.0.4"
+                    ]
                 ],
                 "txt": [
                     [
@@ -21,16 +25,20 @@
                         "test.bam_stat.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,58f74a7ff9d2966142c81a4a4735dbf3"
+                "versions_rseqc": [
+                    [
+                        "RSEQC_BAMSTAT",
+                        "rseqc",
+                        "5.0.4"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-06-21T09:16:13.970299"
+        "timestamp": "2025-12-10T12:09:27.652778872"
     },
     "sarscov2 - [meta] - bam": {
         "content": [
@@ -44,7 +52,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,58f74a7ff9d2966142c81a4a4735dbf3"
+                    [
+                        "RSEQC_BAMSTAT",
+                        "rseqc",
+                        "5.0.4"
+                    ]
                 ],
                 "txt": [
                     [
@@ -54,15 +66,19 @@
                         "test.bam_stat.txt:md5,2675857864c1d1139b2a19d25dc36b09"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,58f74a7ff9d2966142c81a4a4735dbf3"
+                "versions_rseqc": [
+                    [
+                        "RSEQC_BAMSTAT",
+                        "rseqc",
+                        "5.0.4"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2023-12-14T17:00:23.830276754"
+        "timestamp": "2025-12-10T12:09:21.393873778"
     }
 }

modules/nf-core/rseqc/inferexperiment/environment.yml

@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::rseqc=5.0.3
+  - bioconda::rseqc=5.0.4
   - conda-forge::r-base=3.5

modules/nf-core/rseqc/inferexperiment/main.nf

@@ -4,16 +4,16 @@ process RSEQC_INFEREXPERIMENT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.4--pyhdfd78af_1' :
+        'biocontainers/rseqc:5.0.4--pyhdfd78af_1' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai)
     path  bed
 
     output:
     tuple val(meta), path("*.infer_experiment.txt"), emit: txt
-    path  "versions.yml"                           , emit: versions
+    tuple val("${task.process}"), val('rseqc'), eval('infer_experiment.py --version | sed "s/infer_experiment.py //"'), emit: versions_rseqc, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,21 +27,11 @@ process RSEQC_INFEREXPERIMENT {
         -r $bed \\
         $args \\
         > ${prefix}.infer_experiment.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.infer_experiment.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
-    END_VERSIONS
     """
 }

modules/nf-core/rseqc/inferexperiment/meta.yml

@@ -25,6 +25,11 @@ input:
         description: the bam file to calculate statistics of
         pattern: "*.{bam}"
         ontologies: []
+    - bai:
+        type: file
+        description: BAM index file
+        pattern: "*.{bai}"
+        ontologies: []
   - bed:
       type: file
       description: a bed file for the reference gene model
@@ -42,16 +47,34 @@ output:
           description: infer_experiment results report
           pattern: "*.infer_experiment.txt"
           ontologies: []
+  versions_rseqc:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - rseqc:
+          type: string
+          description: The name of the tool
+      - infer_experiment.py --version | sed "s/infer_experiment.py //":
+          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
+      - rseqc:
+          type: string
+          description: The name of the tool
+      - infer_experiment.py --version | sed "s/infer_experiment.py //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+  - "@rhassaine"
 maintainers:
   - "@drpatelh"
   - "@kevinmenden"
+  - "@rhassaine"

modules/nf-core/rseqc/inferexperiment/tests/main.nf.test

@@ -15,11 +15,12 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                     [ id:'test' ], // meta map
-                file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
                 ])
-                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true))
+                input[1] = channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true))
                 """
             }
         }
@@ -37,11 +38,12 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                     [ id:'test' ], // meta map
-                file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
                 ])
-                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true))
+                input[1] = channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true))
                 """
             }
         }