topic migration crispresso2

modules/nf-core/crispresso2/environment.yml

@@ -4,4 +4,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::crispresso2=2.3.3"
+  - bioconda::bowtie2=2.5.4
+  - bioconda::crispresso2=2.3.3
+  - bioconda::fastp=1.0.1
+  - bioconda::samtools=1.22

modules/nf-core/crispresso2/main.nf

@@ -14,7 +14,7 @@ process CRISPRESSO2 {
     tuple val(meta), path("CRISPResso_on_*")        , emit: results
     tuple val(meta), path("*.html")                 , emit: html
     tuple val(meta), path("CRISPResso_on_*/*.txt")  , emit: txt
-    path "versions.yml"                             , emit: versions
+    tuple val("${task.process}"), val('crispresso2'), eval("CRISPResso --version 2>&1 | sed 's/CRISPResso //'"), emit: versions_crispresso2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,34 +32,26 @@ process CRISPRESSO2 {
     }
 
     """
+    export MPLCONFIGDIR=.matplotlib
     CRISPResso \\
         ${read_inputs} \\
         --name ${prefix} \\
         --output_folder . \\
         ${args}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        crispresso2: \$(CRISPResso --version 2>&1 | grep -o 'CRISPResso version [0-9.]*' | sed 's/CRISPResso version //')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     #!/usr/bin/env bash
     set -e
+    export MPLCONFIGDIR=.matplotlib
 
     mkdir -p CRISPResso_on_${prefix}
     touch CRISPResso_on_${prefix}/${prefix}.html
     touch CRISPResso_on_${prefix}/CRISPResso_report.html
     touch CRISPResso_on_${prefix}/CRISPResso_mapping_statistics.txt
     touch CRISPResso_on_${prefix}/quantification_of_editing_frequency.txt
     touch ${prefix}.html
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        crispresso2: 2.3.3
-    END_VERSIONS
     """
 }

modules/nf-core/crispresso2/meta.yml

@@ -15,9 +15,9 @@ tools:
       documentation: "https://docs.crispresso.com"
       tool_dev_url: "https://github.com/pinellolab/CRISPResso2"
       doi: "10.1038/s41587-019-0032-3"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: biotools:crispresso2
-
 input:
   - - meta:
         type: map
@@ -31,7 +31,6 @@ input:
         pattern: "*.{fastq,fq,fastq.gz,fq.gz}"
         ontologies:
           - edam: http://edamontology.org/format_1930 # FASTQ
-
 output:
   results:
     - - meta:
@@ -61,20 +60,33 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'test', single_end:false ]`
-      - "CRISPResso_on_*/*.txt":
+      - CRISPResso_on_*/*.txt:
           type: file
           description: CRISPResso text output files
           pattern: "CRISPResso_on_*/*.txt"
           ontologies:
             - edam: http://edamontology.org/format_2330 # Textual format
+  versions_crispresso2:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - crispresso2:
+          type: string
+          description: The name of the tool
+      - CRISPResso --version 2>&1 | sed 's/CRISPResso //':
+          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
+      - crispresso2:
+          type: string
+          description: The name of the tool
+      - CRISPResso --version 2>&1 | sed 's/CRISPResso //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@sathyasjali"
 maintainers:

modules/nf-core/crispresso2/tests/main.nf.test

@@ -24,12 +24,14 @@ nextflow_process {
         }
 
         then {
-            assertAll(
+        assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("single_end_versions") },
-                { assert process.out.results[0][1].size() > 0 },
-                { assert process.out.html[0][1].size() > 0 },
-                { assert process.out.txt[0][1].size() > 0 }
+                { assert snapshot(
+                    process.out.results[0][1].size(),
+                    file(process.out.html[0][1]).name,
+                    process.out.txt[0][1].size(),
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() },
             )
         }
     }
@@ -55,10 +57,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("paired_end_versions") },
-                { assert process.out.results[0][1].size() > 0 },
-                { assert process.out.html[0][1].size() > 0 },
-                { assert process.out.txt[0][1].size() > 0 }
+                { assert snapshot(
+                    process.out.results[0][1].size(),
+                    process.out.html[0][1].collect{ html -> file(html).name }.sort(),
+                    process.out.txt[0][1].size(),
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() },
             )
         }
     }
@@ -81,10 +85,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("nhej_analysis_versions") },
-                { assert process.out.results[0][1].size() > 0 },
-                { assert process.out.html[0][1].size() > 0 },
-                { assert process.out.txt[0][1].size() > 0 }
+                { assert snapshot(
+                    process.out.results[0][1].size(),
+                    file(process.out.html[0][1]).name,
+                    process.out.txt[0][1].size(),
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() },
             )
         }
     }

modules/nf-core/crispresso2/tests/main.nf.test.snap

@@ -1,38 +1,68 @@
 {
-    "paired_end_versions": {
+    "crispresso2 - paired_end": {
         "content": [
+            2,
             [
-                "versions.yml:md5,2c04a720d2ac80a8651db90eaa1e8c35"
-            ]
+                "CRISPResso_on_paired_test.html",
+                "fastp.html"
+            ],
+            9,
+            {
+                "versions_crispresso2": [
+                    [
+                        "CRISPRESSO2",
+                        "crispresso2",
+                        "2.3.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-13T14:56:09.120398517",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-04T10:40:04.221264"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
-    "nhej_analysis_versions": {
+    "crispresso2 - nhej_analysis": {
         "content": [
-            [
-                "versions.yml:md5,2c04a720d2ac80a8651db90eaa1e8c35"
-            ]
+            2,
+            "CRISPResso_on_nhej_test.html",
+            9,
+            {
+                "versions_crispresso2": [
+                    [
+                        "CRISPRESSO2",
+                        "crispresso2",
+                        "2.3.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-13T15:34:17.493407027",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-04T10:40:15.66427"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
-    "single_end_versions": {
+    "crispresso2 - single_end": {
         "content": [
-            [
-                "versions.yml:md5,2c04a720d2ac80a8651db90eaa1e8c35"
-            ]
+            2,
+            "CRISPResso_on_test.html",
+            9,
+            {
+                "versions_crispresso2": [
+                    [
+                        "CRISPRESSO2",
+                        "crispresso2",
+                        "2.3.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-13T15:32:17.852481198",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-04T10:39:52.068269"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }