Convert sentieon modules to topics and update version

modules/nf-core/sentieon/applyvarcal/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202503.01
+  - bioconda::sentieon=202503.02

modules/nf-core/sentieon/applyvarcal/main.nf

@@ -5,8 +5,8 @@ process SENTIEON_APPLYVARCAL {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0f/0f1dfe59ef66d7326b43db9ab1f39ce6220b358a311078c949a208f9c9815d4e/data'
-        : 'community.wave.seqera.io/library/sentieon:202503.01--1863def31ed8e4d5'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73e9111552beb76e2ad3ad89eb75bed162d7c5b85b2433723ecb4fc96a02674a/data'
+        : 'community.wave.seqera.io/library/sentieon:202503.02--def60555294d04fa'}"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)
@@ -16,7 +16,7 @@ process SENTIEON_APPLYVARCAL {
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
     tuple val(meta), path("*.tbi"),    emit: tbi
-    path "versions.yml",               emit: versions
+    tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon
 
     when:
     task.ext.when == null || task.ext.when
@@ -41,22 +41,12 @@ process SENTIEON_APPLYVARCAL {
         --tranches_file ${tranches} \\
         ${args2} \\
         ${prefix}.vcf.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}_applyvarcal"
     """
     echo | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
-    END_VERSIONS
     """
 }

modules/nf-core/sentieon/applyvarcal/meta.yml

@@ -96,13 +96,28 @@ output:
           description: Index of recalibrated vcf file.
           pattern: "*vcf.gz.tbi"
           ontologies: []
+  versions_sentieon:
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - "sentieon":
+          type: string
+          description: The tool name
+      - 'sentieon driver --version | sed "s/.*-//g"':
+          type: string
+          description: The command used to generate the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions.
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - "sentieon":
+          type: string
+          description: The tool name
+      - 'sentieon driver --version | sed "s/.*-//g"':
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@assp8200"
 maintainers:

modules/nf-core/sentieon/applyvarcal/tests/main.nf.test

@@ -37,8 +37,7 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     path(process.out.vcf[0][1]).vcf.summary,
-                    file(process.out.tbi[0][1]).name,
-                    path(process.out.versions[0]).yaml
+                    file(process.out.tbi[0][1]).name
                     ).match()
                 }
             )
@@ -71,8 +70,7 @@ nextflow_process {
             assert process.success
             assertAll(
                 { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
+                    process.out
                     ).match()
                 }
             )

modules/nf-core/sentieon/applyvarcal/tests/main.nf.test.snap

@@ -2,18 +2,13 @@
     "homo sapiens": {
         "content": [
             "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=733, phased=false, phasedAutodetect=false]",
-            "test_applyvarcal.vcf.gz.tbi",
-            {
-                "SENTIEON_APPLYVARCAL": {
-                    "sentieon": 202503.01
-                }
-            }
+            "test_applyvarcal.vcf.gz.tbi"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-05-09T07:58:39.037594229"
+        "timestamp": "2026-01-19T18:19:13.890563238"
     },
     "homo sapiens -- stub": {
         "content": [
@@ -35,7 +30,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,debf15eb513a4082e53616c5a77e0477"
+                    [
+                        "SENTIEON_APPLYVARCAL",
+                        "sentieon",
+                        "202503.02"
+                    ]
                 ],
                 "tbi": [
                     [
@@ -53,20 +52,19 @@
                         "test_applyvarcal.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,debf15eb513a4082e53616c5a77e0477"
+                "versions_sentieon": [
+                    [
+                        "SENTIEON_APPLYVARCAL",
+                        "sentieon",
+                        "202503.02"
+                    ]
                 ]
-            },
-            {
-                "SENTIEON_APPLYVARCAL": {
-                    "sentieon": 202503.01
-                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-05-09T07:59:06.102870321"
+        "timestamp": "2026-01-19T18:19:21.793386558"
     }
-}
+}

modules/nf-core/sentieon/applyvarcal/tests/nextflow.config

@@ -1,10 +1,3 @@
-process {
-    withName: "SENTIEON_APPLYVARCAL" {
-        ext.args  = params.module_args
-        ext.args2 = params.module_args
-    }
-}
-
 env {
     // NOTE This is how nf-core/sarek users will use Sentieon in real world use
     // TODO: Update to `env('SENTIEON_LICSRVR_IP')` when minimum Nextflow version is >= 26.04.0
@@ -13,6 +6,13 @@ env {
     // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0
     SENTIEON_AUTH_MECH = System.getenv('SENTIEON_AUTH_MECH')
     SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA
-    // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file
+    // NOTE This is how users will test out Sentieon in Sarek with a license file
     // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
 }
+
+process {
+    withName: 'SENTIEON_APPLYVARCAL' {
+        ext.args  = params.module_args
+        ext.args2 = params.module_args2
+    }
+}

modules/nf-core/sentieon/bwaindex/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202503.01
+  - bioconda::sentieon=202503.02

modules/nf-core/sentieon/bwaindex/main.nf

@@ -5,36 +5,34 @@ process SENTIEON_BWAINDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0f/0f1dfe59ef66d7326b43db9ab1f39ce6220b358a311078c949a208f9c9815d4e/data'
-        : 'community.wave.seqera.io/library/sentieon:202503.01--1863def31ed8e4d5'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73e9111552beb76e2ad3ad89eb75bed162d7c5b85b2433723ecb4fc96a02674a/data'
+        : 'community.wave.seqera.io/library/sentieon:202503.02--def60555294d04fa'}"
 
     input:
     tuple val(meta), path(fasta)
 
     output:
     tuple val(meta), path("bwa"), emit: index
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ? "bwa/${task.ext.prefix}" : "bwa/${fasta.baseName}"
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64
+        ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; "
+        : ""
     """
+    ${sentieonLicense}
     mkdir bwa
 
     sentieon \\
         bwa index \\
         ${args} \\
         -p ${prefix} \\
         ${fasta}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
-        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
-    END_VERSIONS
     """
 
     stub:
@@ -46,11 +44,5 @@ process SENTIEON_BWAINDEX {
     touch bwa/genome.bwt
     touch bwa/genome.pac
     touch bwa/genome.sa
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
-        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
-    END_VERSIONS
     """
 }

modules/nf-core/sentieon/bwaindex/meta.yml

@@ -36,16 +36,28 @@ output:
           description: BWA genome index files
           pattern: "*.{amb,ann,bwt,pac,sa}"
           ontologies: []
+  versions_sentieon:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - sentieon:
+          type: string
+          description: The tool name
+      - 'sentieon driver --version | sed "s/.*-//g"':
+          type: string
+          description: The command used to generate 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
+      - sentieon:
+          type: string
+          description: The tool name
+      - 'sentieon driver --version | sed "s/.*-//g"':
+          type: string
+          description: The command used to generate the version of the tool
 authors:
-  - "@drpatelh"
   - "@maxulysse"
 maintainers:
-  - "@drpatelh"
   - "@maxulysse"

modules/nf-core/sentieon/bwaindex/tests/main.nf.test.snap

@@ -17,7 +17,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c217de4e5a992968de304e342fd720f6"
+                    [
+                        "SENTIEON_BWAINDEX",
+                        "sentieon",
+                        "202503.02"
+                    ]
                 ],
                 "index": [
                     [
@@ -33,16 +37,20 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,c217de4e5a992968de304e342fd720f6"
+                "versions_sentieon": [
+                    [
+                        "SENTIEON_BWAINDEX",
+                        "sentieon",
+                        "202503.02"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-08-21T08:16:59.165128416"
+        "timestamp": "2026-01-19T18:27:10.208416609"
     },
     "build index - fasta": {
         "content": [
@@ -62,7 +70,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c217de4e5a992968de304e342fd720f6"
+                    [
+                        "SENTIEON_BWAINDEX",
+                        "sentieon",
+                        "202503.02"
+                    ]
                 ],
                 "index": [
                     [
@@ -78,15 +90,19 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,c217de4e5a992968de304e342fd720f6"
+                "versions_sentieon": [
+                    [
+                        "SENTIEON_BWAINDEX",
+                        "sentieon",
+                        "202503.02"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-08-21T08:16:53.915178368"
+        "timestamp": "2026-01-19T18:27:03.694090374"
     }
 }

modules/nf-core/sentieon/bwaindex/tests/nextflow.config

@@ -6,8 +6,6 @@ env {
     // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0
     SENTIEON_AUTH_MECH = System.getenv('SENTIEON_AUTH_MECH')
     SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA
-    // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file
-    // nextflow secrets set SENTIEON_LICENSE_BASE64 $(cat <sentieon_license_file.lic> | base64 -w 0)
-}
-process {
+    // NOTE This is how users will test out Sentieon in Sarek with a license file
+    // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
 }

modules/nf-core/sentieon/collectvcmetrics/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202503.01
+  - bioconda::sentieon=202503.02