Clair3 version topics migration (nf-core#10975)

* Clair3 version topics migration

* Solve conda tests

* Skip conda packaged_model

* Update snapshot

* Restore snapshot

* Update json

Author: EfraMP

.github/skip_nf_test.json

@@ -29,6 +29,7 @@
         "modules/nf-core/cellrangeratac/mkfastq",
         "modules/nf-core/cellrangeratac/mkref",
         "modules/nf-core/checkqc",
+        "modules/nf-core/clair3",
         "modules/nf-core/coreograph",
         "modules/nf-core/ctatsplicing/prepgenomelib",
         "modules/nf-core/ctatsplicing/startocancerintrons",

modules/nf-core/clair3/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::clair3=1.2.0"
+  - "bioconda::clair3=2.0.0"

modules/nf-core/clair3/main.nf

@@ -3,9 +3,9 @@ process CLAIR3 {
     label 'process_high'
 
     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/e7/e70b0f4389028f4dc88efde1aac7139927c898cf7add680e14724d97fecd3d32/data'
-        : 'community.wave.seqera.io/library/clair3:1.2.0--b1b03d4e9d1b6a2e'}"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    'docker://hkubal/clair3:v2.0.0' :
+    'docker.io/hkubal/clair3:v2.0.0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), val(packaged_model), path(user_model), val(platform)
@@ -19,18 +19,20 @@ process CLAIR3 {
     tuple val(meta), path("${prefix}phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true
     tuple val(meta), path("${prefix}merge_output.gvcf.gz"),           emit: gvcf, optional: true
     tuple val(meta), path("${prefix}merge_output.gvcf.gz.tbi"),       emit: gtbi, optional: true
-    path "versions.yml",                                              emit: versions
+    tuple val("${task.process}"), val('clair3'), eval('run_clair3.sh --version | sed "s/^Clair3 v//"'), emit: versions_clair3, topic: versions
+
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def model = ""
     if (!user_model) {
-        // In seqera containers `MAMBA_ROOT_PREFIX` is always available
-        // whereas `CONDA_PREFIX` may not be
-        // see https://github.com/seqeralabs/wave/issues/886
-        model = "\${CONDA_PREFIX:-\$MAMBA_ROOT_PREFIX}/bin/models/${packaged_model}"
+        if (workflow.containerEngine in ['singularity', 'docker', 'podman']) {
+            model = "/opt/models/${packaged_model}"
+        } else {
+            error "Clair3 packaged models are only available in Docker/Singularity/Podman containers. Please use one of these profiles or provide a user_model instead."
+        }
     }
     if (!packaged_model) {
         model = "${user_model}"
@@ -42,12 +44,12 @@ process CLAIR3 {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     run_clair3.sh \\
-        --bam_fn=${bam} \\
-        --ref_fn=${reference} \\
+        --bam_fn=\${PWD}/${bam} \\
+        --ref_fn=\${PWD}/${reference} \\
         --threads=${task.cpus} \\
         --output=. \\
         --platform=${platform} \\
-        --model=${model} \\
+        --model_path=${model} \\
         ${args}
 
     # Rename to add prefix
@@ -61,11 +63,6 @@ process CLAIR3 {
         mv "\$file" "${prefix}\$file"
     fi
     done
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        clair3: \$(run_clair3.sh  --version |& sed '1!d ; s/Clair3 v//')
-    END_VERSIONS
     """
 
     stub:
@@ -77,10 +74,5 @@ process CLAIR3 {
     touch ${prefix}merge_output.vcf.gz.tbi
     echo "" | gzip > ${prefix}merge_output.gvcf.gz
     touch ${prefix}merge_output.gvcf.gz.tbi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        clair3: \$(run_clair3.sh --version |& sed '1!d ; s/Clair3 v//')
-    END_VERSIONS
     """
 }

modules/nf-core/clair3/meta.yml

@@ -18,9 +18,9 @@ tools:
       documentation: "https://github.com/HKU-BAL/Clair3"
       tool_dev_url: "https://github.com/HKU-BAL/Clair3"
       doi: "10.1038/s43588-022-00387-x"
-      licence: ["BSD-3-clause"]
+      licence:
+        - "BSD-3-clause"
       identifier: biotools:clair3
-
 input:
   - - meta:
         type: map
@@ -42,15 +42,16 @@ input:
         ontologies: []
     - packaged_model:
         type: string
-        description: string containing the name of a prepackaged Clair3 model full list
-          of models and their descriptions is provided at https://github.com/HKU-BAL/Clair3?tab=readme-ov-file#pre-trained-models
+        description: string containing the name of a prepackaged Clair3 model full
+          list of models and their descriptions is provided at
+          https://github.com/HKU-BAL/Clair3?tab=readme-ov-file#pre-trained-models
     - user_model:
         type: directory
         description: directory containing Clair3 model files
     - platform:
         type: string
-        description: val in ['hifi','ont', 'ilmn'] to indicate pacbio, ONT, or illumina
-          respectively
+        description: val in ['hifi','ont', 'ilmn'] to indicate pacbio, ONT, or
+          illumina respectively
   - - meta2:
         type: map
         description: |
@@ -79,7 +80,7 @@ output:
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
           pattern: "*.{vcf,vcf.gz}"
-      - "${prefix}merge_output.vcf.gz":
+      - ${prefix}merge_output.vcf.gz:
           type: map
           description: |
             Groovy Map containing sample information
@@ -92,7 +93,7 @@ output:
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
           pattern: "*.{vcf,vcf.gz}"
-      - "${prefix}merge_output.vcf.gz.tbi":
+      - ${prefix}merge_output.vcf.gz.tbi:
           type: file
           description: index for vcf files
           pattern: "*.{vcf.tbi,vcf.tbi.gz}"
@@ -104,7 +105,7 @@ output:
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
           pattern: "*.{vcf,vcf.gz}"
-      - "${prefix}phased_merge_output.vcf.gz":
+      - ${prefix}phased_merge_output.vcf.gz:
           type: file
           description: phased vcf
           pattern: "*.{vcf,vcf.gz}"
@@ -116,7 +117,7 @@ output:
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
           pattern: "*.{vcf,vcf.gz}"
-      - "${prefix}phased_merge_output.vcf.gz.tbi":
+      - ${prefix}phased_merge_output.vcf.gz.tbi:
           type: file
           description: index for vcf files
           pattern: "*.{vcf.tbi,vcf.tbi.gz}"
@@ -128,7 +129,7 @@ output:
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
           pattern: "*.{vcf,vcf.gz}"
-      - "${prefix}merge_output.gvcf.gz":
+      - ${prefix}merge_output.gvcf.gz:
           type: file
           description: gvcf file
           pattern: "*.{gvcf,gvcf.gz}"
@@ -139,20 +140,33 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-          pattern: "*.{gvcf.tbi,gvcf.gz.tbi}"
-      - "${prefix}merge_output.gvcf.gz.tbi":
+          pattern: "*.{vcf,vcf.gz}"
+      - ${prefix}merge_output.gvcf.gz.tbi:
           type: file
           description: index for gvcf file
           pattern: "*.{vcf.tbi,vcf.tbi.gz}"
           ontologies: []
-
+  versions_clair3:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - clair3:
+          type: string
+          description: The name of the tool
+      - run_clair3.sh --version | sed "s/^Clair3 v//":
+          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
+      - clair3:
+          type: string
+          description: The name of the tool
+      - run_clair3.sh --version | sed "s/^Clair3 v//":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@robert-a-forsyth"
 maintainers:

modules/nf-core/clair3/tests/main.nf.test

@@ -18,7 +18,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test'],
-                    file(params.modules_testdata_base_path + 'generic/models/clair3.hifi.tar.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'generic/models/clair3_v2.hifi.tar.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -69,7 +69,7 @@ nextflow_process {
                         [file(it[1]).name, path(it[1]).vcf.summary]
                     },
                     process.out.gtbi.collect { file(it[1]).name },
-                    process.out.versions)
+                    process.out.findAll { key, val -> key.startsWith('versions') })
                     .match()}
             )
         }
@@ -120,7 +120,7 @@ nextflow_process {
                         [file(it[1]).name, path(it[1]).vcf.summary]
                     },
                     process.out.gtbi.collect { file(it[1]).name },
-                    process.out.versions)
+                    process.out.findAll { key, val -> key.startsWith('versions') })
                     .match()}
             )
         }
@@ -208,7 +208,7 @@ nextflow_process {
                         [file(it[1]).name, path(it[1]).vcf.summary]
                     },
                     process.out.gtbi.collect { file(it[1]).name },
-                    process.out.versions)
+                    process.out.findAll { key, val -> key.startsWith('versions') })
                     .match()}
             )
         }
@@ -253,7 +253,7 @@ nextflow_process {
                         process.out.phased_tbi,
                         process.out.gvcf,
                         process.out.gtbi,
-                        process.out.versions)
+                        process.out.findAll { key, val -> key.startsWith('versions') })
                         .match()}
             )
         }

modules/nf-core/clair3/tests/main.nf.test.snap

@@ -49,15 +49,21 @@
                     "testmerge_output.gvcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ],
-            [
-                "versions.yml:md5,bc9f9c29055f993dc8c5c8a3e8d32d1a"
-            ]
+            {
+                "versions_clair3": [
+                    [
+                        "CLAIR3",
+                        "clair3",
+                        "2.0.0"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-19T12:58:29.886268",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T12:49:24.796196"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2 - bam - packaged_model": {
         "content": [
@@ -82,22 +88,28 @@
             [
 
             ],
-            [
-                "versions.yml:md5,bc9f9c29055f993dc8c5c8a3e8d32d1a"
-            ]
+            {
+                "versions_clair3": [
+                    [
+                        "CLAIR3",
+                        "clair3",
+                        "2.0.0"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-20T04:12:38.663282558",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-02T10:27:38.84502"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2 - bam - user_model": {
         "content": [
             [
                 [
                     "testmerge_output.vcf.gz",
-                    "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=19, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]"
                 ]
             ],
             [
@@ -115,22 +127,28 @@
             [
 
             ],
-            [
-                "versions.yml:md5,bc9f9c29055f993dc8c5c8a3e8d32d1a"
-            ]
+            {
+                "versions_clair3": [
+                    [
+                        "CLAIR3",
+                        "clair3",
+                        "2.0.0"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-19T13:38:03.609361",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-02T10:27:17.499057"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2 - bam - user_model - gvcf": {
         "content": [
             [
                 [
                     "testmerge_output.vcf.gz",
-                    "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=19, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]"
                 ]
             ],
             [
@@ -145,20 +163,26 @@
             [
                 [
                     "testmerge_output.gvcf.gz",
-                    "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=457, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=456, phased=false, phasedAutodetect=false]"
                 ]
             ],
             [
                 "testmerge_output.gvcf.gz.tbi"
             ],
-            [
-                "versions.yml:md5,bc9f9c29055f993dc8c5c8a3e8d32d1a"
-            ]
+            {
+                "versions_clair3": [
+                    [
+                        "CLAIR3",
+                        "clair3",
+                        "2.0.0"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-19T13:39:12.428496",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-02T10:28:13.64925"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }