From 5ed48a9c4a705f2900b150626f41f4927d98ba7b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Feb 2024 10:43:44 +0100
Subject: [PATCH 01/27] Install utils_subworkflows_* from nf-core/modules

---
 nf_core/pipeline-template/modules.json        |  19 +
 .../nf-core/utils_nextflow_pipeline/main.nf   | 126 ++++++
 .../nf-core/utils_nextflow_pipeline/meta.yml  |  38 ++
 .../tests/main.function.nf.test               |  54 +++
 .../tests/main.function.nf.test.snap          |  12 +
 .../tests/main.workflow.nf.test               | 123 ++++++
 .../tests/nextflow.config                     |   9 +
 .../utils_nextflow_pipeline/tests/tags.yml    |   2 +
 .../nf-core/utils_nfcore_pipeline/main.nf     | 395 ++++++++++++++++++
 .../nf-core/utils_nfcore_pipeline/meta.yml    |  20 +
 .../tests/main.function.nf.test               | 114 +++++
 .../tests/main.function.nf.test.snap          | 134 ++++++
 .../tests/main.workflow.nf.test               |  21 +
 .../tests/main.workflow.nf.test.snap          |  15 +
 .../tests/nextflow.config                     |   9 +
 .../utils_nfcore_pipeline/tests/tags.yml      |   2 +
 .../nf-core/utils_nfvalidation_plugin/main.nf |  62 +++
 .../utils_nfvalidation_plugin/meta.yml        |  44 ++
 .../tests/main.nf.test                        | 200 +++++++++
 .../tests/nextflow_schema.json                |  96 +++++
 .../utils_nfvalidation_plugin/tests/tags.yml  |   2 +
 21 files changed, 1497 insertions(+)
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 8660da2d42..5c30ac92fc 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -21,6 +21,25 @@
                         "installed_by": ["modules"]
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "utils_nextflow_pipeline": {
+                        "branch": "master",
+                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "utils_nfcore_pipeline": {
+                        "branch": "master",
+                        "git_sha": "73b63c8e510107010ab13b68cf31189d6cdca8cb",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "utils_nfvalidation_plugin": {
+                        "branch": "master",
+                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
             }
         }
     }
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
new file mode 100644
index 0000000000..ac31f28f66
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -0,0 +1,126 @@
+//
+// Subworkflow with functionality that may be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
+
+/*
+========================================================================================
+    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} ${getWorkflowVersion()}"
+        System.exit(0)
+    }
+
+    //
+    // Dump pipeline parameters to a JSON file
+    //
+    if (dump_parameters && outdir) {
+        dumpParametersToJSON(outdir)
+    }
+
+    //
+    // When running with Conda, warn if channels have not been set-up appropriately
+    //
+    if (check_conda_channels) {
+        checkCondaChannels()
+    }
+
+    emit:
+    dummy_emit = true
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+// Generate version string
+//
+def getWorkflowVersion() {
+    String version_string = ""
+    if (workflow.manifest.version) {
+        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+        version_string += "${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    = JsonOutput.toJson(params)
+    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+
+    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() {
+    Yaml parser = new Yaml()
+    def channels = []
+    try {
+        def config = parser.load("conda config --show channels".execute().text)
+        channels = config.channels
+    } catch(NullPointerException | IOException e) {
+        log.warn "Could not verify conda channel configuration."
+        return
+    }
+
+    // Check that all channels are present
+    // This channel list is ordered by required channel priority.
+    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    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 = false
+    def n = required_channels_in_order.size()
+    for (int i = 0; i < n - 1; i++) {
+        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+    }
+
+    if (channels_missing | channel_priority_violation) {
+        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            "  There is a problem with your Conda configuration!\n\n" +
+            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
+            "  Please refer to https://bioconda.github.io/\n" +
+            "  The observed channel order is \n" +
+            "  ${channels}\n" +
+            "  but the following channel order is required:\n" +
+            "  ${required_channels_in_order}\n" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+    }
+}
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
new file mode 100644
index 0000000000..e5c3a0a828
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
@@ -0,0 +1,38 @@
+# 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
new file mode 100644
index 0000000000..8ed4310cac
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
@@ -0,0 +1,54 @@
+
+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() }
+            )
+        }
+    }
+}
\ No newline at end of file
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
new file mode 100644
index 0000000000..db2030f8b0
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,12 @@
+{
+    "Test Function getWorkflowVersion": {
+        "content": [
+            "v9.9.9"
+        ],
+        "timestamp": "2024-01-19T11:32:36.031083"
+    },
+    "Test Function checkCondaChannels": {
+        "content": null,
+        "timestamp": "2024-01-19T11:32:50.456"
+    }
+}
\ 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
new file mode 100644
index 0000000000..f7c54bc68f
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,123 @@
+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 {
+            params {
+                outdir = "tests/results"
+            }
+            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 {
+            params {
+                outdir = "tests/results"
+            }
+            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 {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
+            )
+        }
+    }
+
+    test("Should dump params") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            workflow {
+                """
+                print_version        = false
+                dump_parameters      = true
+                outdir               = params.outdir
+                check_conda_channels = false
+
+                input[0] = false
+                input[1] = true
+                input[2] = params.outdir
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should not create params JSON if no output directory") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            workflow {
+                """
+                print_version        = false
+                dump_parameters      = true
+                outdir               = params.outdir
+                check_conda_channels = false
+
+                input[0] = false
+                input[1] = true
+                input[2] = null
+                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
new file mode 100644
index 0000000000..53574ffec4
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+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'
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
new file mode 100644
index 0000000000..f84761125a
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nextflow_pipeline:
+  - subworkflows/nf-core/utils_nextflow_pipeline/**
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
new file mode 100644
index 0000000000..6d805bb3fd
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -0,0 +1,395 @@
+//
+// Subworkflow with utility functions specific to the nf-core pipeline template
+//
+
+import org.yaml.snakeyaml.Yaml
+import nextflow.extension.FilesEx
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFCORE_PIPELINE {
+
+    main:
+    valid_config = checkConfigProvided()
+
+    emit:
+    valid_config
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+//  Warn if a -profile or Nextflow config has not been provided to run the pipeline
+//
+def checkConfigProvided() {
+    valid_config = true
+    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
+}
+
+//
+// Citation string for pipeline
+//
+def workflowCitation() {
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+        "* The pipeline\n" +
+        "  ${workflow.manifest.doi}\n\n" +
+        "* The nf-core framework\n" +
+        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+        "* Software dependencies\n" +
+        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+}
+
+//
+// Generate workflow version string
+//
+def getWorkflowVersion() {
+    String version_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) {
+    Yaml yaml = new Yaml()
+    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: $workflow.nextflow.version
+    """.stripIndent().trim()
+}
+
+//
+// Get channel of software versions used in pipeline in YAML format
+//
+def softwareVersionsToYAML(ch_versions) {
+    return ch_versions
+                .unique()
+                .map { processVersionsFromYAML(it) }
+                .unique()
+                .mix(Channel.of(workflowVersionToYAML()))
+}
+
+//
+// Get workflow summary for MultiQC
+//
+def paramsSummaryMultiqc(summary_params) {
+    def summary_section = ''
+    for (group in summary_params.keySet()) {
+        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
+        if (group_params) {
+            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
+            summary_section += "    <dl class=\"dl-horizontal\">\n"
+            for (param in group_params.keySet()) {
+                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"
+        }
+    }
+
+    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text        += "section_name: '${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
+}
+
+//
+// nf-core logo
+//
+def nfCoreLogo(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    String.format(
+        """\n
+        ${dashedLine(monochrome_logs)}
+                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                ${colors.green}`._,._,\'${colors.reset}
+        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
+        ${dashedLine(monochrome_logs)}
+        """.stripIndent()
+    )
+}
+
+//
+// Return dashed line
+//
+def dashedLine(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+}
+
+//
+// ANSII colours used for terminal logging
+//
+def logColours(monochrome_logs=true) {
+    Map colorcodes = [:]
+
+    // 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
+}
+
+//
+// Construct and send completion email
+//
+def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true) {
+
+    // Set up the e-mail variables
+    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    if (!workflow.success) {
+        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+    }
+
+    def summary = [:]
+    for (group in summary_params.keySet()) {
+        summary << summary_params[group]
+    }
+
+    def misc_fields = [:]
+    misc_fields['Date Started']              = workflow.start
+    misc_fields['Date Completed']            = workflow.complete
+    misc_fields['Pipeline script file path'] = workflow.scriptFile
+    misc_fields['Pipeline script hash ID']   = workflow.scriptId
+    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
+    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    misc_fields['Nextflow Version']           = workflow.nextflow.version
+    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+    def email_fields = [:]
+    email_fields['version']      = getWorkflowVersion()
+    email_fields['runName']      = workflow.runName
+    email_fields['success']      = workflow.success
+    email_fields['dateComplete'] = workflow.complete
+    email_fields['duration']     = workflow.duration
+    email_fields['exitStatus']   = workflow.exitStatus
+    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    email_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    email_fields['commandLine']  = workflow.commandLine
+    email_fields['projectDir']   = workflow.projectDir
+    email_fields['summary']      = summary << misc_fields
+
+    // Check if we are only sending emails on failure
+    def email_address = email
+    if (!email && email_on_fail && !workflow.success) {
+        email_address = email_on_fail
+    }
+
+    // Render the TXT template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    def tf           = new File("${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("${workflow.projectDir}/assets/email_template.html")
+    def html_template = engine.createTemplate(hf).make(email_fields)
+    def email_html    = html_template.toString()
+
+    // Render the sendmail template
+    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}" ]
+    def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
+    def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+    def sendmail_html          = sendmail_template.toString()
+
+    // Send the HTML e-mail
+    Map colors = logColours(monochrome_logs)
+    if (email_address) {
+        try {
+            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            // Try to send HTML e-mail using sendmail
+            def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+            sendmail_tf.withWriter { w -> w << sendmail_html }
+            [ 'sendmail', '-t' ].execute() << sendmail_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+        } catch (all) {
+            // Catch failures and try with plaintext
+            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            mail_cmd.execute() << email_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+        }
+    }
+
+    // Write summary e-mail HTML to a file
+    def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
+    output_hf.withWriter { w -> w << email_html }
+    FilesEx.copyTo(output_hf.toPath(), "${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 }
+    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    output_tf.delete()
+}
+
+//
+// Print pipeline summary on completion
+//
+def completionSummary(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    if (workflow.success) {
+        if (workflow.stats.ignoredCount == 0) {
+            log.info "-${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 = [:]
+    for (group in summary_params.keySet()) {
+        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
new file mode 100644
index 0000000000..dd1462b232
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
@@ -0,0 +1,20 @@
+# 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: []
+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
new file mode 100644
index 0000000000..f7ea05fcd7
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -0,0 +1,114 @@
+
+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 workflowCitation") {
+
+        function "workflowCitation"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function nfCoreLogo") {
+
+        function "nfCoreLogo"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function dashedLine") {
+
+        function "dashedLine"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        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() }
+            )
+        }
+    }
+}
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
new file mode 100644
index 0000000000..afb9ab4dca
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,134 @@
+{
+    "Test Function checkConfigProvided": {
+        "content": [
+            true
+        ],
+        "timestamp": "2024-01-19T11:34:13.548431224"
+    },
+    "Test Function nfCoreLogo": {
+        "content": [
+            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
+        ],
+        "timestamp": "2024-01-19T11:34:38.840454873"
+    },
+    "Test Function workflowCitation": {
+        "content": [
+            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
+        ],
+        "timestamp": "2024-01-19T11:34:22.24352016"
+    },
+    "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": ""
+            }
+        ],
+        "timestamp": "2024-01-19T11:35:04.418416984"
+    },
+    "Test Function dashedLine": {
+        "content": [
+            "-\u001b[2m----------------------------------------------------\u001b[0m-"
+        ],
+        "timestamp": "2024-01-19T11:34:55.420000755"
+    },
+    "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"
+            }
+        ],
+        "timestamp": "2024-01-19T11:35:13.436366565"
+    }
+}
\ 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
new file mode 100644
index 0000000000..c5f7776a67
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,21 @@
+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") {
+
+        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
new file mode 100644
index 0000000000..d07ce54c51
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
@@ -0,0 +1,15 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "valid_config": [
+                    true
+                ]
+            }
+        ],
+        "timestamp": "2024-01-19T11:35:22.538940073"
+    }
+}
\ 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
new file mode 100644
index 0000000000..d0a926bf6d
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+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/tests/tags.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
new file mode 100644
index 0000000000..ac8523c9a2
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfcore_pipeline:
+  - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
new file mode 100644
index 0000000000..2585b65d1b
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
@@ -0,0 +1,62 @@
+//
+// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
+//
+
+/*
+========================================================================================
+    IMPORT NF-VALIDATION PLUGIN
+========================================================================================
+*/
+
+include { paramsHelp         } from 'plugin/nf-validation'
+include { paramsSummaryLog   } from 'plugin/nf-validation'
+include { validateParameters } from 'plugin/nf-validation'
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFVALIDATION_PLUGIN {
+
+    take:
+    print_help       // boolean: print help
+    workflow_command //  string: default commmand used to run pipeline
+    pre_help_text    //  string: string to be printed before help text and summary log
+    post_help_text   //  string: string to be printed after help text and summary log
+    validate_params  // boolean: validate parameters
+    schema_filename  //    path: JSON schema file, null to use default value
+
+    main:
+
+    log.debug "Using schema file: ${schema_filename}"
+
+    // Default values for strings
+    pre_help_text    = pre_help_text    ?: ''
+    post_help_text   = post_help_text   ?: ''
+    workflow_command = workflow_command ?: ''
+
+    //
+    // Print help message if needed
+    //
+    if (print_help) {
+        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
+        System.exit(0)
+    }
+
+    //
+    // Print parameter summary to stdout
+    //
+    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
+
+    //
+    // Validate parameters relative to the parameter JSON schema
+    //
+    if (validate_params){
+        validateParameters(parameters_schema: schema_filename)
+    }
+
+    emit:
+    dummy_emit = true
+}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
new file mode 100644
index 0000000000..3d4a6b04f5
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
@@ -0,0 +1,44 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFVALIDATION_PLUGIN"
+description: Use nf-validation to initiate and validate a pipeline
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - validation
+components: []
+input:
+  - print_help:
+      type: boolean
+      description: |
+        Print help message and exit
+  - workflow_command:
+      type: string
+      description: |
+        The command to run the workflow e.g. "nextflow run main.nf"
+  - pre_help_text:
+      type: string
+      description: |
+        Text to print before the help message
+  - post_help_text:
+      type: string
+      description: |
+        Text to print after the help message
+  - validate_params:
+      type: boolean
+      description: |
+        Validate the parameters and error if invalid.
+  - schema_filename:
+      type: string
+      description: |
+        The filename of the schema to validate against.
+output:
+  - dummy_emit:
+      type: boolean
+      description: |
+        Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
+  - "@maxulysse"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
new file mode 100644
index 0000000000..517ee54e48
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -0,0 +1,200 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFVALIDATION_PLUGIN"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "plugin/nf-validation"
+    tag "'plugin/nf-validation'"
+    tag "utils_nfvalidation_plugin"
+    tag "subworkflows/utils_nfvalidation_plugin"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+
+            workflow {
+                """
+                help             = false
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should run help") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.exitStatus == 0 },
+                { assert workflow.stdout.any { it.contains('Input/output options') } },
+                { assert workflow.stdout.any { it.contains('--outdir') } }
+            )
+        }
+    }
+
+    test("Should run help with command") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = "nextflow run noorg/doesntexist"
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.exitStatus == 0 },
+                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
+                { assert workflow.stdout.any { it.contains('Input/output options') } },
+                { assert workflow.stdout.any { it.contains('--outdir') } }
+            )
+        }
+    }
+
+    test("Should run help with extra text") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = "nextflow run noorg/doesntexist"
+                pre_help_text    = "pre-help-text"
+                post_help_text   = "post-help-text"
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.exitStatus == 0 },
+                { assert workflow.stdout.any { it.contains('pre-help-text') } },
+                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
+                { assert workflow.stdout.any { it.contains('Input/output options') } },
+                { assert workflow.stdout.any { it.contains('--outdir') } },
+                { assert workflow.stdout.any { it.contains('post-help-text') } }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+                outdir          = 1
+            }
+            workflow {
+                """
+                help             = false
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = true
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
new file mode 100644
index 0000000000..7626c1c93e
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
@@ -0,0 +1,96 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+    "title": ". pipeline parameters",
+    "description": "",
+    "type": "object",
+    "definitions": {
+        "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": [
+        {
+            "$ref": "#/definitions/input_output_options"
+        },
+        {
+            "$ref": "#/definitions/generic_options"
+        }
+    ]
+}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
new file mode 100644
index 0000000000..60b1cfff49
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfvalidation_plugin:
+  - subworkflows/nf-core/utils_nfvalidation_plugin/**

From 53487ec543a4fc5446fc29fd4a4ed2d84517116b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Feb 2024 12:44:32 +0100
Subject: [PATCH 02/27] Remove lib directory from pipeline template

---
 .../lib/NfcoreTemplate.groovy                 | 356 ------------------
 nf_core/pipeline-template/lib/Utils.groovy    |  47 ---
 .../pipeline-template/lib/WorkflowMain.groovy |  80 ----
 .../lib/WorkflowPipeline.groovy               | 123 ------
 4 files changed, 606 deletions(-)
 delete mode 100755 nf_core/pipeline-template/lib/NfcoreTemplate.groovy
 delete mode 100644 nf_core/pipeline-template/lib/Utils.groovy
 delete mode 100755 nf_core/pipeline-template/lib/WorkflowMain.groovy
 delete mode 100755 nf_core/pipeline-template/lib/WorkflowPipeline.groovy

diff --git a/nf_core/pipeline-template/lib/NfcoreTemplate.groovy b/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
deleted file mode 100755
index 0f8d021a03..0000000000
--- a/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
+++ /dev/null
@@ -1,356 +0,0 @@
-//
-// This file holds several functions used within the nf-core pipeline template.
-//
-
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
-class NfcoreTemplate {
-
-    //
-    // Check AWS Batch related parameters have been specified correctly
-    //
-    public static void awsBatch(workflow, params) {
-        if (workflow.profile.contains('awsbatch')) {
-            // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
-            assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
-            // Check outdir paths to be S3 buckets if running on AWSBatch
-            assert params.outdir.startsWith('s3:')       : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
-        }
-    }
-
-    //
-    //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
-    //
-    public static void checkConfigProvided(workflow, log) {
-        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-                    "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-                    "Please refer to the quick start section and usage docs for the pipeline.\n "
-        }
-    }
-
-    //
-    // Generate version string
-    //
-    public static String version(workflow) {
-        String version_string = ""
-
-        if (workflow.manifest.version) {
-            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-            version_string += "${prefix_v}${workflow.manifest.version}"
-        }
-
-        if (workflow.commitId) {
-            def git_shortsha = workflow.commitId.substring(0, 7)
-            version_string += "-g${git_shortsha}"
-        }
-
-        return version_string
-    }
-
-    //
-    // Construct and send completion email
-    //
-    public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
-
-        // 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 = [:]
-        for (group in summary_params.keySet()) {
-            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']      = NfcoreTemplate.version(workflow)
-        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 = null
-        try {
-            if (workflow.success) {
-                mqc_report = multiqc_report.getVal()
-                if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                    if (mqc_report.size() > 1) {
-                        log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
-                    }
-                    mqc_report = mqc_report[0]
-                }
-            }
-        } catch (all) {
-            if (multiqc_report) {
-                log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
-            }
-        }
-
-        // Check if we are only sending emails on failure
-        def email_address = params.email
-        if (!params.email && params.email_on_fail && !workflow.success) {
-            email_address = params.email_on_fail
-        }
-
-        // Render the TXT template
-        def engine       = new groovy.text.GStringTemplateEngine()
-        def tf           = new File("$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("$projectDir/assets/email_template.html")
-        def html_template = engine.createTemplate(hf).make(email_fields)
-        def email_html    = html_template.toString()
-
-        // Render the sendmail template
-        def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
-        def sf                     = new File("$projectDir/assets/sendmail_template.txt")
-        def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
-        def sendmail_html          = sendmail_template.toString()
-
-        // Send the HTML e-mail
-        Map colors = logColours(params.monochrome_logs)
-        if (email_address) {
-            try {
-                if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
-                // Try to send HTML e-mail using sendmail
-                def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
-                sendmail_tf.withWriter { w -> w << sendmail_html }
-                [ 'sendmail', '-t' ].execute() << sendmail_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-            } catch (all) {
-                // Catch failures and try with plaintext
-                def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-                if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
-                    mail_cmd += [ '-A', mqc_report ]
-                }
-                mail_cmd.execute() << email_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
-            }
-        }
-
-        // Write summary e-mail HTML to a file
-        def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
-        output_hf.withWriter { w -> w << email_html }
-        FilesEx.copyTo(output_hf.toPath(), "${params.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 }
-        FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt");
-        output_tf.delete()
-    }
-
-    //
-    // Construct and send a notification to a web server as JSON
-    // e.g. Microsoft Teams and Slack
-    //
-    public static void IM_notification(workflow, params, summary_params, projectDir, log) {
-        def hook_url = params.hook_url
-
-        def summary = [:]
-        for (group in summary_params.keySet()) {
-            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']      = NfcoreTemplate.version(workflow)
-        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("$projectDir/assets/${json_path}")
-        def json_template = engine.createTemplate(hf).make(msg_fields)
-        def json_message  = json_template.toString()
-
-        // POST
-        def post = new URL(hook_url).openConnection();
-        post.setRequestMethod("POST")
-        post.setDoOutput(true)
-        post.setRequestProperty("Content-Type", "application/json")
-        post.getOutputStream().write(json_message.getBytes("UTF-8"));
-        def postRC = post.getResponseCode();
-        if (! postRC.equals(200)) {
-            log.warn(post.getErrorStream().getText());
-        }
-    }
-
-    //
-    // Dump pipeline parameters in a json file
-    //
-    public static void dump_parameters(workflow, params) {
-        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-        def filename   = "params_${timestamp}.json"
-        def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-        def jsonStr    = JsonOutput.toJson(params)
-        temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
-
-        FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
-        temp_pf.delete()
-    }
-
-    //
-    // Print pipeline summary on completion
-    //
-    public static void summary(workflow, params, log) {
-        Map colors = logColours(params.monochrome_logs)
-        if (workflow.success) {
-            if (workflow.stats.ignoredCount == 0) {
-                log.info "-${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}-"
-        }
-    }
-
-    //
-    // ANSII Colours used for terminal logging
-    //
-    public static Map logColours(Boolean monochrome_logs) {
-        Map colorcodes = [:]
-
-        // 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
-    }
-
-    //
-    // Does what is says on the tin
-    //
-    public static String dashedLine(monochrome_logs) {
-        Map colors = logColours(monochrome_logs)
-        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-    }
-
-    //
-    // nf-core logo
-    //
-    public static String logo(workflow, monochrome_logs) {
-        Map colors = logColours(monochrome_logs)
-        String workflow_version = NfcoreTemplate.version(workflow)
-        String.format(
-            """\n
-            ${dashedLine(monochrome_logs)}{% if branded %}
-                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                    ${colors.green}`._,._,\'${colors.reset}{% endif %}
-            ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
-            ${dashedLine(monochrome_logs)}
-            """.stripIndent()
-        )
-    }
-}
diff --git a/nf_core/pipeline-template/lib/Utils.groovy b/nf_core/pipeline-template/lib/Utils.groovy
deleted file mode 100644
index 8d030f4e84..0000000000
--- a/nf_core/pipeline-template/lib/Utils.groovy
+++ /dev/null
@@ -1,47 +0,0 @@
-//
-// This file holds several Groovy functions that could be useful for any Nextflow pipeline
-//
-
-import org.yaml.snakeyaml.Yaml
-
-class Utils {
-
-    //
-    // When running with -profile conda, warn if channels have not been set-up appropriately
-    //
-    public static void checkCondaChannels(log) {
-        Yaml parser = new Yaml()
-        def channels = []
-        try {
-            def config = parser.load("conda config --show channels".execute().text)
-            channels = config.channels
-        } catch(NullPointerException | IOException e) {
-            log.warn "Could not verify conda channel configuration."
-            return
-        }
-
-        // Check that all channels are present
-        // This channel list is ordered by required channel priority.
-        def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
-        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 = false
-        def n = required_channels_in_order.size()
-        for (int i = 0; i < n - 1; i++) {
-            channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
-        }
-
-        if (channels_missing | channel_priority_violation) {
-            log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                "  There is a problem with your Conda configuration!\n\n" +
-                "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-                "  Please refer to https://bioconda.github.io/\n" +
-                "  The observed channel order is \n" +
-                "  ${channels}\n" +
-                "  but the following channel order is required:\n" +
-                "  ${required_channels_in_order}\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        }
-    }
-}
diff --git a/nf_core/pipeline-template/lib/WorkflowMain.groovy b/nf_core/pipeline-template/lib/WorkflowMain.groovy
deleted file mode 100755
index a254b2b22a..0000000000
--- a/nf_core/pipeline-template/lib/WorkflowMain.groovy
+++ /dev/null
@@ -1,80 +0,0 @@
-//
-// This file holds several functions specific to the main.nf workflow in the {{ name }} pipeline
-//
-
-import nextflow.Nextflow
-
-class WorkflowMain {
-
-    //
-    // Citation string for pipeline
-    //
-    public static String citation(workflow) {
-        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            // TODO nf-core: Add Zenodo DOI for pipeline after first release
-            //"* The pipeline\n" +
-            //"  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
-            "* The nf-core framework\n" +
-            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-            "* Software dependencies\n" +
-            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-    }
-
-
-    //
-    // Validate parameters and print summary to screen
-    //
-    public static void initialise(workflow, params, log, args) {
-
-        // Print workflow version and exit on --version
-        if (params.version) {
-            String workflow_version = NfcoreTemplate.version(workflow)
-            log.info "${workflow.manifest.name} ${workflow_version}"
-            System.exit(0)
-        }
-
-        // Check that a -profile or Nextflow config has been provided to run the pipeline
-        NfcoreTemplate.checkConfigProvided(workflow, log)
-        // Check that the profile doesn't contain spaces and doesn't end with a trailing comma
-        checkProfile(workflow.profile, args, log)
-
-        // Check that conda channels are set-up correctly
-        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-            Utils.checkCondaChannels(log)
-        }
-
-        // Check AWS batch settings
-        NfcoreTemplate.awsBatch(workflow, params)
-
-        // Check input has been provided
-        if (!params.input) {
-            Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
-        }
-    }
-
-    {%- if igenomes %}
-    //
-    // Get attribute from genome config file e.g. fasta
-    //
-    public static Object getGenomeAttribute(params, attribute) {
-        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-            if (params.genomes[ params.genome ].containsKey(attribute)) {
-                return params.genomes[ params.genome ][ attribute ]
-            }
-        }
-        return null
-    }
-    {%- endif %}
-
-    //
-    // Exit pipeline if --profile contains spaces
-    //
-    private static void checkProfile(profile, args, log) {
-        if (profile.endsWith(',')) {
-            Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
-        }
-        if (args[0]) {
-            log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n      Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
-        }
-    }
-}
diff --git a/nf_core/pipeline-template/lib/WorkflowPipeline.groovy b/nf_core/pipeline-template/lib/WorkflowPipeline.groovy
deleted file mode 100755
index f9a7859ef5..0000000000
--- a/nf_core/pipeline-template/lib/WorkflowPipeline.groovy
+++ /dev/null
@@ -1,123 +0,0 @@
-//
-// This file holds several functions specific to the workflow/{{ short_name }}.nf in the {{ name }} pipeline
-//
-
-import nextflow.Nextflow
-import groovy.text.SimpleTemplateEngine
-
-class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} {
-
-    //
-    // Check and validate parameters
-    //
-    public static void initialise(params, log) {
-{% if igenomes %}
-        genomeExistsError(params, log)
-{% endif %}
-
-        if (!params.fasta) {
-            Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
-        }
-    }
-
-    //
-    // Get workflow summary for MultiQC
-    //
-    public static String paramsSummaryMultiqc(workflow, summary) {
-        String summary_section = ''
-        for (group in summary.keySet()) {
-            def group_params = summary.get(group)  // This gets the parameters of that particular group
-            if (group_params) {
-                summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
-                summary_section += "    <dl class=\"dl-horizontal\">\n"
-                for (param in group_params.keySet()) {
-                    summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
-                }
-                summary_section += "    </dl>\n"
-            }
-        }
-
-        String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
-        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
-    }
-
-    //
-    // Generate methods description for MultiQC
-    //
-
-    public static String toolCitationText(params) {
-
-        // TODO nf-core: Optionally add in-text citation tools to this list.
-        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
-        // Uncomment function in methodsDescriptionText to render in MultiQC report
-        def citation_text = [
-                "Tools used in the workflow included:",
-                "FastQC (Andrews 2010),",
-                "MultiQC (Ewels et al. 2016)",
-                "."
-            ].join(' ').trim()
-
-        return citation_text
-    }
-
-    public static String toolBibliographyText(params) {
-
-        // TODO Optionally add bibliographic entries to this list.
-        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
-        // Uncomment function in methodsDescriptionText to render in MultiQC report
-        def reference_text = [
-                "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
-                "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
-            ].join(' ').trim()
-
-        return reference_text
-    }
-
-    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) {
-        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
-        def meta = [:]
-        meta.workflow = run_workflow.toMap()
-        meta["manifest_map"] = run_workflow.manifest.toMap()
-
-        // Pipeline DOI
-        meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
-        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
-
-        // Tool references
-        meta["tool_citations"] = ""
-        meta["tool_bibliography"] = ""
-
-        // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
-        //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-        //meta["tool_bibliography"] = toolBibliographyText(params)
-
-
-        def methods_text = mqc_methods_yaml.text
-
-        def engine =  new SimpleTemplateEngine()
-        def description_html = engine.createTemplate(methods_text).make(meta)
-
-        return description_html
-    }
-    {%- if igenomes %}
-
-    //
-    // Exit pipeline if incorrect --genome key provided
-    //
-    private static void genomeExistsError(params, log) {
-        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-            def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-                "  Currently, the available genome keys are:\n" +
-                "  ${params.genomes.keySet().join(", ")}\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-            Nextflow.error(error_string)
-        }
-    }
-{% endif -%}}

From 99fb69f5263c5a63244682821fcf777bc6c899d3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Feb 2024 12:44:56 +0100
Subject: [PATCH 03/27] Change output channel name in input_check subworkflow

---
 nf_core/pipeline-template/subworkflows/local/input_check.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/input_check.nf b/nf_core/pipeline-template/subworkflows/local/input_check.nf
index 0aecf87fb7..562f44cc69 100644
--- a/nf_core/pipeline-template/subworkflows/local/input_check.nf
+++ b/nf_core/pipeline-template/subworkflows/local/input_check.nf
@@ -13,10 +13,10 @@ workflow INPUT_CHECK {
         .csv
         .splitCsv ( header:true, sep:',' )
         .map { create_fastq_channel(it) }
-        .set { reads }
+        .set { samplesheet }
 
     emit:
-    reads                                     // channel: [ val(meta), [ reads ] ]
+    samplesheet                               // channel: [ val(meta), [ reads ] ]
     versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
 }
 

From bae90f0f350ac2bc48991b1c938b98e28f7e0d75 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Feb 2024 12:46:07 +0100
Subject: [PATCH 04/27] Delete custom/dumpsoftwareversions module

---
 nf_core/pipeline-template/modules.json        |  27 +++--
 .../dumpsoftwareversions/environment.yml      |   7 --
 .../custom/dumpsoftwareversions/main.nf       |  24 -----
 .../custom/dumpsoftwareversions/meta.yml      |  37 -------
 .../templates/dumpsoftwareversions.py         | 102 ------------------
 .../dumpsoftwareversions/tests/main.nf.test   |  43 --------
 .../tests/main.nf.test.snap                   |  33 ------
 .../dumpsoftwareversions/tests/tags.yml       |   2 -
 8 files changed, 16 insertions(+), 259 deletions(-)
 delete mode 100644 nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/environment.yml
 delete mode 100644 nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
 delete mode 100644 nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml
 delete mode 100755 nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
 delete mode 100644 nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
 delete mode 100644 nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
 delete mode 100644 nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 5c30ac92fc..c558969239 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -5,20 +5,19 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
-                        "installed_by": ["modules"]
-                    },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -27,20 +26,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "73b63c8e510107010ab13b68cf31189d6cdca8cb",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/environment.yml
deleted file mode 100644
index 9b3272bc11..0000000000
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: custom_dumpsoftwareversions
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::multiqc=1.19
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
deleted file mode 100644
index f2187611cc..0000000000
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_single'
-
-    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.19--pyhdfd78af_0' }"
-
-    input:
-    path versions
-
-    output:
-    path "software_versions.yml"    , emit: yml
-    path "software_versions_mqc.yml", emit: mqc_yml
-    path "versions.yml"             , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    template 'dumpsoftwareversions.py'
-}
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml
deleted file mode 100644
index 5f15a5fde0..0000000000
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: custom_dumpsoftwareversions
-description: Custom module used to dump software versions within the nf-core pipeline template
-keywords:
-  - custom
-  - dump
-  - version
-tools:
-  - custom:
-      description: Custom module used to dump software versions within the nf-core pipeline template
-      homepage: https://github.com/nf-core/tools
-      documentation: https://github.com/nf-core/tools
-      licence: ["MIT"]
-input:
-  - versions:
-      type: file
-      description: YML file containing software versions
-      pattern: "*.yml"
-output:
-  - yml:
-      type: file
-      description: Standard YML file containing software versions
-      pattern: "software_versions.yml"
-  - mqc_yml:
-      type: file
-      description: MultiQC custom content YML file containing software versions
-      pattern: "software_versions_mqc.yml"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@drpatelh"
-  - "@grst"
-maintainers:
-  - "@drpatelh"
-  - "@grst"
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
deleted file mode 100755
index e55b8d43a9..0000000000
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ /dev/null
@@ -1,102 +0,0 @@
-#!/usr/bin/env python
-
-
-"""Provide functions to merge multiple versions.yml files."""
-
-
-import platform
-from textwrap import dedent
-
-import yaml
-
-
-def _make_versions_html(versions):
-    """Generate a tabular HTML output of all versions for MultiQC."""
-    html = [
-        dedent(
-            """\\
-            <style>
-            #nf-core-versions tbody:nth-child(even) {
-                background-color: #f2f2f2;
-            }
-            </style>
-            <table class="table" style="width:100%" id="nf-core-versions">
-                <thead>
-                    <tr>
-                        <th> Process Name </th>
-                        <th> Software </th>
-                        <th> Version  </th>
-                    </tr>
-                </thead>
-            """
-        )
-    ]
-    for process, tmp_versions in sorted(versions.items()):
-        html.append("<tbody>")
-        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
-            html.append(
-                dedent(
-                    f"""\\
-                    <tr>
-                        <td><samp>{process if (i == 0) else ''}</samp></td>
-                        <td><samp>{tool}</samp></td>
-                        <td><samp>{version}</samp></td>
-                    </tr>
-                    """
-                )
-            )
-        html.append("</tbody>")
-    html.append("</table>")
-    return "\\n".join(html)
-
-
-def main():
-    """Load all version files and generate merged output."""
-    versions_this_module = {}
-    versions_this_module["${task.process}"] = {
-        "python": platform.python_version(),
-        "yaml": yaml.__version__,
-    }
-
-    with open("$versions") as f:
-        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-    # aggregate versions by the module name (derived from fully-qualified process name)
-    versions_by_module = {}
-    for process, process_versions in versions_by_process.items():
-        module = process.split(":")[-1]
-        try:
-            if versions_by_module[module] != process_versions:
-                raise AssertionError(
-                    "We assume that software versions are the same between all modules. "
-                    "If you see this error-message it means you discovered an edge-case "
-                    "and should open an issue in nf-core/tools. "
-                )
-        except KeyError:
-            versions_by_module[module] = process_versions
-
-    versions_by_module["Workflow"] = {
-        "Nextflow": "$workflow.nextflow.version",
-        "$workflow.manifest.name": "$workflow.manifest.version",
-    }
-
-    versions_mqc = {
-        "id": "software_versions",
-        "section_name": "${workflow.manifest.name} Software Versions",
-        "section_href": "https://github.com/${workflow.manifest.name}",
-        "plot_type": "html",
-        "description": "are collected at run time from the software output.",
-        "data": _make_versions_html(versions_by_module),
-    }
-
-    with open("software_versions.yml", "w") as f:
-        yaml.dump(versions_by_module, f, default_flow_style=False)
-    with open("software_versions_mqc.yml", "w") as f:
-        yaml.dump(versions_mqc, f, default_flow_style=False)
-
-    with open("versions.yml", "w") as f:
-        yaml.dump(versions_this_module, f, default_flow_style=False)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
deleted file mode 100644
index b1e1630bb3..0000000000
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
+++ /dev/null
@@ -1,43 +0,0 @@
-nextflow_process {
-
-    name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS"
-    script "../main.nf"
-    process "CUSTOM_DUMPSOFTWAREVERSIONS"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "custom"
-    tag "dumpsoftwareversions"
-    tag "custom/dumpsoftwareversions"
-
-    test("Should run without failures") {
-        when {
-            process {
-                """
-                def tool1_version = '''
-                TOOL1:
-                    tool1: 0.11.9
-                '''.stripIndent()
-
-                def tool2_version = '''
-                TOOL2:
-                    tool2: 1.9
-                '''.stripIndent()
-
-                input[0] = Channel.of(tool1_version, tool2_version).collectFile()
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.versions,
-                    file(process.out.mqc_yml[0]).readLines()[0..10],
-                    file(process.out.yml[0]).readLines()[0..7]
-                    ).match()
-                }
-            )
-        }
-    }
-}
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
deleted file mode 100644
index 5f59a936d7..0000000000
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
+++ /dev/null
@@ -1,33 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            [
-                "versions.yml:md5,76d454d92244589d32455833f7c1ba6d"
-            ],
-            [
-                "data: \"<style>\\n#nf-core-versions tbody:nth-child(even) {\\n    background-color: #f2f2f2;\\n\\",
-                "  }\\n</style>\\n<table class=\\\"table\\\" style=\\\"width:100%\\\" id=\\\"nf-core-versions\\\"\\",
-                "  >\\n    <thead>\\n        <tr>\\n            <th> Process Name </th>\\n            <th>\\",
-                "  \\ Software </th>\\n            <th> Version  </th>\\n        </tr>\\n    </thead>\\n\\",
-                "  \\n<tbody>\\n<tr>\\n    <td><samp>CUSTOM_DUMPSOFTWAREVERSIONS</samp></td>\\n    <td><samp>python</samp></td>\\n\\",
-                "  \\    <td><samp>3.11.7</samp></td>\\n</tr>\\n\\n<tr>\\n    <td><samp></samp></td>\\n \\",
-                "  \\   <td><samp>yaml</samp></td>\\n    <td><samp>5.4.1</samp></td>\\n</tr>\\n\\n</tbody>\\n\\",
-                "  <tbody>\\n<tr>\\n    <td><samp>TOOL1</samp></td>\\n    <td><samp>tool1</samp></td>\\n\\",
-                "  \\    <td><samp>0.11.9</samp></td>\\n</tr>\\n\\n</tbody>\\n<tbody>\\n<tr>\\n    <td><samp>TOOL2</samp></td>\\n\\",
-                "  \\    <td><samp>tool2</samp></td>\\n    <td><samp>1.9</samp></td>\\n</tr>\\n\\n</tbody>\\n\\",
-                "  <tbody>\\n<tr>\\n    <td><samp>Workflow</samp></td>\\n    <td><samp>Nextflow</samp></td>\\n\\"
-            ],
-            [
-                "CUSTOM_DUMPSOFTWAREVERSIONS:",
-                "  python: 3.11.7",
-                "  yaml: 5.4.1",
-                "TOOL1:",
-                "  tool1: 0.11.9",
-                "TOOL2:",
-                "  tool2: '1.9'",
-                "Workflow:"
-            ]
-        ],
-        "timestamp": "2024-01-09T23:01:18.710682"
-    }
-}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
deleted file mode 100644
index 405aa24ae3..0000000000
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-custom/dumpsoftwareversions:
-  - modules/nf-core/custom/dumpsoftwareversions/**

From a78d41b2a1647b70f4d5bf63c7bd6738f5412c16 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Feb 2024 12:46:25 +0100
Subject: [PATCH 05/27] Delete fasta from test.config

---
 nf_core/pipeline-template/conf/test.config | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config
index 49bfe8a6db..499c72054b 100644
--- a/nf_core/pipeline-template/conf/test.config
+++ b/nf_core/pipeline-template/conf/test.config
@@ -24,11 +24,8 @@ params {
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
-    {% if igenomes -%}
+    {% if igenomes %}
     // Genome references
     genome = 'R64-1-1'
-    {%- else -%}
-    // Fasta references
-    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
     {%- endif %}
 }

From 7343ce4adc481671e9cb50252aa6a84f45597cf3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Feb 2024 12:46:46 +0100
Subject: [PATCH 06/27] Add local subworkflow for pipeline utilities

---
 .../utils_nfcore_pipeline_pipeline/main.nf    | 177 ++++++++++++++++++
 1 file changed, 177 insertions(+)
 create mode 100644 nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

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
new file mode 100644
index 0000000000..945d270741
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -0,0 +1,177 @@
+//
+// Subworkflow with functionality specific to the nf-core/pipeline pipeline
+//
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-validation'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
+include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
+include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
+include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { INPUT_CHECK               } from '../../local/input_check'
+
+/*
+========================================================================================
+    SUBWORKFLOW TO INITIALISE PIPELINE
+========================================================================================
+*/
+
+workflow PIPELINE_INITIALISATION {
+
+    take:
+    version         // boolean: Display version and exit
+    help            // boolean: Display help text
+    validate_params // boolean: Boolean whether to validate parameters against the schema at runtime
+    monochrome_logs // boolean: Do not use coloured log outputs
+    outdir          //  string: The output directory where the results will be saved
+    input           //  string: Path to input samplesheet
+
+    main:
+
+    ch_versions = Channel.empty()
+  
+    //
+    // 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
+    )
+
+    //
+    // Validate parameters and generate parameter summary to stdout
+    //
+    pre_help_text = nfCoreLogo(monochrome_logs)
+    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
+    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+    UTILS_NFVALIDATION_PLUGIN (
+        help,
+        workflow_command,
+        pre_help_text,
+        post_help_text,
+        validate_params,
+        "nextflow_schema.json"
+    )
+
+    //
+    // Check config provided to the pipeline
+    //
+    UTILS_NFCORE_PIPELINE ()
+
+    //
+    // Custom validation for pipeline parameters
+    //
+    validateInputParameters()
+
+    //
+    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
+    //
+    INPUT_CHECK (
+        file(input)
+    )
+    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
+    // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
+    // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
+    // ! There is currently no tooling to help you write a sample sheet schema
+
+    emit:
+    samplesheet = INPUT_CHECK.out.samplesheet
+    versions    = ch_versions
+}
+
+/*
+========================================================================================
+    SUBWORKFLOW FOR PIPELINE COMPLETION
+========================================================================================
+*/
+
+workflow PIPELINE_COMPLETION {
+
+    take:
+    email           //  string: email address
+    email_on_fail   //  string: email address sent on pipeline failure
+    plaintext_email // boolean: Send plain-text email instead of HTML
+    outdir          //    path: Path to output directory where results will be published
+    monochrome_logs // boolean: Disable ANSI colour codes in log output
+    hook_url        //  string: hook URL for notifications
+
+    main:
+
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+
+    //
+    // Completion email and summary
+    //
+    workflow.onComplete {
+        if (email || email_on_fail) {
+            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs)
+        }
+
+        completionSummary(monochrome_logs)
+
+        if (hook_url) {
+            imNotification(summary_params, hook_url)
+        }
+    }
+
+    //
+    // Log warning if exceeding resource requests
+    //
+    workflow.onError {
+        if (workflow.errorReport.contains("Process requirement exceeds available memory")) {
+            log.warning "🛑 Default resources exceed availability 🛑 "
+            log.warning "💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡"
+        }
+    }
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+// Check and validate pipeline parameters
+//
+def validateInputParameters() {
+    genomeExistsError()
+}
+
+//
+// Get attribute from genome config file e.g. fasta
+//
+def getGenomeAttribute(attribute) {
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[ params.genome ].containsKey(attribute)) {
+            return params.genomes[ params.genome ][ attribute ]
+        }
+    }
+    return null
+}
+
+//
+// Exit pipeline if incorrect --genome key provided
+//
+def genomeExistsError() {
+    if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
+            "  Currently, the available genome keys are:\n" +
+            "  ${params.genomes.keySet().join(", ")}\n" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        error(error_string)
+    }
+}
\ No newline at end of file

From 090a395097cc233dff30a82f8ea726cb1a417219 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Feb 2024 12:47:59 +0100
Subject: [PATCH 07/27] Update main workflows in pipeline to use utils_*
 subworkflows

---
 nf_core/pipeline-template/main.nf             |  95 ++++++++-----
 .../pipeline-template/workflows/pipeline.nf   | 127 ++++--------------
 2 files changed, 89 insertions(+), 133 deletions(-)

diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 78da158856..2fb327b221 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -12,7 +12,19 @@
 */
 
 nextflow.enable.dsl = 2
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_pipeline_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_pipeline_pipeline'
 {% if igenomes %}
+include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_pipeline_pipeline'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
@@ -22,59 +34,72 @@ nextflow.enable.dsl = 2
 // TODO nf-core: Remove this line if you don't need a FASTA file
 //   This is an example of how to use getGenomeAttribute() to fetch parameters
 //   from igenomes.config using `--genome`
-params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
+params.fasta = getGenomeAttribute('fasta')
 {% endif %}
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    VALIDATE & PRINT PARAMETER SUMMARY
+    NAMED WORKFLOWS FOR PIPELINE
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
+//
+// WORKFLOW: Run main analysis pipeline depending on type of input
+//
+workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
 
-// Print help message if needed
-if (params.help) {
-    def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
-    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
-    System.exit(0)
-}
+    take:
+    samplesheet // channel: samplesheet read in from --input
 
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
+    main:
 
-WorkflowMain.initialise(workflow, params, log, args)
+    //
+    // WORKFLOW: Run pipeline
+    //
+    {{ short_name|upper }} ( 
+        samplesheet 
+    )
 
+}
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOW FOR PIPELINE
+    RUN MAIN WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { {{ short_name|upper }} } from './workflows/{{ short_name }}'
+workflow {
 
-//
-// WORKFLOW: Run main {{ name }} analysis pipeline
-//
-workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
-    {{ short_name|upper }} ()
-}
+    main:
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN ALL WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+    //
+    // SUBWORKFLOW: Run initialisation tasks
+    //
+    PIPELINE_INITIALISATION (
+        params.version,
+        params.help,
+        params.validate_params,
+        params.monochrome_logs,
+        params.outdir,
+        params.input
+    )
 
-//
-// WORKFLOW: Execute a single named workflow for the pipeline
-// See: https://github.com/nf-core/rnaseq/issues/619
-//
-workflow {
-    {{ prefix_nodash|upper }}_{{ short_name|upper }} ()
+    //
+    // WORKFLOW: Run main workflow
+    //
+    {{ prefix_nodash|upper }}_{{ short_name|upper }} (
+        PIPELINE_INITIALISATION.out.samplesheet
+    )
+
+    //
+    // SUBWORKFLOW: Run completion tasks
+    //
+    PIPELINE_COMPLETION (
+        params.email,
+        params.email_on_fail,
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url
+    )
 }
 
 /*
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 4583f2a9d6..85c9dd22a1 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -1,54 +1,14 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    PRINT PARAMS SUMMARY
+    IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-def summary_params = paramsSummaryMap(workflow)
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.initialise(params, log)
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
-ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT LOCAL MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
-//
-include { INPUT_CHECK } from '../subworkflows/local/input_check'
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// MODULE: Installed directly from nf-core/modules
-//
-include { FASTQC                      } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { FASTQC                 } from '../modules/nf-core/fastqc/main'
+include { MULTIQC                } from '../modules/nf-core/multiqc/main'
+include { paramsSummaryMap       } from 'plugin/nf-validation'
+include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -56,50 +16,42 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// Info required for completion email and summary
-def multiqc_report = []
-
 workflow {{ short_name|upper }} {
 
-    ch_versions = Channel.empty()
+    take:
+    ch_samplesheet // channel: samplesheet read in from --input
 
-    //
-    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
-    //
-    INPUT_CHECK (
-        file(params.input)
-    )
-    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
-    // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
-    // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
-    // ! There is currently no tooling to help you write a sample sheet schema
+    main:
+
+    ch_versions = Channel.empty()
+    ch_multiqc_files = Channel.empty()
 
     //
     // MODULE: Run FastQC
     //
     FASTQC (
-        INPUT_CHECK.out.reads
+        ch_samplesheet
     )
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
-    )
+    //
+    // Collate and save software versions
+    //
+    softwareVersionsToYAML(ch_versions)
+        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
+        .set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
-    workflow_summary    = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.paramsSummaryMultiqc(workflow, summary_params)
-    ch_workflow_summary = Channel.value(workflow_summary)
-
-    methods_description    = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
-    ch_methods_description = Channel.value(methods_description)
-
-    ch_multiqc_files = Channel.empty()
+    ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
+    ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
 
     MULTIQC (
         ch_multiqc_files.collect(),
@@ -107,31 +59,10 @@ workflow {{ short_name|upper }} {
         ch_multiqc_custom_config.toList(),
         ch_multiqc_logo.toList()
     )
-    multiqc_report = MULTIQC.out.report.toList()
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    COMPLETION EMAIL AND SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
-    }
-    NfcoreTemplate.dump_parameters(workflow, params)
-    NfcoreTemplate.summary(workflow, params, log)
-    if (params.hook_url) {
-        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
-    }
-}
 
-workflow.onError {
-    if (workflow.errorReport.contains("Process requirement exceeds available memory")) {
-        println("🛑 Default resources exceed availability 🛑 ")
-        println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡")
-    }
+    emit:
+    multiqc_report = MULTIQC.out.report // channel: /path/to/multiqc_report.html
+    versions       = ch_versions        // channel: [ path(versions.yml) ]
 }
 
 /*

From fdf3e547c10405cd21aa66a1e1ff0c8663fd6f70 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Feb 2024 14:55:35 +0100
Subject: [PATCH 08/27] Disable native version detection in MultiQC

---
 nf_core/pipeline-template/assets/multiqc_config.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml
index 39943ffe49..b13b7ae074 100644
--- a/nf_core/pipeline-template/assets/multiqc_config.yml
+++ b/nf_core/pipeline-template/assets/multiqc_config.yml
@@ -17,3 +17,5 @@ report_section_order:
     order: -1002
 
 export_plots: true
+
+disable_version_detection: true

From 52149765512cc0a5c2c749f82fc1656536a4e4d4 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Feb 2024 16:13:54 +0100
Subject: [PATCH 09/27] Add checkProfileProvided function back in

---
 nf_core/pipeline-template/main.nf              |  1 +
 .../utils_nfcore_pipeline_pipeline/main.nf     | 17 ++++++++++-------
 .../nf-core/utils_nfcore_pipeline/main.nf      | 18 ++++++++++++++++++
 3 files changed, 29 insertions(+), 7 deletions(-)

diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 2fb327b221..c56dc5d443 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -78,6 +78,7 @@ workflow {
         params.help,
         params.validate_params,
         params.monochrome_logs,
+        args,
         params.outdir,
         params.input
     )
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 945d270741..d33aae5330 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
@@ -29,12 +29,13 @@ include { INPUT_CHECK               } from '../../local/input_check'
 workflow PIPELINE_INITIALISATION {
 
     take:
-    version         // boolean: Display version and exit
-    help            // boolean: Display help text
-    validate_params // boolean: Boolean whether to validate parameters against the schema at runtime
-    monochrome_logs // boolean: Do not use coloured log outputs
-    outdir          //  string: The output directory where the results will be saved
-    input           //  string: Path to input samplesheet
+    version           // boolean: Display version and exit
+    help              // boolean: Display help text
+    validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
+    monochrome_logs   // boolean: Do not use coloured log outputs
+    nextflow_cli_args //   array: List of positional nextflow CLI args
+    outdir            //  string: The output directory where the results will be saved
+    input             //  string: Path to input samplesheet
 
     main:
 
@@ -68,7 +69,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE ()
+    UTILS_NFCORE_PIPELINE (
+        nextflow_cli_args
+    )
 
     //
     // Custom validation for pipeline parameters
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
index 6d805bb3fd..c1aecf6e42 100644
--- 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
@@ -13,8 +13,12 @@ import nextflow.extension.FilesEx
 
 workflow UTILS_NFCORE_PIPELINE {
 
+    take:
+    nextflow_cli_args
+
     main:
     valid_config = checkConfigProvided()
+    checkProfileProvided(nextflow_cli_args)
 
     emit:
     valid_config
@@ -43,6 +47,20 @@ def checkConfigProvided() {
     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"
+    }
+}
+
 //
 // Citation string for pipeline
 //

From 7832a441f3fda016d55f989095f9aae11d4ff4a8 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 9 Feb 2024 20:02:31 +0100
Subject: [PATCH 10/27] update utils_nfcore_pipeline in the template

---
 nf_core/pipeline-template/conf/test.config    |  2 +-
 nf_core/pipeline-template/modules.json        | 24 ++++++-------------
 .../nf-core/utils_nfcore_pipeline/meta.yml    |  6 ++++-
 .../tests/main.function.nf.test               | 20 ++++++++++++++++
 .../tests/main.function.nf.test.snap          |  4 ++++
 .../tests/main.workflow.nf.test               |  8 +++++++
 6 files changed, 45 insertions(+), 19 deletions(-)

diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config
index 499c72054b..32b9619ebb 100644
--- a/nf_core/pipeline-template/conf/test.config
+++ b/nf_core/pipeline-template/conf/test.config
@@ -24,7 +24,7 @@ params {
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
-    {% if igenomes %}
+    {% if igenomes -%}
     // Genome references
     genome = 'R64-1-1'
     {%- endif %}
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index c558969239..d1e54dbbf7 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -8,16 +8,12 @@
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -26,26 +22,20 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "73b63c8e510107010ab13b68cf31189d6cdca8cb",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "git_sha": "db321a792c88d145afa0ae214fc7da70fcd7d591",
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
         }
     }
-}
\ No newline at end of file
+}
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
index dd1462b232..d08d24342d 100644
--- 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
@@ -7,7 +7,11 @@ keywords:
   - initialise
   - version
 components: []
-input: []
+input:
+  - nextflow_cli_args:
+      type: list
+      description: |
+        Nextflow CLI positional arguments
 output:
   - success:
       type: boolean
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
index f7ea05fcd7..1dc317f8f7 100644
--- 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
@@ -21,6 +21,26 @@ nextflow_function {
         }
     }
 
+    test("Test Function checkProfileProvided") {
+
+        function "checkProfileProvided"
+
+        when {
+            function {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
     test("Test Function workflowCitation") {
 
         function "workflowCitation"
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
index afb9ab4dca..10f948e629 100644
--- 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
@@ -1,4 +1,8 @@
 {
+    "Test Function checkProfileProvided": {
+        "content": null,
+        "timestamp": "2024-02-09T15:43:55.145717"
+    },
     "Test Function checkConfigProvided": {
         "content": [
             true
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
index c5f7776a67..8940d32d1e 100644
--- 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
@@ -11,6 +11,14 @@ nextflow_workflow {
 
     test("Should run without failures") {
 
+        when {
+            workflow {
+                """
+                input[0] = []
+                """
+            }
+        }
+
         then {
             assertAll(
                 { assert workflow.success },

From 91b15295719cded218565aef1fbfa939c90ca736 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Sat, 10 Feb 2024 10:57:53 +0100
Subject: [PATCH 11/27] add multiqc report to completion email

---
 nf_core/pipeline-template/main.nf             | 10 +++++---
 .../utils_nfcore_pipeline_pipeline/main.nf    |  7 +++---
 .../nf-core/utils_nfcore_pipeline/main.nf     | 23 +++++++++++++++++--
 3 files changed, 32 insertions(+), 8 deletions(-)

diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index c56dc5d443..c31927f236 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -55,10 +55,13 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
     //
     // WORKFLOW: Run pipeline
     //
-    {{ short_name|upper }} ( 
-        samplesheet 
+    {{ short_name|upper }} (
+        samplesheet
     )
 
+    emit:
+    multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
+
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -99,7 +102,8 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url
+        params.hook_url,
+        {{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report
     )
 }
 
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 d33aae5330..b1046ed9db 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
@@ -40,7 +40,7 @@ workflow PIPELINE_INITIALISATION {
     main:
 
     ch_versions = Channel.empty()
-  
+
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
@@ -109,6 +109,7 @@ workflow PIPELINE_COMPLETION {
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
+    multiqc_report  //  string: Path to MultiQC report
 
     main:
 
@@ -119,7 +120,7 @@ workflow PIPELINE_COMPLETION {
     //
     workflow.onComplete {
         if (email || email_on_fail) {
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs)
+            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
         }
 
         completionSummary(monochrome_logs)
@@ -177,4 +178,4 @@ def genomeExistsError() {
             "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         error(error_string)
     }
-}
\ No newline at end of file
+}
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
index c1aecf6e42..54769d5b58 100644
--- 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
@@ -249,7 +249,7 @@ def logColours(monochrome_logs=true) {
 //
 // Construct and send completion email
 //
-def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true) {
+def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=[]) {
 
     // Set up the e-mail variables
     def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
@@ -287,6 +287,24 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['projectDir']   = workflow.projectDir
     email_fields['summary']      = summary << misc_fields
 
+    // On success try attach the multiqc report
+    def mqc_report = null
+    try {
+        if (workflow.success) {
+            mqc_report = multiqc_report.getVal()
+            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+                if (mqc_report.size() > 1) {
+                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                }
+                mqc_report = mqc_report[0]
+            }
+        }
+    } catch (all) {
+        if (multiqc_report) {
+            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+        }
+    }
+
     // Check if we are only sending emails on failure
     def email_address = email
     if (!email && email_on_fail && !workflow.success) {
@@ -305,7 +323,8 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def email_html    = html_template.toString()
 
     // Render the sendmail template
-    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}" ]
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${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()

From 48c7026f18c92d267998341ba952eba9c8d58f08 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Feb 2024 13:50:54 +0100
Subject: [PATCH 12/27] add methodsDescriptionText to multiqc report

---
 .../utils_nfcore_pipeline_pipeline/main.nf    | 56 +++++++++++++++++++
 .../pipeline-template/workflows/pipeline.nf   | 18 +++---
 2 files changed, 67 insertions(+), 7 deletions(-)

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 b1046ed9db..3a76444eef 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
@@ -179,3 +179,59 @@ def genomeExistsError() {
         error(error_string)
     }
 }
+
+//
+// Generate methods description for MultiQC
+//
+def toolCitationText() {
+    // TODO nf-core: Optionally add in-text citation tools to this list.
+    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
+    // Uncomment function in methodsDescriptionText to render in MultiQC report
+    def citation_text = [
+            "Tools used in the workflow included:",
+            "FastQC (Andrews 2010),",
+            "MultiQC (Ewels et al. 2016)",
+            "."
+        ].join(' ').trim()
+
+    return citation_text
+}
+
+def toolBibliographyText() {
+    // TODO nf-core: Optionally add bibliographic entries to this list.
+    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
+    // Uncomment function in methodsDescriptionText to render in MultiQC report
+    def reference_text = [
+            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
+            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
+        ].join(' ').trim()
+
+    return reference_text
+}
+
+def methodsDescriptionText(mqc_methods_yaml) {
+    // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+    def meta = [:]
+    meta.workflow = workflow.toMap()
+    meta["manifest_map"] = workflow.manifest.toMap()
+
+    // Pipeline DOI
+    meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
+    meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+
+    // Tool references
+    meta["tool_citations"] = ""
+    meta["tool_bibliography"] = ""
+
+    // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
+    meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    meta["tool_bibliography"] = toolBibliographyText()
+
+
+    def methods_text = mqc_methods_yaml.text
+
+    def engine =  new groovy.text.SimpleTemplateEngine()
+    def description_html = engine.createTemplate(methods_text).make(meta)
+
+    return description_html
+}
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 85c9dd22a1..30b0085514 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -9,6 +9,7 @@ include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_pipeline_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -45,13 +46,16 @@ workflow {{ short_name|upper }} {
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-    ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
-    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
+    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
+    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
+    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
+    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
 
     MULTIQC (
         ch_multiqc_files.collect(),

From bbf3fac4d9f60931096e8c978eb8939b0f7a0bfc Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Feb 2024 15:44:39 +0100
Subject: [PATCH 13/27] update template subworkflows

---
 nf_core/pipeline-template/modules.json        |  2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 42 +++++++++++--------
 2 files changed, 26 insertions(+), 18 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index d1e54dbbf7..96cb7942e9 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -26,7 +26,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "db321a792c88d145afa0ae214fc7da70fcd7d591",
+                        "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
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
index 54769d5b58..a8b55d6fe1 100644
--- 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
@@ -246,10 +246,33 @@ def logColours(monochrome_logs=true) {
     return colorcodes
 }
 
+//
+// Attach the multiqc report to email
+//
+def attachMultiqcReport(multiqc_report) {
+    def mqc_report = null
+    try {
+        if (workflow.success) {
+            mqc_report = multiqc_report.getVal()
+            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+                if (mqc_report.size() > 1) {
+                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                }
+                mqc_report = mqc_report[0]
+            }
+        }
+    } catch (all) {
+        if (multiqc_report) {
+            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+        }
+    }
+    return mqc_report
+}
+
 //
 // Construct and send completion email
 //
-def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=[]) {
+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"
@@ -288,22 +311,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['summary']      = summary << misc_fields
 
     // On success try attach the multiqc report
-    def mqc_report = null
-    try {
-        if (workflow.success) {
-            mqc_report = multiqc_report.getVal()
-            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
-                }
-                mqc_report = mqc_report[0]
-            }
-        }
-    } catch (all) {
-        if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
-        }
-    }
+    def mqc_report = attachMultiqcReport(multiqc_report)
 
     // Check if we are only sending emails on failure
     def email_address = email

From 125cc59f1e2f84182773ca2158479047487dff03 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Feb 2024 17:40:42 +0100
Subject: [PATCH 14/27] remove warn exceeding resources

---
 .../local/utils_nfcore_pipeline_pipeline/main.nf       | 10 ----------
 1 file changed, 10 deletions(-)

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 3a76444eef..8f71247cb4 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
@@ -129,16 +129,6 @@ workflow PIPELINE_COMPLETION {
             imNotification(summary_params, hook_url)
         }
     }
-
-    //
-    // Log warning if exceeding resource requests
-    //
-    workflow.onError {
-        if (workflow.errorReport.contains("Process requirement exceeds available memory")) {
-            log.warning "🛑 Default resources exceed availability 🛑 "
-            log.warning "💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡"
-        }
-    }
 }
 
 /*

From c64ed821225b974fc90006f595ea74d11418ad44 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Feb 2024 18:40:41 +0100
Subject: [PATCH 15/27] fix SimpleTemplateEngine error by writing to the file

---
 .../local/utils_nfcore_pipeline_pipeline/main.nf            | 4 ++--
 nf_core/pipeline-template/workflows/pipeline.nf             | 6 +++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

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 8f71247cb4..488306e538 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
@@ -214,8 +214,8 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["tool_bibliography"] = ""
 
     // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
-    meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-    meta["tool_bibliography"] = toolBibliographyText()
+    // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    // meta["tool_bibliography"] = toolBibliographyText()
 
 
     def methods_text = mqc_methods_yaml.text
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 30b0085514..6c016168c5 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -53,9 +53,13 @@ workflow {{ short_name|upper }} {
     ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+    methods_description_file              = new File('methods_description_mqc.yaml')
+    ch_methods_description.map{
+        methods_description_file << it
+    }
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
+    ch_multiqc_files                      = ch_multiqc_files.mix(Channel.fromPath(methods_description_file, checkIfExists: true))
 
     MULTIQC (
         ch_multiqc_files.collect(),

From e56999f3a8928188d4dbcd9f2b493322c4830372 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Feb 2024 11:32:53 +0100
Subject: [PATCH 16/27] use nf-validation to create input channel

---
 .../assets/schema_input.json                  |  21 +-
 .../bin/check_samplesheet.py                  | 259 ------------------
 nf_core/pipeline-template/conf/modules.config |   8 -
 .../modules/local/samplesheet_check.nf        |  31 ---
 .../pipeline-template/nextflow_schema.json    |   1 +
 .../subworkflows/local/input_check.nf         |  44 ---
 .../utils_nfcore_pipeline_pipeline/main.nf    |  48 +++-
 7 files changed, 48 insertions(+), 364 deletions(-)
 delete mode 100755 nf_core/pipeline-template/bin/check_samplesheet.py
 delete mode 100644 nf_core/pipeline-template/modules/local/samplesheet_check.nf
 delete mode 100644 nf_core/pipeline-template/subworkflows/local/input_check.nf

diff --git a/nf_core/pipeline-template/assets/schema_input.json b/nf_core/pipeline-template/assets/schema_input.json
index 509048bd8a..e76b95fa99 100644
--- a/nf_core/pipeline-template/assets/schema_input.json
+++ b/nf_core/pipeline-template/assets/schema_input.json
@@ -10,25 +10,22 @@
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "meta": ["id"]
             },
             "fastq_1": {
                 "type": "string",
+                "format": "file-path",
+                "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
-                "anyOf": [
-                    {
-                        "type": "string",
-                        "pattern": "^\\S+\\.f(ast)?q\\.gz$"
-                    },
-                    {
-                        "type": "string",
-                        "maxLength": 0
-                    }
-                ]
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             }
         },
         "required": ["sample", "fastq_1"]
diff --git a/nf_core/pipeline-template/bin/check_samplesheet.py b/nf_core/pipeline-template/bin/check_samplesheet.py
deleted file mode 100755
index 4a758fe003..0000000000
--- a/nf_core/pipeline-template/bin/check_samplesheet.py
+++ /dev/null
@@ -1,259 +0,0 @@
-#!/usr/bin/env python
-
-
-"""Provide a command line tool to validate and transform tabular samplesheets."""
-
-
-import argparse
-import csv
-import logging
-import sys
-from collections import Counter
-from pathlib import Path
-
-logger = logging.getLogger()
-
-
-class RowChecker:
-    """
-    Define a service that can validate and transform each given row.
-
-    Attributes:
-        modified (list): A list of dicts, where each dict corresponds to a previously
-            validated and transformed row. The order of rows is maintained.
-
-    """
-
-    VALID_FORMATS = (
-        ".fq.gz",
-        ".fastq.gz",
-    )
-
-    def __init__(
-        self,
-        sample_col="sample",
-        first_col="fastq_1",
-        second_col="fastq_2",
-        single_col="single_end",
-        **kwargs,
-    ):
-        """
-        Initialize the row checker with the expected column names.
-
-        Args:
-            sample_col (str): The name of the column that contains the sample name
-                (default "sample").
-            first_col (str): The name of the column that contains the first (or only)
-                FASTQ file path (default "fastq_1").
-            second_col (str): The name of the column that contains the second (if any)
-                FASTQ file path (default "fastq_2").
-            single_col (str): The name of the new column that will be inserted and
-                records whether the sample contains single- or paired-end sequencing
-                reads (default "single_end").
-
-        """
-        super().__init__(**kwargs)
-        self._sample_col = sample_col
-        self._first_col = first_col
-        self._second_col = second_col
-        self._single_col = single_col
-        self._seen = set()
-        self.modified = []
-
-    def validate_and_transform(self, row):
-        """
-        Perform all validations on the given row and insert the read pairing status.
-
-        Args:
-            row (dict): A mapping from column headers (keys) to elements of that row
-                (values).
-
-        """
-        self._validate_sample(row)
-        self._validate_first(row)
-        self._validate_second(row)
-        self._validate_pair(row)
-        self._seen.add((row[self._sample_col], row[self._first_col]))
-        self.modified.append(row)
-
-    def _validate_sample(self, row):
-        """Assert that the sample name exists and convert spaces to underscores."""
-        if len(row[self._sample_col]) <= 0:
-            raise AssertionError("Sample input is required.")
-        # Sanitize samples slightly.
-        row[self._sample_col] = row[self._sample_col].replace(" ", "_")
-
-    def _validate_first(self, row):
-        """Assert that the first FASTQ entry is non-empty and has the right format."""
-        if len(row[self._first_col]) <= 0:
-            raise AssertionError("At least the first FASTQ file is required.")
-        self._validate_fastq_format(row[self._first_col])
-
-    def _validate_second(self, row):
-        """Assert that the second FASTQ entry has the right format if it exists."""
-        if len(row[self._second_col]) > 0:
-            self._validate_fastq_format(row[self._second_col])
-
-    def _validate_pair(self, row):
-        """Assert that read pairs have the same file extension. Report pair status."""
-        if row[self._first_col] and row[self._second_col]:
-            row[self._single_col] = False
-            first_col_suffix = Path(row[self._first_col]).suffixes[-2:]
-            second_col_suffix = Path(row[self._second_col]).suffixes[-2:]
-            if first_col_suffix != second_col_suffix:
-                raise AssertionError("FASTQ pairs must have the same file extensions.")
-        else:
-            row[self._single_col] = True
-
-    def _validate_fastq_format(self, filename):
-        """Assert that a given filename has one of the expected FASTQ extensions."""
-        if not any(filename.endswith(extension) for extension in self.VALID_FORMATS):
-            raise AssertionError(
-                f"The FASTQ file has an unrecognized extension: {filename}\n"
-                f"It should be one of: {', '.join(self.VALID_FORMATS)}"
-            )
-
-    def validate_unique_samples(self):
-        """
-        Assert that the combination of sample name and FASTQ filename is unique.
-
-        In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the
-        number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment.
-
-        """
-        if len(self._seen) != len(self.modified):
-            raise AssertionError("The pair of sample name and FASTQ must be unique.")
-        seen = Counter()
-        for row in self.modified:
-            sample = row[self._sample_col]
-            seen[sample] += 1
-            row[self._sample_col] = f"{sample}_T{seen[sample]}"
-
-
-def read_head(handle, num_lines=10):
-    """Read the specified number of lines from the current position in the file."""
-    lines = []
-    for idx, line in enumerate(handle):
-        if idx == num_lines:
-            break
-        lines.append(line)
-    return "".join(lines)
-
-
-def sniff_format(handle):
-    """
-    Detect the tabular format.
-
-    Args:
-        handle (text file): A handle to a `text file`_ object. The read position is
-        expected to be at the beginning (index 0).
-
-    Returns:
-        csv.Dialect: The detected tabular format.
-
-    .. _text file:
-        https://docs.python.org/3/glossary.html#term-text-file
-
-    """
-    peek = read_head(handle)
-    handle.seek(0)
-    sniffer = csv.Sniffer()
-    dialect = sniffer.sniff(peek)
-    return dialect
-
-
-def check_samplesheet(file_in, file_out):
-    """
-    Check that the tabular samplesheet has the structure expected by nf-core pipelines.
-
-    Validate the general shape of the table, expected columns, and each row. Also add
-    an additional column which records whether one or two FASTQ reads were found.
-
-    Args:
-        file_in (pathlib.Path): The given tabular samplesheet. The format can be either
-            CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``.
-        file_out (pathlib.Path): Where the validated and transformed samplesheet should
-            be created; always in CSV format.
-
-    Example:
-        This function checks that the samplesheet follows the following structure,
-        see also the `viral recon samplesheet`_::
-
-            sample,fastq_1,fastq_2
-            SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
-            SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
-            SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
-
-    .. _viral recon samplesheet:
-        https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
-
-    """
-    required_columns = {"sample", "fastq_1", "fastq_2"}
-    # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
-    with file_in.open(newline="") as in_handle:
-        reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle))
-        # Validate the existence of the expected header columns.
-        if not required_columns.issubset(reader.fieldnames):
-            req_cols = ", ".join(required_columns)
-            logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.")
-            sys.exit(1)
-        # Validate each row.
-        checker = RowChecker()
-        for i, row in enumerate(reader):
-            try:
-                checker.validate_and_transform(row)
-            except AssertionError as error:
-                logger.critical(f"{str(error)} On line {i + 2}.")
-                sys.exit(1)
-        checker.validate_unique_samples()
-    header = list(reader.fieldnames)
-    header.insert(1, "single_end")
-    # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
-    with file_out.open(mode="w", newline="") as out_handle:
-        writer = csv.DictWriter(out_handle, header, delimiter=",")
-        writer.writeheader()
-        for row in checker.modified:
-            writer.writerow(row)
-
-
-def parse_args(argv=None):
-    """Define and immediately parse command line arguments."""
-    parser = argparse.ArgumentParser(
-        description="Validate and transform a tabular samplesheet.",
-        epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv",
-    )
-    parser.add_argument(
-        "file_in",
-        metavar="FILE_IN",
-        type=Path,
-        help="Tabular input samplesheet in CSV or TSV format.",
-    )
-    parser.add_argument(
-        "file_out",
-        metavar="FILE_OUT",
-        type=Path,
-        help="Transformed output samplesheet in CSV format.",
-    )
-    parser.add_argument(
-        "-l",
-        "--log-level",
-        help="The desired log level (default WARNING).",
-        choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"),
-        default="WARNING",
-    )
-    return parser.parse_args(argv)
-
-
-def main(argv=None):
-    """Coordinate argument parsing and program execution."""
-    args = parse_args(argv)
-    logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s")
-    if not args.file_in.is_file():
-        logger.error(f"The given input file {args.file_in} was not found!")
-        sys.exit(2)
-    args.file_out.parent.mkdir(parents=True, exist_ok=True)
-    check_samplesheet(args.file_in, args.file_out)
-
-
-if __name__ == "__main__":
-    sys.exit(main())
diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config
index d91c6aba0b..e3ea8fa6c4 100644
--- a/nf_core/pipeline-template/conf/modules.config
+++ b/nf_core/pipeline-template/conf/modules.config
@@ -18,14 +18,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: SAMPLESHEET_CHECK {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: FASTQC {
         ext.args = '--quiet'
     }
diff --git a/nf_core/pipeline-template/modules/local/samplesheet_check.nf b/nf_core/pipeline-template/modules/local/samplesheet_check.nf
deleted file mode 100644
index 77be6dfff4..0000000000
--- a/nf_core/pipeline-template/modules/local/samplesheet_check.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-process SAMPLESHEET_CHECK {
-    tag "$samplesheet"
-    label 'process_single'
-
-    conda "conda-forge::python=3.8.3"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'biocontainers/python:3.8.3' }"
-
-    input:
-    path samplesheet
-
-    output:
-    path '*.csv'       , emit: csv
-    path "versions.yml", emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script: // This script is bundled with the pipeline, in {{ name }}/bin/
-    """
-    check_samplesheet.py \\
-        $samplesheet \\
-        samplesheet.valid.csv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
-    """
-}
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 080797b4eb..1b603dcf85 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -16,6 +16,7 @@
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
+                    "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
diff --git a/nf_core/pipeline-template/subworkflows/local/input_check.nf b/nf_core/pipeline-template/subworkflows/local/input_check.nf
deleted file mode 100644
index 562f44cc69..0000000000
--- a/nf_core/pipeline-template/subworkflows/local/input_check.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-//
-// Check input samplesheet and get read channels
-//
-
-include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
-
-workflow INPUT_CHECK {
-    take:
-    samplesheet // file: /path/to/samplesheet.csv
-
-    main:
-    SAMPLESHEET_CHECK ( samplesheet )
-        .csv
-        .splitCsv ( header:true, sep:',' )
-        .map { create_fastq_channel(it) }
-        .set { samplesheet }
-
-    emit:
-    samplesheet                               // channel: [ val(meta), [ reads ] ]
-    versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
-}
-
-// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
-def create_fastq_channel(LinkedHashMap row) {
-    // create meta map
-    def meta = [:]
-    meta.id         = row.sample
-    meta.single_end = row.single_end.toBoolean()
-
-    // add path(s) of the fastq file(s) to the meta map
-    def fastq_meta = []
-    if (!file(row.fastq_1).exists()) {
-        exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
-    }
-    if (meta.single_end) {
-        fastq_meta = [ meta, [ file(row.fastq_1) ] ]
-    } else {
-        if (!file(row.fastq_2).exists()) {
-            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
-        }
-        fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
-    }
-    return fastq_meta
-}
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 488306e538..5dd87e8f47 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
@@ -10,6 +10,7 @@
 
 include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-validation'
+include { fromSamplesheet           } from 'plugin/nf-validation'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
@@ -18,7 +19,6 @@ include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
-include { INPUT_CHECK               } from '../../local/input_check'
 
 /*
 ========================================================================================
@@ -79,18 +79,31 @@ workflow PIPELINE_INITIALISATION {
     validateInputParameters()
 
     //
-    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
+    // Create channel from input file provided through params.input
     //
-    INPUT_CHECK (
-        file(input)
-    )
-    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
-    // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
-    // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
-    // ! There is currently no tooling to help you write a sample sheet schema
+    Channel
+        .fromSamplesheet("input")
+        .map {
+            meta, fastq_1, fastq_2 ->
+                if (!fastq_2) {
+                    return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
+                } else {
+                    return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
+                }
+        }
+        .groupTuple()
+        .map {
+            validateInputSamplesheet(it)
+        }
+        .map {
+            meta, fastqs ->
+                return [ meta, fastqs.flatten() ]
+        }
+        .set { ch_samplesheet }
+        ch_samplesheet.view()
 
     emit:
-    samplesheet = INPUT_CHECK.out.samplesheet
+    samplesheet = ch_samplesheet
     versions    = ch_versions
 }
 
@@ -144,6 +157,21 @@ def validateInputParameters() {
     genomeExistsError()
 }
 
+//
+// Validate channels from input samplesheet
+//
+def validateInputSamplesheet(input) {
+    def (metas, fastqs) = input[1..2]
+
+    // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
+    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
+    if (!endedness_ok) {
+        error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
+    }
+
+    return [ metas[0], fastqs ]
+}
+
 //
 // Get attribute from genome config file e.g. fasta
 //

From 75f833f28c19215031bd5e12d66ecb8f251a30ad Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Feb 2024 11:44:55 +0100
Subject: [PATCH 17/27] linting: warn if groovy files in lib exist

---
 nf_core/lint/files_exist.py     | 14 +++++++-------
 nf_core/lint/files_unchanged.py |  2 --
 2 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/nf_core/lint/files_exist.py b/nf_core/lint/files_exist.py
index ecd7bc4bbd..ab29c4c39e 100644
--- a/nf_core/lint/files_exist.py
+++ b/nf_core/lint/files_exist.py
@@ -52,9 +52,6 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
         docs/output.md
         docs/README.md
         docs/usage.md
-        lib/NfcoreTemplate.groovy
-        lib/Utils.groovy
-        lib/WorkflowMain.groovy
         nextflow_schema.json
         nextflow.config
         README.md
@@ -165,9 +162,6 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
         [Path("docs", "README.md")],
         [Path("docs", "README.md")],
         [Path("docs", "usage.md")],
-        [Path("lib", "NfcoreTemplate.groovy")],
-        [Path("lib", "Utils.groovy")],
-        [Path("lib", "WorkflowMain.groovy")],
     ]
 
     files_warn = [
@@ -200,7 +194,13 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
         Path("lib", "Completion.groovy"),
         Path("lib", "Workflow.groovy"),
     ]
-    files_warn_ifexists = [Path(".travis.yml")]
+    files_warn_ifexists = [
+        Path(".travis.yml"),
+        Path("lib", "NfcoreTemplate.groovy"),
+        Path("lib", "Utils.groovy"),
+        Path("lib", "WorkflowMain.groovy"),
+        Path("lib", "NfcoreTemplate.groovy"),
+    ]
     files_fail_ifinconfig: List[Tuple[Path, Dict[str, str]]] = [
         (Path("lib", "nfcore_external_java_deps.jar"), {"plugins": "nf-validation"}),
     ]
diff --git a/nf_core/lint/files_unchanged.py b/nf_core/lint/files_unchanged.py
index 7f63973f16..3038c8af51 100644
--- a/nf_core/lint/files_unchanged.py
+++ b/nf_core/lint/files_unchanged.py
@@ -40,7 +40,6 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
         docs/images/nf-core-PIPELINE_logo_light.png
         docs/images/nf-core-PIPELINE_logo_dark.png
         docs/README.md'
-        lib/NfcoreTemplate.groovy
         ['LICENSE', 'LICENSE.md', 'LICENCE', 'LICENCE.md'], # NB: British / American spelling
 
     Files that can have additional content but must include the template contents::
@@ -104,7 +103,6 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
         [Path("docs", "images", f"nf-core-{short_name}_logo_light.png")],
         [Path("docs", "images", f"nf-core-{short_name}_logo_dark.png")],
         [Path("docs", "README.md")],
-        [Path("lib", "NfcoreTemplate.groovy")],
     ]
     files_partial = [
         [Path(".gitignore"), Path(".prettierignore"), Path("pyproject.toml")],

From a62c307b7e13df2008d20f9247c03b31d59802b3 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Feb 2024 15:56:02 +0100
Subject: [PATCH 18/27] fix pytests

---
 tests/lint/files_exist.py    |  8 ++++++--
 tests/modules/lint.py        |  2 --
 tests/modules/update.py      | 24 ++++++++++++------------
 tests/subworkflows/lint.py   |  3 +++
 tests/subworkflows/remove.py | 12 ++++++++----
 5 files changed, 29 insertions(+), 20 deletions(-)

diff --git a/tests/lint/files_exist.py b/tests/lint/files_exist.py
index d3a6a25e82..5081522899 100644
--- a/tests/lint/files_exist.py
+++ b/tests/lint/files_exist.py
@@ -61,7 +61,9 @@ def test_files_exist_pass_conditional(self):
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
     lint_obj._load()
     lint_obj.nf_config["plugins"] = []
-    Path(new_pipeline, "lib/nfcore_external_java_deps.jar").touch()
+    lib_dir = Path(new_pipeline, "lib")
+    lib_dir.mkdir()
+    (lib_dir / "nfcore_external_java_deps.jar").touch()
     results = lint_obj.files_exist()
     assert results["failed"] == []
     assert results["ignored"] == []
@@ -71,7 +73,9 @@ def test_files_exist_fail_conditional(self):
     new_pipeline = self._make_pipeline_copy()
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
     lint_obj._load()
-    Path(new_pipeline, "lib/nfcore_external_java_deps.jar").touch()
+    lib_dir = Path(new_pipeline, "lib")
+    lib_dir.mkdir()
+    (lib_dir / "nfcore_external_java_deps.jar").touch()
     results = lint_obj.files_exist()
     assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
     assert results["ignored"] == []
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index a5d8567b76..9bd280ddd8 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -40,7 +40,6 @@ def test_modules_lint_empty(self):
     """Test linting a pipeline with no modules installed"""
     self.mods_remove.remove("fastqc", force=True)
     self.mods_remove.remove("multiqc", force=True)
-    self.mods_remove.remove("custom/dumpsoftwareversions", force=True)
     with pytest.raises(LookupError):
         nf_core.modules.ModuleLint(dir=self.pipeline_dir)
 
@@ -58,7 +57,6 @@ def test_modules_lint_no_gitlab(self):
     """Test linting a pipeline with no modules installed"""
     self.mods_remove.remove("fastqc", force=True)
     self.mods_remove.remove("multiqc", force=True)
-    self.mods_remove.remove("custom/dumpsoftwareversions", force=True)
     with pytest.raises(LookupError):
         nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
 
diff --git a/tests/modules/update.py b/tests/modules/update.py
index 5208070fa5..5cf24b56f0 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -317,13 +317,13 @@ def test_update_only_show_differences(self, mock_prompt):
 
     mod_json = modules_json.get_modules_json()
     # Loop through all modules and check that they are NOT updated (according to the modules.json file)
-    # Modules that can be updated but shouldn't are custom/dumpsoftwareversions and fastqc
+    # A module that can be updated but shouldn't is fastqc
     # Module multiqc is already up to date so don't check
-    for mod in ["custom/dumpsoftwareversions", "fastqc"]:
-        correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
-        current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
-        assert correct_git_sha != current_git_sha
-        assert cmp_module(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True
+    mod = "fastqc"
+    correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
+    current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
+    assert correct_git_sha != current_git_sha
+    assert cmp_module(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True
 
 
 # Mock questionary answer: do not update module, only show diffs
@@ -357,19 +357,19 @@ def test_update_only_show_differences_when_patch(self, mock_prompt):
     patch_obj = ModulePatch(self.pipeline_dir)
     patch_obj.patch("fastqc")
     # Check that a patch file with the correct name has been created
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "fastqc.diff"}
+    assert "fastqc.diff" in set(os.listdir(module_path))
 
     # Update all modules
     assert update_obj.update() is True
 
     mod_json = modules_json.get_modules_json()
     # Loop through all modules and check that they are NOT updated (according to the modules.json file)
-    # Modules that can be updated but shouldn't are custom/dumpsoftwareversions and fastqc
+    # A module that can be updated but shouldn't is fastqc
     # Module multiqc is already up to date so don't check
-    for mod in ["custom/dumpsoftwareversions", "fastqc"]:
-        correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
-        current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
-        assert correct_git_sha != current_git_sha
+    mod = "fastqc"
+    correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
+    current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
+    assert correct_git_sha != current_git_sha
 
 
 def cmp_module(dir1, dir2):
diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py
index b53fef7f0e..8804f8bf6f 100644
--- a/tests/subworkflows/lint.py
+++ b/tests/subworkflows/lint.py
@@ -19,6 +19,9 @@ def test_subworkflows_lint(self):
 
 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_nfvalidation_plugin", force=True)
     with pytest.raises(LookupError):
         nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
 
diff --git a/tests/subworkflows/remove.py b/tests/subworkflows/remove.py
index dec67875bd..c6a3b98454 100644
--- a/tests/subworkflows/remove.py
+++ b/tests/subworkflows/remove.py
@@ -20,13 +20,15 @@ def test_subworkflows_remove_subworkflow(self):
     mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
     assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
     mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert Path.exists(subworkflow_path) is False
     assert Path.exists(bam_sort_stats_samtools_path) is False
     assert Path.exists(bam_stats_samtools_path) is False
     assert Path.exists(samtools_index_path) is False
     assert mod_json_before != mod_json_after
     # assert subworkflows key is removed from modules.json
-    assert "subworkflows" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"].keys()
+    assert (
+        "bam_sort_stats_samtools"
+        not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys()
+    )
     assert "samtools/index" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"].keys()
 
 
@@ -44,13 +46,15 @@ def test_subworkflows_remove_subworkflow_keep_installed_module(self):
     assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
     mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json()
 
-    assert Path.exists(subworkflow_path) is False
     assert Path.exists(bam_sort_stats_samtools_path) is False
     assert Path.exists(bam_stats_samtools_path) is False
     assert Path.exists(samtools_index_path) is True
     assert mod_json_before != mod_json_after
     # assert subworkflows key is removed from modules.json
-    assert "subworkflows" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"].keys()
+    assert (
+        "bam_sort_stats_samtools"
+        not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys()
+    )
     assert (
         "samtools/index"
         in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"].keys()

From 0dd064af5d426b607f7ff2bffe427f0104744e16 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Feb 2024 16:03:55 +0100
Subject: [PATCH 19/27] rename local subworkflow from the template

---
 nf_core/create.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/create.py b/nf_core/create.py
index 8038a995c5..c094d33a22 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -292,7 +292,7 @@ def render_template(self):
         short_name = self.template_params["short_name"]
         rename_files = {
             "workflows/pipeline.nf": f"workflows/{short_name}.nf",
-            "lib/WorkflowPipeline.groovy": f"lib/Workflow{short_name[0].upper()}{short_name[1:]}.groovy",
+            "subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf": f"subworkflows/local/utils_nfcore_{short_name}_pipeline/main.nf",
         }
 
         # Set the paths to skip according to customization

From 5b5b30aa5ca0de2805935ab94baeff2fc9e87840 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Feb 2024 16:09:36 +0100
Subject: [PATCH 20/27] fix editorconfig errors in the template

---
 nf_core/pipeline-template/.editorconfig   | 7 +++++++
 nf_core/pipeline-template/nextflow.config | 6 +++---
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index dd991a0e95..cf8bcff952 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -19,6 +19,13 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 indent_size = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
 
 [/assets/email*]
 indent_size = unset
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 3153ff70d6..0f840fc60b 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -18,9 +18,9 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
-    {% else %}
+    {% else -%}
     fasta                      = null
-    {%- endif %}
+    {%- endif -%}
 
     // MultiQC options
     multiqc_config             = null
@@ -49,7 +49,7 @@ params {
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
-    {% endif %}
+    {%- endif %}
 
     // Max resource options
     // Defaults only, expecting to be overwritten

From 71a0eec0a631d3ff15ca2af94378602fc214f0ca Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Feb 2024 11:06:01 +0100
Subject: [PATCH 21/27] rename local subworkflow with jinja

---
 nf_core/pipeline-template/main.nf               | 6 +++---
 nf_core/pipeline-template/workflows/pipeline.nf | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index c31927f236..2590f7467b 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -20,10 +20,10 @@ nextflow.enable.dsl = 2
 */
 
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_pipeline_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_pipeline_pipeline'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 {% if igenomes %}
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_pipeline_pipeline'
+include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 6c016168c5..81fdf9f27d 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -9,7 +9,7 @@ include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_pipeline_pipeline'
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

From ff69ee3893b356d0cd0c5ca3512a8261a0ccbae7 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Feb 2024 12:12:27 +0100
Subject: [PATCH 22/27] fix more pytests

---
 tests/subworkflows/update.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 32a69ba180..9ddc9bec0c 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -171,9 +171,9 @@ def test_update_with_config_fix_all(self):
     with open(Path(self.pipeline_dir, config_fn), "w") as f:
         yaml.dump(tools_config, f)
 
-    # Update all subworkflows in the pipeline
-    update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
-    assert update_obj.update() is True
+    # Update fastq_align_bowtie2
+    update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=False, update_deps=True, show_diff=False)
+    assert update_obj.update("fastq_align_bowtie2") is True
 
     # Check that the git sha for fastq_align_bowtie2 is correctly downgraded
     mod_json = ModulesJson(self.pipeline_dir).get_modules_json()

From b3259449641cfbf3740d9e3589e09275210fb322 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Feb 2024 14:42:18 +0100
Subject: [PATCH 23/27] fix creating a template without igenomes

---
 .prettierignore                                            | 1 +
 nf_core/create.py                                          | 1 +
 nf_core/pipeline-template/nextflow.config                  | 1 -
 nf_core/pipeline-template/nextflow_schema.json             | 6 ++++--
 .../local/utils_nfcore_pipeline_pipeline/main.nf           | 7 ++++++-
 5 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/.prettierignore b/.prettierignore
index a55074abfb..b923532bd7 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -6,6 +6,7 @@ testing
 nf_core/module-template/meta.yml
 nf_core/module-template/tests/tags.yml
 nf_core/subworkflow-template/tests/tags.yml
+nf_core/pipeline-template/nextflow_schema.json
 # don't run on things handled by ruff
 *.py
 *.pyc
diff --git a/nf_core/create.py b/nf_core/create.py
index c094d33a22..fa900cdb06 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -497,6 +497,7 @@ def fix_linting(self):
         # Add the lint content to the preexisting nf-core config
         config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
         nf_core_yml["lint"] = lint_config
+        print("added linting config")
         with open(self.outdir / config_fn, "w") as fh:
             yaml.dump(nf_core_yml, fh, default_flow_style=False, sort_keys=False)
 
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 0f840fc60b..17e75f18a4 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -18,7 +18,6 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
-    {% else -%}
     fasta                      = null
     {%- endif -%}
 
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 1b603dcf85..de841550e3 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -43,6 +43,7 @@
                 }
             }
         },
+        {%- if igenomes %}
         "reference_genome_options": {
             "title": "Reference genome options",
             "type": "object",
@@ -74,6 +75,7 @@
                 }
             }
         },
+        {%- endif %}
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",
@@ -273,9 +275,9 @@
         {
             "$ref": "#/definitions/input_output_options"
         },
-        {
+        {%- if igenomes %}{
             "$ref": "#/definitions/reference_genome_options"
-        },
+        },{% endif %}
         {
             "$ref": "#/definitions/institutional_config_options"
         },
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 5dd87e8f47..8b911d1667 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
@@ -73,10 +73,12 @@ workflow PIPELINE_INITIALISATION {
         nextflow_cli_args
     )
 
+    {%- if igenomes %}
     //
     // Custom validation for pipeline parameters
     //
     validateInputParameters()
+    {%- endif %}
 
     //
     // Create channel from input file provided through params.input
@@ -100,7 +102,6 @@ workflow PIPELINE_INITIALISATION {
                 return [ meta, fastqs.flatten() ]
         }
         .set { ch_samplesheet }
-        ch_samplesheet.view()
 
     emit:
     samplesheet = ch_samplesheet
@@ -150,12 +151,14 @@ workflow PIPELINE_COMPLETION {
 ========================================================================================
 */
 
+{%- if igenomes %}
 //
 // Check and validate pipeline parameters
 //
 def validateInputParameters() {
     genomeExistsError()
 }
+{%- endif -%}
 
 //
 // Validate channels from input samplesheet
@@ -172,6 +175,7 @@ def validateInputSamplesheet(input) {
     return [ metas[0], fastqs ]
 }
 
+{%- if igenomes %}
 //
 // Get attribute from genome config file e.g. fasta
 //
@@ -197,6 +201,7 @@ def genomeExistsError() {
         error(error_string)
     }
 }
+{%- endif -%}
 
 //
 // Generate methods description for MultiQC

From 3bd4cfe42e26ba1ee6c436687973299ea131537e Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Feb 2024 15:52:25 +0100
Subject: [PATCH 24/27] return multiqc description as string

---
 .../local/utils_nfcore_pipeline_pipeline/main.nf            | 2 +-
 nf_core/pipeline-template/workflows/pipeline.nf             | 6 +-----
 2 files changed, 2 insertions(+), 6 deletions(-)

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 8b911d1667..24d4c2d7e1 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
@@ -256,5 +256,5 @@ def methodsDescriptionText(mqc_methods_yaml) {
     def engine =  new groovy.text.SimpleTemplateEngine()
     def description_html = engine.createTemplate(methods_text).make(meta)
 
-    return description_html
+    return description_html.toString()
 }
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 81fdf9f27d..f7de301ce5 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -53,13 +53,9 @@ workflow {{ short_name|upper }} {
     ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    methods_description_file              = new File('methods_description_mqc.yaml')
-    ch_methods_description.map{
-        methods_description_file << it
-    }
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files                      = ch_multiqc_files.mix(Channel.fromPath(methods_description_file, checkIfExists: true))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
 
     MULTIQC (
         ch_multiqc_files.collect(),

From 9c89874c563e07d3a17536b1b0017b7def9e5363 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Feb 2024 16:31:26 +0100
Subject: [PATCH 25/27] fix prettier inconsistencies in the pipeline template

---
 nf_core/pipeline-template/.editorconfig        | 2 --
 nf_core/pipeline-template/nextflow_schema.json | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index cf8bcff952..dd9ffa5387 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -18,14 +18,12 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-indent_size = unset
 [/subworkflows/nf-core/**]
 charset = unset
 end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-indent_size = unset
 
 [/assets/email*]
 indent_size = unset
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index de841550e3..77b1a7a070 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -275,7 +275,7 @@
         {
             "$ref": "#/definitions/input_output_options"
         },
-        {%- if igenomes %}{
+        {% if igenomes %}{
             "$ref": "#/definitions/reference_genome_options"
         },{% endif %}
         {

From 7f7e920dcbeea7317b92b1000dcc112a52bcb91c Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Feb 2024 16:43:28 +0100
Subject: [PATCH 26/27] fix more linting tests

---
 nf_core/lint/files_exist.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/nf_core/lint/files_exist.py b/nf_core/lint/files_exist.py
index ab29c4c39e..3e98526266 100644
--- a/nf_core/lint/files_exist.py
+++ b/nf_core/lint/files_exist.py
@@ -66,7 +66,6 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
         conf/igenomes.config
         .github/workflows/awstest.yml
         .github/workflows/awsfulltest.yml
-        lib/WorkflowPIPELINE.groovy
         pyproject.toml
 
     Files that *must not* be present, due to being renamed or removed in the template:
@@ -88,6 +87,11 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
         lib/Checks.groovy
         lib/Completion.groovy
         lib/Workflow.groovy
+        lib/WorkflowPIPELINE.groovy
+        lib/NfcoreTemplate.groovy
+        lib/Utils.groovy
+        lib/WorkflowMain.groovy
+
 
     Files that *should not* be present:
 
@@ -171,7 +175,6 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
         [Path("conf", "igenomes.config")],
         [Path(".github", "workflows", "awstest.yml")],
         [Path(".github", "workflows", "awsfulltest.yml")],
-        [Path("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy")],
         [Path("modules.json")],
         [Path("pyproject.toml")],
     ]
@@ -200,6 +203,7 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
         Path("lib", "Utils.groovy"),
         Path("lib", "WorkflowMain.groovy"),
         Path("lib", "NfcoreTemplate.groovy"),
+        Path("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy"),
     ]
     files_fail_ifinconfig: List[Tuple[Path, Dict[str, str]]] = [
         (Path("lib", "nfcore_external_java_deps.jar"), {"plugins": "nf-validation"}),

From 28c0196477d8aa21f6ea82d1906163b3e519e773 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 15 Feb 2024 13:09:08 +0100
Subject: [PATCH 27/27] apply suggestions from code review

---
 nf_core/create.py                               | 1 -
 nf_core/lint/files_exist.py                     | 5 +----
 nf_core/pipeline-template/workflows/pipeline.nf | 4 ++--
 3 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/nf_core/create.py b/nf_core/create.py
index fa900cdb06..c094d33a22 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -497,7 +497,6 @@ def fix_linting(self):
         # Add the lint content to the preexisting nf-core config
         config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
         nf_core_yml["lint"] = lint_config
-        print("added linting config")
         with open(self.outdir / config_fn, "w") as fh:
             yaml.dump(nf_core_yml, fh, default_flow_style=False, sort_keys=False)
 
diff --git a/nf_core/lint/files_exist.py b/nf_core/lint/files_exist.py
index 3e98526266..5d62a23bf8 100644
--- a/nf_core/lint/files_exist.py
+++ b/nf_core/lint/files_exist.py
@@ -196,15 +196,12 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
         Path("lib", "Checks.groovy"),
         Path("lib", "Completion.groovy"),
         Path("lib", "Workflow.groovy"),
-    ]
-    files_warn_ifexists = [
-        Path(".travis.yml"),
-        Path("lib", "NfcoreTemplate.groovy"),
         Path("lib", "Utils.groovy"),
         Path("lib", "WorkflowMain.groovy"),
         Path("lib", "NfcoreTemplate.groovy"),
         Path("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy"),
     ]
+    files_warn_ifexists = [Path(".travis.yml")]
     files_fail_ifinconfig: List[Tuple[Path, Dict[str, str]]] = [
         (Path("lib", "nfcore_external_java_deps.jar"), {"plugins": "nf-validation"}),
     ]
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index f7de301ce5..68adbaa328 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -65,8 +65,8 @@ workflow {{ short_name|upper }} {
     )
 
     emit:
-    multiqc_report = MULTIQC.out.report // channel: /path/to/multiqc_report.html
-    versions       = ch_versions        // channel: [ path(versions.yml) ]
+    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    versions       = ch_versions                 // channel: [ path(versions.yml) ]
 }
 
 /*