diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 77797f41a3..d7bbaa8025 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -23,6 +23,22 @@ include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ s
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 {%- if igenomes %}
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
+{%- endif %}
+
+// Import nf-core-utils plugin functions
+include { getWorkflowVersion      } from 'plugin/nf-core-utils'
+include { dumpParametersToJSON    } from 'plugin/nf-core-utils'
+include { checkCondaChannels      } from 'plugin/nf-core-utils'
+{%- if email %}
+include { completionEmail         } from 'plugin/nf-core-utils'
+{%- endif %}
+include { completionSummary       } from 'plugin/nf-core-utils'
+{%- if adaptivecard or slackreport %}
+include { imNotification          } from 'plugin/nf-core-utils'
+{%- endif %}
+include { checkConfigProvided     } from 'plugin/nf-core-utils'
+include { checkProfileProvided    } from 'plugin/nf-core-utils'
+{%- if igenomes %}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 8ae5c19c7e..eb1a237651 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -13,30 +13,14 @@
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
+                        "git_sha": "c9a31c472ef2d86802eb44f27322955849859361",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}
                 }
             },
             "subworkflows": {
-                "nf-core": {
-                    "utils_nextflow_pipeline": {
-                        "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfcore_pipeline": {
-                        "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["subworkflows"]
-                    }{% if nf_schema %},
-                    "utils_nfschema_plugin": {
-                        "branch": "master",
-                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
-                        "installed_by": ["subworkflows"]
-                    }{% endif %}
-                }
+                "nf-core": {}
             }
         }
     }
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index ccd9a797cb..4f883757a9 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -322,6 +322,7 @@ manifest {
 // Nextflow plugins
 plugins {
     id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-core-utils@0.3.0' // Utility functions for nf-core pipelines
 }
 
 validation {
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index e6c485d1eb..47960573ff 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -8,19 +8,25 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-{% if nf_schema %}include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+{% if nf_schema %}include { paramsSummaryLog          } from 'plugin/nf-schema'
+include { validateParameters        } from 'plugin/nf-schema'
 include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { samplesheetToList         } from 'plugin/nf-schema'
 include { paramsHelp                } from 'plugin/nf-schema'{% endif %}
 {%- if email %}
-include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+include { completionEmail           } from 'plugin/nf-core-utils'
 {%- endif %}
-include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary         } from 'plugin/nf-core-utils'
 {%- if adaptivecard or slackreport %}
-include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification            } from 'plugin/nf-core-utils'
 {%- endif %}
-include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { checkConfigProvided       } from 'plugin/nf-core-utils'
+include { checkProfileProvided      } from 'plugin/nf-core-utils'
+include { getWorkflowVersion        } from 'plugin/nf-core-utils'
+include { dumpParametersToJSON      } from 'plugin/nf-core-utils'
+include { checkCondaChannels        } from 'plugin/nf-core-utils'
+include { processVersionsFromFile   } from 'plugin/nf-core-utils'
+include { workflowVersionToChannel  } from 'plugin/nf-core-utils'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -48,58 +54,36 @@ 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(workflow.manifest.version, workflow.commitId)}")
+        System.exit(0)
+    }
+
+    if (outdir) {
+        dumpParametersToJSON(outdir, params)
+    }
+
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        checkCondaChannels()
+    }
 
     {%- if nf_schema %}
 
     //
     // Validate parameters and generate parameter summary to stdout
     //
+    log.info paramsSummaryLog(workflow)
 
-    {%- if is_nfcore %}
-    before_text = """
--\033[2m----------------------------------------------------\033[0m-
-                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
-\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
-\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
-\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
-                                        \033[0;32m`._,._,\'\033[0m
-\033[0;35m  {{ name }} ${workflow.manifest.version}\033[0m
--\033[2m----------------------------------------------------\033[0m-
-"""
-    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
-* The nf-core framework
-    https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
-    https://github.com/{{ name }}/blob/{{ default_branch }}/CITATIONS.md
-"""{% endif %}
-    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,
-        {% if is_nfcore -%}before_text{%- else %}""{%- endif %},
-        {% if is_nfcore -%}after_text{%- else %}""{%- endif %},
-        command
-    )
+    if (validate_params) {
+        validateParameters()
+    }
     {%- endif %}
 
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE (
-        nextflow_cli_args
-    )
+    checkConfigProvided()
+    checkProfileProvided(nextflow_cli_args, monochrome_logs)
 
     {%- if igenomes %}
 
@@ -188,7 +172,7 @@ workflow PIPELINE_COMPLETION {
                 plaintext_email,
                 outdir,
                 monochrome_logs,
-                {% if multiqc %}multiqc_reports.getVal(),{% else %}[]{% endif %}
+                {% if multiqc %}multiqc_reports.getVal(){% else %}[]{% endif %}
             )
         }
         {%- endif %}
@@ -213,6 +197,57 @@ workflow PIPELINE_COMPLETION {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+//
+// Get channel of software versions used in pipeline in YAML format
+//
+def softwareVersionsToYAML(ch_versions) {
+    return ch_versions.unique()
+        .map { version -> processVersionsFromFile([version.toString()]) }
+        .unique()
+        .mix(Channel.fromList(workflowVersionToChannel(workflow.session)).map { it ->
+            """
+    Workflow:
+        ${it[1]}: ${it[2]}
+            """.stripIndent().trim()
+        })
+}
+
+{%- if multiqc %}
+//
+// Get workflow summary for MultiQC
+//
+def paramsSummaryMultiqc(summary_params) {
+    def summary_section = ''
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                group_params
+                    .keySet()
+                    .sort()
+                    .each { param ->
+                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                    }
+                summary_section += "    </dl>\n"
+            }
+        }
+
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
+    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${summary_section}"
+
+    return yaml_file_text
+}
+{%- endif %}
+
 {%- if igenomes %}
 //
 // Check and validate pipeline parameters
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
deleted file mode 100644
index d6e593e852..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ /dev/null
@@ -1,126 +0,0 @@
-//
-// Subworkflow with functionality that may be useful for any Nextflow pipeline
-//
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow UTILS_NEXTFLOW_PIPELINE {
-    take:
-    print_version        // boolean: print version
-    dump_parameters      // boolean: dump parameters
-    outdir               //    path: base directory used to publish pipeline results
-    check_conda_channels // boolean: check conda channels
-
-    main:
-
-    //
-    // Print workflow version and exit on --version
-    //
-    if (print_version) {
-        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
-        System.exit(0)
-    }
-
-    //
-    // Dump pipeline parameters to a JSON file
-    //
-    if (dump_parameters && outdir) {
-        dumpParametersToJSON(outdir)
-    }
-
-    //
-    // When running with Conda, warn if channels have not been set-up appropriately
-    //
-    if (check_conda_channels) {
-        checkCondaChannels()
-    }
-
-    emit:
-    dummy_emit = true
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// Generate version string
-//
-def getWorkflowVersion() {
-    def version_string = "" as String
-    if (workflow.manifest.version) {
-        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-        version_string += "${prefix_v}${workflow.manifest.version}"
-    }
-
-    if (workflow.commitId) {
-        def git_shortsha = workflow.commitId.substring(0, 7)
-        version_string += "-g${git_shortsha}"
-    }
-
-    return version_string
-}
-
-//
-// Dump pipeline parameters to a JSON file
-//
-def dumpParametersToJSON(outdir) {
-    def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
-    def filename  = "params_${timestamp}.json"
-    def temp_pf   = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr   = groovy.json.JsonOutput.toJson(params)
-    temp_pf.text  = groovy.json.JsonOutput.prettyPrint(jsonStr)
-
-    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
-    temp_pf.delete()
-}
-
-//
-// When running with -profile conda, warn if channels have not been set-up appropriately
-//
-def checkCondaChannels() {
-    def parser = new org.yaml.snakeyaml.Yaml()
-    def channels = []
-    try {
-        def config = parser.load("conda config --show channels".execute().text)
-        channels = config.channels
-    }
-    catch (NullPointerException e) {
-        log.debug(e)
-        log.warn("Could not verify conda channel configuration.")
-        return null
-    }
-    catch (IOException e) {
-        log.debug(e)
-        log.warn("Could not verify conda channel configuration.")
-        return null
-    }
-
-    // Check that all channels are present
-    // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda']
-    def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
-
-    // Check that they are in the right order
-    def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order }
-
-    if (channels_missing | channel_priority_violation) {
-        log.warn """\
-        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-            There is a problem with your Conda configuration!
-            You will need to set-up the conda-forge and bioconda channels correctly.
-            Please refer to https://bioconda.github.io/
-            The observed channel order is
-            ${channels}
-            but the following channel order is required:
-            ${required_channels_in_order}
-        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        """.stripIndent(true)
-    }
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
deleted file mode 100644
index e5c3a0a828..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NEXTFLOW_PIPELINE"
-description: Subworkflow with functionality that may be useful for any Nextflow pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - version
-components: []
-input:
-  - print_version:
-      type: boolean
-      description: |
-        Print the version of the pipeline and exit
-  - dump_parameters:
-      type: boolean
-      description: |
-        Dump the parameters of the pipeline to a JSON file
-  - output_directory:
-      type: directory
-      description: Path to output dir to write JSON file to.
-      pattern: "results/"
-  - check_conda_channel:
-      type: boolean
-      description: |
-        Check if the conda channel priority is correct.
-output:
-  - dummy_emit:
-      type: boolean
-      description: |
-        Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@adamrtalbot"
-  - "@drpatelh"
-maintainers:
-  - "@adamrtalbot"
-  - "@drpatelh"
-  - "@maxulysse"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
deleted file mode 100644
index 68718e4f59..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
+++ /dev/null
@@ -1,54 +0,0 @@
-
-nextflow_function {
-
-    name "Test Functions"
-    script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
-    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
-    tag 'subworkflows'
-    tag 'utils_nextflow_pipeline'
-    tag 'subworkflows/utils_nextflow_pipeline'
-
-    test("Test Function getWorkflowVersion") {
-
-        function "getWorkflowVersion"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function dumpParametersToJSON") {
-
-        function "dumpParametersToJSON"
-
-        when {
-            function {
-                """
-                // define inputs of the function here. Example:
-                input[0] = "$outputDir"
-                """.stripIndent()
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success }
-            )
-        }
-    }
-
-    test("Test Function checkCondaChannels") {
-
-        function "checkCondaChannels"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
deleted file mode 100644
index e3f0baf473..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
+++ /dev/null
@@ -1,20 +0,0 @@
-{
-    "Test Function getWorkflowVersion": {
-        "content": [
-            "v9.9.9"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:02:05.308243"
-    },
-    "Test Function checkCondaChannels": {
-        "content": null,
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:02:12.425833"
-    }
-}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
deleted file mode 100644
index 02dbf094cd..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ /dev/null
@@ -1,113 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NEXTFLOW_PIPELINE"
-    script "../main.nf"
-    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
-    workflow "UTILS_NEXTFLOW_PIPELINE"
-    tag 'subworkflows'
-    tag 'utils_nextflow_pipeline'
-    tag 'subworkflows/utils_nextflow_pipeline'
-
-    test("Should run no inputs") {
-
-        when {
-            workflow {
-                """
-                print_version        = false
-                dump_parameters      = false
-                outdir               = null
-                check_conda_channels = false
-
-                input[0] = print_version
-                input[1] = dump_parameters
-                input[2] = outdir
-                input[3] = check_conda_channels
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should print version") {
-
-        when {
-            workflow {
-                """
-                print_version        = true
-                dump_parameters      = false
-                outdir               = null
-                check_conda_channels = false
-
-                input[0] = print_version
-                input[1] = dump_parameters
-                input[2] = outdir
-                input[3] = check_conda_channels
-                """
-            }
-        }
-
-        then {
-            expect {
-                with(workflow) {
-                    assert success
-                    assert "nextflow_workflow v9.9.9" in stdout
-                }
-            }
-        }
-    }
-
-    test("Should dump params") {
-
-        when {
-            workflow {
-                """
-                print_version        = false
-                dump_parameters      = true
-                outdir               = 'results'
-                check_conda_channels = false
-
-                input[0] = false
-                input[1] = true
-                input[2] = outdir
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should not create params JSON if no output directory") {
-
-        when {
-            workflow {
-                """
-                print_version        = false
-                dump_parameters      = true
-                outdir               = null
-                check_conda_channels = false
-
-                input[0] = false
-                input[1] = true
-                input[2] = outdir
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
deleted file mode 100644
index a09572e5bb..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
-    nextflowVersion = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
deleted file mode 100644
index bfd258760d..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ /dev/null
@@ -1,419 +0,0 @@
-//
-// Subworkflow with utility functions specific to the nf-core pipeline template
-//
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow UTILS_NFCORE_PIPELINE {
-    take:
-    nextflow_cli_args
-
-    main:
-    valid_config = checkConfigProvided()
-    checkProfileProvided(nextflow_cli_args)
-
-    emit:
-    valid_config
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-//  Warn if a -profile or Nextflow config has not been provided to run the pipeline
-//
-def checkConfigProvided() {
-    def valid_config = true as Boolean
-    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn(
-            "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n "
-        )
-        valid_config = false
-    }
-    return valid_config
-}
-
-//
-// Exit pipeline if --profile contains spaces
-//
-def checkProfileProvided(nextflow_cli_args) {
-    if (workflow.profile.endsWith(',')) {
-        error(
-            "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
-        )
-    }
-    if (nextflow_cli_args[0]) {
-        log.warn(
-            "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
-        )
-    }
-}
-
-//
-// Generate workflow version string
-//
-def getWorkflowVersion() {
-    def version_string = "" as String
-    if (workflow.manifest.version) {
-        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-        version_string += "${prefix_v}${workflow.manifest.version}"
-    }
-
-    if (workflow.commitId) {
-        def git_shortsha = workflow.commitId.substring(0, 7)
-        version_string += "-g${git_shortsha}"
-    }
-
-    return version_string
-}
-
-//
-// Get software versions for pipeline
-//
-def processVersionsFromYAML(yaml_file) {
-    def yaml = new org.yaml.snakeyaml.Yaml()
-    def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] }
-    return yaml.dumpAsMap(versions).trim()
-}
-
-//
-// Get workflow version for pipeline
-//
-def workflowVersionToYAML() {
-    return """
-    Workflow:
-        ${workflow.manifest.name}: ${getWorkflowVersion()}
-        Nextflow: ${workflow.nextflow.version}
-    """.stripIndent().trim()
-}
-
-//
-// Get channel of software versions used in pipeline in YAML format
-//
-def softwareVersionsToYAML(ch_versions) {
-    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
-}
-
-//
-// Get workflow summary for MultiQC
-//
-def paramsSummaryMultiqc(summary_params) {
-    def summary_section = ''
-    summary_params
-        .keySet()
-        .each { group ->
-            def group_params = summary_params.get(group)
-            // This gets the parameters of that particular group
-            if (group_params) {
-                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
-                summary_section += "    <dl class=\"dl-horizontal\">\n"
-                group_params
-                    .keySet()
-                    .sort()
-                    .each { param ->
-                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
-                    }
-                summary_section += "    </dl>\n"
-            }
-        }
-
-    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
-    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
-    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text     += "plot_type: 'html'\n"
-    yaml_file_text     += "data: |\n"
-    yaml_file_text     += "${summary_section}"
-
-    return yaml_file_text
-}
-
-//
-// ANSII colours used for terminal logging
-//
-def logColours(monochrome_logs=true) {
-    def colorcodes = [:] as Map
-
-    // Reset / Meta
-    colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
-    colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
-    colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
-    colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
-    colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
-    colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
-    colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
-
-    // Regular Colors
-    colorcodes['black']  = monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']    = monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']  = monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']   = monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']   = monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']  = monochrome_logs ? '' : "\033[0;37m"
-
-    // Bold
-    colorcodes['bblack']  = monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']    = monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']  = monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']   = monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']   = monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']  = monochrome_logs ? '' : "\033[1;37m"
-
-    // Underline
-    colorcodes['ublack']  = monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']    = monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']  = monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']   = monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']   = monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']  = monochrome_logs ? '' : "\033[4;37m"
-
-    // High Intensity
-    colorcodes['iblack']  = monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']    = monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']  = monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']   = monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']   = monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']  = monochrome_logs ? '' : "\033[0;97m"
-
-    // Bold High Intensity
-    colorcodes['biblack']  = monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']    = monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']  = monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']   = monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']   = monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']  = monochrome_logs ? '' : "\033[1;97m"
-
-    return colorcodes
-}
-
-// Return a single report from an object that may be a Path or List
-//
-def getSingleReport(multiqc_reports) {
-    if (multiqc_reports instanceof Path) {
-        return multiqc_reports
-    } else if (multiqc_reports instanceof List) {
-        if (multiqc_reports.size() == 0) {
-            log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
-            return null
-        } else if (multiqc_reports.size() == 1) {
-            return multiqc_reports.first()
-        } else {
-            log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
-            return multiqc_reports.first()
-        }
-    } else {
-        return null
-    }
-}
-
-//
-// Construct and send completion email
-//
-def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
-
-    // Set up the e-mail variables
-    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
-    if (!workflow.success) {
-        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
-    }
-
-    def summary = [:]
-    summary_params
-        .keySet()
-        .sort()
-        .each { group ->
-            summary << summary_params[group]
-        }
-
-    def misc_fields = [:]
-    misc_fields['Date Started']              = workflow.start
-    misc_fields['Date Completed']            = workflow.complete
-    misc_fields['Pipeline script file path'] = workflow.scriptFile
-    misc_fields['Pipeline script hash ID']   = workflow.scriptId
-    if (workflow.repository) {
-        misc_fields['Pipeline repository Git URL']    = workflow.repository
-    }
-    if (workflow.commitId) {
-        misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-    }
-    if (workflow.revision) {
-        misc_fields['Pipeline Git branch/tag']        = workflow.revision
-    }
-    misc_fields['Nextflow Version']          = workflow.nextflow.version
-    misc_fields['Nextflow Build']            = workflow.nextflow.build
-    misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
-
-    def email_fields = [:]
-    email_fields['version']      = getWorkflowVersion()
-    email_fields['runName']      = workflow.runName
-    email_fields['success']      = workflow.success
-    email_fields['dateComplete'] = workflow.complete
-    email_fields['duration']     = workflow.duration
-    email_fields['exitStatus']   = workflow.exitStatus
-    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-    email_fields['errorReport']  = (workflow.errorReport ?: 'None')
-    email_fields['commandLine']  = workflow.commandLine
-    email_fields['projectDir']   = workflow.projectDir
-    email_fields['summary']      = summary << misc_fields
-
-    // On success try attach the multiqc report
-    def mqc_report = getSingleReport(multiqc_report)
-
-    // Check if we are only sending emails on failure
-    def email_address = email
-    if (!email && email_on_fail && !workflow.success) {
-        email_address = email_on_fail
-    }
-
-    // Render the TXT template
-    def engine       = new groovy.text.GStringTemplateEngine()
-    def tf           = new File("${workflow.projectDir}/assets/email_template.txt")
-    def txt_template = engine.createTemplate(tf).make(email_fields)
-    def email_txt    = txt_template.toString()
-
-    // Render the HTML template
-    def hf            = new File("${workflow.projectDir}/assets/email_template.html")
-    def html_template = engine.createTemplate(hf).make(email_fields)
-    def email_html    = html_template.toString()
-
-    // Render the sendmail template
-    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
-    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
-    def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
-    def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
-    def sendmail_html          = sendmail_template.toString()
-
-    // Send the HTML e-mail
-    def colors = logColours(monochrome_logs) as Map
-    if (email_address) {
-        try {
-            if (plaintext_email) {
-                new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
-            }
-            // Try to send HTML e-mail using sendmail
-            def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
-            sendmail_tf.withWriter { w -> w << sendmail_html }
-            ['sendmail', '-t'].execute() << sendmail_html
-            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
-        }
-        catch (Exception msg) {
-            log.debug(msg.toString())
-            log.debug("Trying with mail instead of sendmail")
-            // Catch failures and try with plaintext
-            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
-            mail_cmd.execute() << email_html
-            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-")
-        }
-    }
-
-    // Write summary e-mail HTML to a file
-    def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
-    output_hf.withWriter { w -> w << email_html }
-    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html")
-    output_hf.delete()
-
-    // Write summary e-mail TXT to a file
-    def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
-    output_tf.withWriter { w -> w << email_txt }
-    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt")
-    output_tf.delete()
-}
-
-//
-// Print pipeline summary on completion
-//
-def completionSummary(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    if (workflow.success) {
-        if (workflow.stats.ignoredCount == 0) {
-            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-")
-        }
-        else {
-            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-")
-        }
-    }
-    else {
-        log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
-    }
-}
-
-//
-// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
-//
-def imNotification(summary_params, hook_url) {
-    def summary = [:]
-    summary_params
-        .keySet()
-        .sort()
-        .each { group ->
-            summary << summary_params[group]
-        }
-
-    def misc_fields = [:]
-    misc_fields['start']          = workflow.start
-    misc_fields['complete']       = workflow.complete
-    misc_fields['scriptfile']     = workflow.scriptFile
-    misc_fields['scriptid']       = workflow.scriptId
-    if (workflow.repository) {
-        misc_fields['repository'] = workflow.repository
-    }
-    if (workflow.commitId) {
-        misc_fields['commitid']   = workflow.commitId
-    }
-    if (workflow.revision) {
-        misc_fields['revision']   = workflow.revision
-    }
-    misc_fields['nxf_version']    = workflow.nextflow.version
-    misc_fields['nxf_build']      = workflow.nextflow.build
-    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
-
-    def msg_fields = [:]
-    msg_fields['version']      = getWorkflowVersion()
-    msg_fields['runName']      = workflow.runName
-    msg_fields['success']      = workflow.success
-    msg_fields['dateComplete'] = workflow.complete
-    msg_fields['duration']     = workflow.duration
-    msg_fields['exitStatus']   = workflow.exitStatus
-    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
-    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
-    msg_fields['projectDir']   = workflow.projectDir
-    msg_fields['summary']      = summary << misc_fields
-
-    // Render the JSON template
-    def engine       = new groovy.text.GStringTemplateEngine()
-    // Different JSON depending on the service provider
-    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
-    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
-    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
-    def json_template = engine.createTemplate(hf).make(msg_fields)
-    def json_message  = json_template.toString()
-
-    // POST
-    def post = new URL(hook_url).openConnection()
-    post.setRequestMethod("POST")
-    post.setDoOutput(true)
-    post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"))
-    def postRC = post.getResponseCode()
-    if (!postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText())
-    }
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
deleted file mode 100644
index d08d24342d..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NFCORE_PIPELINE"
-description: Subworkflow with utility functions specific to the nf-core pipeline template
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - version
-components: []
-input:
-  - nextflow_cli_args:
-      type: list
-      description: |
-        Nextflow CLI positional arguments
-output:
-  - success:
-      type: boolean
-      description: |
-        Dummy output to indicate success
-authors:
-  - "@adamrtalbot"
-maintainers:
-  - "@adamrtalbot"
-  - "@maxulysse"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
deleted file mode 100644
index f117040cbd..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ /dev/null
@@ -1,126 +0,0 @@
-
-nextflow_function {
-
-    name "Test Functions"
-    script "../main.nf"
-    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "utils_nfcore_pipeline"
-    tag "subworkflows/utils_nfcore_pipeline"
-
-    test("Test Function checkConfigProvided") {
-
-        function "checkConfigProvided"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function checkProfileProvided") {
-
-        function "checkProfileProvided"
-
-        when {
-            function {
-                """
-                input[0] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function without logColours") {
-
-        function "logColours"
-
-        when {
-            function {
-                """
-                input[0] = true
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function with logColours") {
-        function "logColours"
-
-        when {
-            function {
-                """
-                input[0] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function getSingleReport with a single file") {
-        function "getSingleReport"
-
-        when {
-            function {
-                """
-                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert function.result.contains("test.tsv") }
-            )
-        }
-    }
-
-    test("Test Function getSingleReport with multiple files") {
-        function "getSingleReport"
-
-        when {
-            function {
-                """
-                input[0] = [
-                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
-                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
-                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert function.result.contains("test.tsv") },
-                { assert !function.result.contains("network.tsv") },
-                { assert !function.result.contains("expression.tsv") }
-            )
-        }
-    }
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
deleted file mode 100644
index 02c6701413..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ /dev/null
@@ -1,136 +0,0 @@
-{
-    "Test Function checkProfileProvided": {
-        "content": null,
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:03.360873"
-    },
-    "Test Function checkConfigProvided": {
-        "content": [
-            true
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:02:59.729647"
-    },
-    "Test Function without logColours": {
-        "content": [
-            {
-                "reset": "",
-                "bold": "",
-                "dim": "",
-                "underlined": "",
-                "blink": "",
-                "reverse": "",
-                "hidden": "",
-                "black": "",
-                "red": "",
-                "green": "",
-                "yellow": "",
-                "blue": "",
-                "purple": "",
-                "cyan": "",
-                "white": "",
-                "bblack": "",
-                "bred": "",
-                "bgreen": "",
-                "byellow": "",
-                "bblue": "",
-                "bpurple": "",
-                "bcyan": "",
-                "bwhite": "",
-                "ublack": "",
-                "ured": "",
-                "ugreen": "",
-                "uyellow": "",
-                "ublue": "",
-                "upurple": "",
-                "ucyan": "",
-                "uwhite": "",
-                "iblack": "",
-                "ired": "",
-                "igreen": "",
-                "iyellow": "",
-                "iblue": "",
-                "ipurple": "",
-                "icyan": "",
-                "iwhite": "",
-                "biblack": "",
-                "bired": "",
-                "bigreen": "",
-                "biyellow": "",
-                "biblue": "",
-                "bipurple": "",
-                "bicyan": "",
-                "biwhite": ""
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:17.969323"
-    },
-    "Test Function with logColours": {
-        "content": [
-            {
-                "reset": "\u001b[0m",
-                "bold": "\u001b[1m",
-                "dim": "\u001b[2m",
-                "underlined": "\u001b[4m",
-                "blink": "\u001b[5m",
-                "reverse": "\u001b[7m",
-                "hidden": "\u001b[8m",
-                "black": "\u001b[0;30m",
-                "red": "\u001b[0;31m",
-                "green": "\u001b[0;32m",
-                "yellow": "\u001b[0;33m",
-                "blue": "\u001b[0;34m",
-                "purple": "\u001b[0;35m",
-                "cyan": "\u001b[0;36m",
-                "white": "\u001b[0;37m",
-                "bblack": "\u001b[1;30m",
-                "bred": "\u001b[1;31m",
-                "bgreen": "\u001b[1;32m",
-                "byellow": "\u001b[1;33m",
-                "bblue": "\u001b[1;34m",
-                "bpurple": "\u001b[1;35m",
-                "bcyan": "\u001b[1;36m",
-                "bwhite": "\u001b[1;37m",
-                "ublack": "\u001b[4;30m",
-                "ured": "\u001b[4;31m",
-                "ugreen": "\u001b[4;32m",
-                "uyellow": "\u001b[4;33m",
-                "ublue": "\u001b[4;34m",
-                "upurple": "\u001b[4;35m",
-                "ucyan": "\u001b[4;36m",
-                "uwhite": "\u001b[4;37m",
-                "iblack": "\u001b[0;90m",
-                "ired": "\u001b[0;91m",
-                "igreen": "\u001b[0;92m",
-                "iyellow": "\u001b[0;93m",
-                "iblue": "\u001b[0;94m",
-                "ipurple": "\u001b[0;95m",
-                "icyan": "\u001b[0;96m",
-                "iwhite": "\u001b[0;97m",
-                "biblack": "\u001b[1;90m",
-                "bired": "\u001b[1;91m",
-                "bigreen": "\u001b[1;92m",
-                "biyellow": "\u001b[1;93m",
-                "biblue": "\u001b[1;94m",
-                "bipurple": "\u001b[1;95m",
-                "bicyan": "\u001b[1;96m",
-                "biwhite": "\u001b[1;97m"
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:21.714424"
-    }
-}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
deleted file mode 100644
index 8940d32d1e..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
+++ /dev/null
@@ -1,29 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NFCORE_PIPELINE"
-    script "../main.nf"
-    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
-    workflow "UTILS_NFCORE_PIPELINE"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "utils_nfcore_pipeline"
-    tag "subworkflows/utils_nfcore_pipeline"
-
-    test("Should run without failures") {
-
-        when {
-            workflow {
-                """
-                input[0] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
-        }
-    }
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
deleted file mode 100644
index 859d1030fb..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
+++ /dev/null
@@ -1,19 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    true
-                ],
-                "valid_config": [
-                    true
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:25.726491"
-    }
-}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
deleted file mode 100644
index d0a926bf6d..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
deleted file mode 100644
index ee4738c8d1..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ /dev/null
@@ -1,74 +0,0 @@
-//
-// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
-//
-
-include { paramsSummaryLog   } from 'plugin/nf-schema'
-include { validateParameters } from 'plugin/nf-schema'
-include { paramsHelp         } from 'plugin/nf-schema'
-
-workflow UTILS_NFSCHEMA_PLUGIN {
-
-    take:
-    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
-    validate_params     // boolean:  validate the parameters
-    parameters_schema   // string:   path to the parameters JSON schema.
-                        //           this has to be the same as the schema given to `validation.parametersSchema`
-                        //           when this input is empty it will automatically use the configured schema or
-                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
-                        //           for meta pipelines
-    help                // boolean:  show help message
-    help_full           // boolean:  show full help message
-    show_hidden         // boolean:  show hidden parameters in help message
-    before_text         // string:   text to show before the help message and parameters summary
-    after_text          // string:   text to show after the help message and parameters summary
-    command             // string:   an example command of the pipeline
-
-    main:
-
-    if(help || help_full) {
-        help_options = [
-            beforeText: before_text,
-            afterText: after_text,
-            command: command,
-            showHidden: show_hidden,
-            fullHelp: help_full,
-        ]
-        if(parameters_schema) {
-            help_options << [parametersSchema: parameters_schema]
-        }
-        log.info paramsHelp(
-            help_options,
-            params.help instanceof String ? params.help : "",
-        )
-        exit 0
-    }
-
-    //
-    // Print parameter summary to stdout. This will display the parameters
-    // that differ from the default given in the JSON schema
-    //
-
-    summary_options = [:]
-    if(parameters_schema) {
-        summary_options << [parametersSchema: parameters_schema]
-    }
-    log.info before_text
-    log.info paramsSummaryLog(summary_options, input_workflow)
-    log.info after_text
-
-    //
-    // Validate the parameters using nextflow_schema.json or the schema
-    // given via the validation.parametersSchema configuration option
-    //
-    if(validate_params) {
-        validateOptions = [:]
-        if(parameters_schema) {
-            validateOptions << [parametersSchema: parameters_schema]
-        }
-        validateParameters(validateOptions)
-    }
-
-    emit:
-    dummy_emit = true
-}
-
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
deleted file mode 100644
index f7d9f02885..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "utils_nfschema_plugin"
-description: Run nf-schema to validate parameters and create a summary of changed parameters
-keywords:
-  - validation
-  - JSON schema
-  - plugin
-  - parameters
-  - summary
-components: []
-input:
-  - input_workflow:
-      type: object
-      description: |
-        The workflow object of the used pipeline.
-        This object contains meta data used to create the params summary log
-  - validate_params:
-      type: boolean
-      description: Validate the parameters and error if invalid.
-  - parameters_schema:
-      type: string
-      description: |
-        Path to the parameters JSON schema.
-        This has to be the same as the schema given to the `validation.parametersSchema` config
-        option. When this input is empty it will automatically use the configured schema or
-        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
-        for meta pipelines.
-output:
-  - dummy_emit:
-      type: boolean
-      description: Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@nvnieuwk"
-maintainers:
-  - "@nvnieuwk"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
deleted file mode 100644
index c977917aac..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ /dev/null
@@ -1,173 +0,0 @@
-nextflow_workflow {
-
-    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
-    script "../main.nf"
-    workflow "UTILS_NFSCHEMA_PLUGIN"
-
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "subworkflows/utils_nfschema_plugin"
-    tag "plugin/nf-schema"
-
-    config "./nextflow.config"
-
-    test("Should run nothing") {
-
-        when {
-
-            params {
-                test_data   = ''
-            }
-
-            workflow {
-                """
-                validate_params = false
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = ""
-                input[3] = false
-                input[4] = false
-                input[5] = false
-                input[6] = ""
-                input[7] = ""
-                input[8] = ""
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should validate params") {
-
-        when {
-
-            params {
-                test_data   = ''
-                outdir      = null
-            }
-
-            workflow {
-                """
-                validate_params = true
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = ""
-                input[3] = false
-                input[4] = false
-                input[5] = false
-                input[6] = ""
-                input[7] = ""
-                input[8] = ""
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
-            )
-        }
-    }
-
-    test("Should run nothing - custom schema") {
-
-        when {
-
-            params {
-                test_data   = ''
-            }
-
-            workflow {
-                """
-                validate_params = false
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
-                input[3] = false
-                input[4] = false
-                input[5] = false
-                input[6] = ""
-                input[7] = ""
-                input[8] = ""
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should validate params - custom schema") {
-
-        when {
-
-            params {
-                test_data   = ''
-                outdir      = null
-            }
-
-            workflow {
-                """
-                validate_params = true
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
-                input[3] = false
-                input[4] = false
-                input[5] = false
-                input[6] = ""
-                input[7] = ""
-                input[8] = ""
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
-            )
-        }
-    }
-
-    test("Should create a help message") {
-
-        when {
-
-            params {
-                test_data   = ''
-                outdir      = null
-            }
-
-            workflow {
-                """
-                validate_params = true
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
-                input[3] = true
-                input[4] = false
-                input[5] = false
-                input[6] = "Before"
-                input[7] = "After"
-                input[8] = "nextflow run test/test"
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
deleted file mode 100644
index 8d8c73718a..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-plugins {
-    id "nf-schema@2.5.1"
-}
-
-validation {
-    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
-    monochromeLogs = true
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
deleted file mode 100644
index 331e0d2f44..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
+++ /dev/null
@@ -1,96 +0,0 @@
-{
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
-    "title": ". pipeline parameters",
-    "description": "",
-    "type": "object",
-    "$defs": {
-        "input_output_options": {
-            "title": "Input/output options",
-            "type": "object",
-            "fa_icon": "fas fa-terminal",
-            "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["outdir"],
-            "properties": {
-                "validate_params": {
-                    "type": "boolean",
-                    "description": "Validate parameters?",
-                    "default": true,
-                    "hidden": true
-                },
-                "outdir": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
-                    "fa_icon": "fas fa-folder-open"
-                },
-                "test_data_base": {
-                    "type": "string",
-                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules",
-                    "description": "Base for test data directory",
-                    "hidden": true
-                },
-                "test_data": {
-                    "type": "string",
-                    "description": "Fake test data param",
-                    "hidden": true
-                }
-            }
-        },
-        "generic_options": {
-            "title": "Generic options",
-            "type": "object",
-            "fa_icon": "fas fa-file-import",
-            "description": "Less common options for the pipeline, typically set in a config file.",
-            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
-            "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
-                "version": {
-                    "type": "boolean",
-                    "description": "Display version and exit.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
-                "logo": {
-                    "type": "boolean",
-                    "default": true,
-                    "description": "Display nf-core logo in console output.",
-                    "fa_icon": "fas fa-image",
-                    "hidden": true
-                },
-                "singularity_pull_docker_container": {
-                    "type": "boolean",
-                    "description": "Pull Singularity container from Docker?",
-                    "hidden": true
-                },
-                "publish_dir_mode": {
-                    "type": "string",
-                    "default": "copy",
-                    "description": "Method used to save pipeline results to output directory.",
-                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
-                    "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
-                    "hidden": true
-                },
-                "monochrome_logs": {
-                    "type": "boolean",
-                    "description": "Use monochrome_logs",
-                    "hidden": true
-                }
-            }
-        }
-    },
-    "allOf": [
-        {
-            "$ref": "#/$defs/input_output_options"
-        },
-        {
-            "$ref": "#/$defs/generic_options"
-        }
-    ]
-}
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 6126f9ec69..22d360dfe0 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -12,8 +12,8 @@ include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endi
 {%- if nf_schema %}
 include { paramsSummaryMap       } from 'plugin/nf-schema'{% endif %}
 {%- if multiqc %}
-include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
-include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { paramsSummaryMultiqc   } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
+include { softwareVersionsToYAML } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 {%- if citations or multiqc %}
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
 {%- endif %}
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index 54ad7e7fc7..8d2a58ec6a 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -20,10 +20,7 @@ def test_subworkflows_lint(self):
         assert len(subworkflow_lint.warned) >= 0
 
     def test_subworkflows_lint_empty(self):
-        """Test linting a pipeline with no subworkflows installed"""
-        self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True)
-        self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True)
-        self.subworkflow_remove.remove("utils_nfschema_plugin", force=True)
+        """Test linting a pipeline with no nf-core subworkflows installed."""
         nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
         assert "No subworkflows from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text