Updare fgbio/copyumifromreadname

modules/nf-core/fgbio/copyumifromreadname/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::fgbio=2.4.0
+  - bioconda::fgbio=3.0.0

modules/nf-core/fgbio/copyumifromreadname/main.nf

@@ -3,22 +3,21 @@ process FGBIO_COPYUMIFROMREADNAME {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' :
-        'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }"
+    container workflow.containerEngine in ['singularity', 'apptainer'] ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f3f7e07c7f261ec7fd86168d8a273624cc0aace8e28eb20e37ddfb2f8f9c75b/data' :
+        'community.wave.seqera.io/library/fgbio:3.0.0--c1b70e1869d6fa49'
 
     input:
     tuple val(meta), path(bam), path(bai)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
     tuple val(meta), path("*.bai"), emit: bai
-    path "versions.yml"           , emit: versions
+    tuple val(task.process), val("fgbio"), eval("fgbio --version 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+'"), topic: versions, emit: versions_fgbio
 
     when:
     task.ext.when == null || task.ext.when
 
-
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}_umi_extracted"
@@ -41,24 +40,12 @@ process FGBIO_COPYUMIFROMREADNAME {
         ${args} \\
         --input ${bam} \\
         --output ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
-    END_VERSIONS
     """
 
-
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}_umi_extracted"
     """
-
     touch ${prefix}.bam
     touch ${prefix}.bai
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fgbio: \$(fgbio --version)
-    END_VERSIONS
     """
 }

modules/nf-core/fgbio/copyumifromreadname/meta.yml

@@ -66,14 +66,27 @@ output:
           pattern: "*.{bai}"
           ontologies:
             - edam: "http://edamontology.org/format_3327" # BAI
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_fgbio:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fgbio:
+          type: string
+          description: The tool name
+      - fgbio --version 2>&1 | grep -oE '[0-9]+(\\.[0-9]+:
+          type: string
+          description: The command used to generate the version of the tool
+topics:
+  - versions:
+      - - process:
+            type: string
+            description: The process the versions were collected from
+        - tool:
+            type: string
+            description: The tool name
+        - version:
+            type: string
+            description: The version of the tool
 authors:
   - "@sppearce"
 maintainers:

modules/nf-core/fgbio/copyumifromreadname/tests/main.nf.test

@@ -31,8 +31,7 @@ nextflow_process {
             assert process.success
             assertAll(
                 { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
+                    process.out
                     ).match()
                 }
             )
@@ -64,7 +63,6 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     process.out,
-                    path(process.out.versions[0]).yaml
                     ).match()
                 }
             )

modules/nf-core/fgbio/copyumifromreadname/tests/main.nf.test.snap

@@ -19,7 +19,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,1440a1d99b4c503c037f5325445eb7e6"
+                    [
+                        "FGBIO_COPYUMIFROMREADNAME",
+                        "fgbio",
+                        "3.0.0"
+                    ]
                 ],
                 "bai": [
                     [
@@ -37,21 +41,20 @@
                         "test_umi_extracted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,1440a1d99b4c503c037f5325445eb7e6"
+                "versions_fgbio": [
+                    [
+                        "FGBIO_COPYUMIFROMREADNAME",
+                        "fgbio",
+                        "3.0.0"
+                    ]
                 ]
-            },
-            {
-                "FGBIO_COPYUMIFROMREADNAME": {
-                    "fgbio": null
-                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-04-21T10:27:36.454432228"
+        "timestamp": "2025-11-10T10:20:22.199167232"
     },
     "sarscov2 - bam": {
         "content": [
@@ -73,7 +76,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,047dd6edb85ae3f51a255523a2bfcfc6"
+                    [
+                        "FGBIO_COPYUMIFROMREADNAME",
+                        "fgbio",
+                        "3.0.0"
+                    ]
                 ],
                 "bai": [
                     [
@@ -91,20 +98,19 @@
                         "test_umi_extracted.bam:md5,245b5f4c2002dc6560353c5183247df3"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,047dd6edb85ae3f51a255523a2bfcfc6"
+                "versions_fgbio": [
+                    [
+                        "FGBIO_COPYUMIFROMREADNAME",
+                        "fgbio",
+                        "3.0.0"
+                    ]
                 ]
-            },
-            {
-                "FGBIO_COPYUMIFROMREADNAME": {
-                    "fgbio": "2.4.0"
-                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-04-21T10:27:16.185419539"
+        "timestamp": "2025-11-10T10:20:12.521127046"
     }
 }