fix lint

Author: robert-a-forsyth

.github/workflows/nf-test.yml

@@ -76,7 +76,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.10.4"
+          - "25.04.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

README.md

@@ -5,7 +5,7 @@
 [![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

nextflow.config

@@ -14,12 +14,12 @@ params {
     input                       = null
 
     // Small variant calling options
-    germline_var_keep           = 'clair'
-    somatic_var_keep            = 'clair'
+    germline_var_keep           = 'deepvariant,clair'
+    somatic_var_keep            = 'deepsomatic,clair'
     germline_var_combine        = 'all'
     somatic_var_combine         = 'all'
-    prioritize_caller_germline  = 'clair'
-    prioritize_caller_somatic   = 'clair'
+    prioritize_caller_germline  = 'deepvariant'
+    prioritize_caller_somatic   = 'deepsomatic'
     generate_gvcf               = false
 
     // Longphase options

nextflow_schema.json

@@ -514,10 +514,6 @@
                 "show_hidden": {
                     "type": "boolean",
                     "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
-                },
-                "use_gpu": {
-                    "type": "boolean",
-                    "description": "Use GPU for supported tools (e.g. DeepVariant, DeepSomatic, Clair3)"
                 }
             }
         }
@@ -567,9 +563,6 @@
         }
     ],
     "properties": {
-        "generate_gvcf": {
-            "type": "boolean"
-        },
         "skip_modkit": {
             "type": "boolean"
         }

ro-crate-metadata.json

@@ -327,10 +327,10 @@
                 "sample3.stats:md5,d7a8552a8a41a217954a0c825d468a60"
             ]
         ],
-        "timestamp": "2026-04-29T08:22:27.451985797",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.0"
-        }
+            "nf-test": "0.9.3",
+            "nextflow": "26.04.1"
+        },
+        "timestamp": "2026-05-27T15:36:59.598391521"
     }
 }