Remove vendored nf-core utils subworkflows, use plugin imports

Replace three subworkflows/nf-core/utils_* subworkflows with direct imports
from plugin/nf-core-utils and plugin/nf-schema, matching the pattern used
by rnavar and createpanelrefs pipelines.

- utils_nextflow_pipeline: version display, params dump, conda check
- utils_nfcore_pipeline: config validation, email, versions YAML
- utils_nfschema_plugin: parameter validation, help display

All functionality preserved in the local utils subworkflow using plugin
functions directly.

Author: maxulysse

modules.json

@@ -141,25 +141,7 @@
                     }
                 }
             },
-            "subworkflows": {
-                "nf-core": {
-                    "utils_nextflow_pipeline": {
-                        "branch": "master",
-                        "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfcore_pipeline": {
-                        "branch": "master",
-                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfschema_plugin": {
-                        "branch": "master",
-                        "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
-                        "installed_by": ["subworkflows"]
-                    }
-                }
-            }
+            "subworkflows": {}
         }
     }
 }

subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf

@@ -8,14 +8,19 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFSCHEMA_PLUGIN   } from '../../nf-core/utils_nfschema_plugin'
+include { checkCondaChannels      } from 'plugin/nf-core-utils'
+include { checkConfigProvided     } from 'plugin/nf-core-utils'
+include { checkProfileProvided    } from 'plugin/nf-core-utils'
+include { completionEmail         } from 'plugin/nf-core-utils'
+include { completionSummary       } from 'plugin/nf-core-utils'
+include { dumpParametersToJSON    } from 'plugin/nf-core-utils'
+include { getWorkflowVersion      } from 'plugin/nf-core-utils'
+include { softwareVersionsToYAML  } from 'plugin/nf-core-utils'
+include { paramsHelp              } from 'plugin/nf-schema'
+include { paramsSummaryLog        } from 'plugin/nf-schema'
 include { paramsSummaryMap        } from 'plugin/nf-schema'
 include { samplesheetToList       } from 'plugin/nf-schema'
-include { paramsHelp              } from 'plugin/nf-schema'
-include { completionEmail         } from '../../nf-core/utils_nfcore_pipeline'
-include { completionSummary       } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NFCORE_PIPELINE   } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
+include { validateParameters      } from 'plugin/nf-schema'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -45,12 +50,15 @@ workflow PIPELINE_INITIALISATION {
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
-    UTILS_NEXTFLOW_PIPELINE(
-        version,
-        true,
-        outdir,
-        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1,
-    )
+    if (version) {
+        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
+        System.exit(0)
+    }
+    def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
+    dumpParametersToJSON(params, "${outdir}/pipeline_info/params_${timestamp}.json")
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        checkCondaChannels()
+    }
 
     //
     // Validate parameters and generate parameter summary to stdout
@@ -80,20 +88,29 @@ workflow PIPELINE_INITIALISATION {
         before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '')
     }
 
-    command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-
-    UTILS_NFSCHEMA_PLUGIN(
-        workflow,
-        validate_params,
-        null,
-        help,
-        help_full,
-        show_hidden,
-        before_text,
-        after_text,
-        command,
-        null,
-    )
+    def command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+
+    if (help || help_full) {
+        log.info paramsHelp(
+            [
+                beforeText: before_text,
+                afterText: after_text,
+                command: command,
+                showHidden: show_hidden,
+                fullHelp: help_full,
+            ],
+            (help instanceof String && help != "true") ? help : "",
+        )
+        System.exit(0)
+    }
+
+    log.info before_text
+    log.info paramsSummaryLog(workflow, parameters_schema: "nextflow_schema.json")
+    log.info after_text
+
+    if (validate_params) {
+        validateParameters(parameters_schema: "nextflow_schema.json")
+    }
 
     extra_text = """
 \033[1;37mExtra informations\033[0m
@@ -110,7 +127,8 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE(nextflow_cli_args)
+    checkConfigProvided()
+    checkProfileProvided(nextflow_cli_args)
 
     //
     // Custom validation for pipeline parameters