From cf14aa170425a326ff58393a681b3e2d1631052d Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 21 Sep 2023 13:35:56 +0100
Subject: [PATCH 1/9] Pipeline template: Use INIITIALISE subworkflow instead of
 WorkflowMain.initialise()

Changes:
 - Guts WorkflowMain, particularly the initialise() method
 - Replaces it with INIITIALISE subworkflow

- Should be easier to maintain via nf-core/modules (more regular updates)
- Uses more native Nextflow for bioinformatics developers to follow

Should incidentally fix #2289
---
 CHANGELOG.md                                  |  1 +
 .../pipeline-template/lib/WorkflowMain.groovy | 46 ----------------
 nf_core/pipeline-template/main.nf             | 19 +------
 nf_core/pipeline-template/modules.json        |  9 +++
 .../subworkflows/nf-core/initialise/main.nf   | 55 +++++++++++++++++++
 .../subworkflows/nf-core/initialise/meta.yml  | 13 +++++
 .../pipeline-template/workflows/pipeline.nf   |  9 ---
 7 files changed, 80 insertions(+), 72 deletions(-)
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/initialise/main.nf
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/initialise/meta.yml

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ef51b9962..02025f19a8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@
 - ([#2415](https://github.com/nf-core/tools/pull/2415#issuecomment-1709847086)) Add autoMounts for apptainer.
 - Remove `igenomes_base` from the schema, so that nf-validation doesn't create a file path and throw errors offline for s3 objects.
 - Update Gitpod profile resources to reflect base environment settings.
+- Use INITIALISE subworkflow to start pipeline and validate parameters etc.
 
 ### Download
 
diff --git a/nf_core/pipeline-template/lib/WorkflowMain.groovy b/nf_core/pipeline-template/lib/WorkflowMain.groovy
index 5824dae2fb..9049d0b27c 100755
--- a/nf_core/pipeline-template/lib/WorkflowMain.groovy
+++ b/nf_core/pipeline-template/lib/WorkflowMain.groovy
@@ -2,54 +2,8 @@
 // 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) {
-
-        // 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 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
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 3d632eb8c5..b520d1f815 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -30,23 +30,7 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
-
-// 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)
-}
-
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
-
-WorkflowMain.initialise(workflow, params, log)
+include { INITIALISE } from './subworkflows/nf-core/initialise/main.nf'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -60,6 +44,7 @@ include { {{ short_name|upper }} } from './workflows/{{ short_name }}'
 // WORKFLOW: Run main {{ name }} analysis pipeline
 //
 workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
+    INITIALISE()
     {{ short_name|upper }} ()
 }
 
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 2154873150..99c00c5dc5 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -21,6 +21,15 @@
                         "installed_by": ["modules"]
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "initialise": {
+                        "branch": "master",
+                        "git_sha": "709d34798f0fd91052be97ebb83f2a76d2174ba0",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
             }
         }
     }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/initialise/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/initialise/main.nf
new file mode 100644
index 0000000000..85b6cd8e79
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/initialise/main.nf
@@ -0,0 +1,55 @@
+// This is a reimplementation of the basic initialise methods in the nf-core template
+// The role of this subworkflow is to check the input parameters and print help messages
+// Use this to start your nf-core pipeline
+
+include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
+
+workflow INITIALISE {
+
+    // Print workflow version and exit on --version
+    if (params.version) {
+        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${git_shortsha}"
+        }
+        log.info "${workflow.manifest.name} ${version_string}"
+        System.exit(0)
+    }
+
+    // Print citation for nf-core
+    def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+        "* The nf-core framework\n" +
+        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+        "* Software dependencies\n" +
+        "  ${workflow.manifest.homePage}/blob/master/CITATIONS.md"
+    log.info citation
+
+    // Print help message if needed
+    if (params.help) {
+        def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker"
+        log.info paramsHelp(command)
+        System.exit(0)
+    }
+
+    if ( params.validate_parameters != false ){
+        validateParameters()
+    }
+
+    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+        log.warn "[$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 "
+    }
+
+    log.info paramsSummaryLog(workflow)
+}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/initialise/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/initialise/meta.yml
new file mode 100644
index 0000000000..b1ee015df8
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/initialise/meta.yml
@@ -0,0 +1,13 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "initialise"
+description: Validate input parameters and print help messages
+keywords:
+  - admin
+  - check
+  - help
+  - version
+modules:
+input:
+output:
+authors:
+  - "@adamrtalbot"
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 9dfb0155f1..fb2ba96404 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -6,15 +6,6 @@
 
 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

From e9be0298415d90b16dfcbcc5a70e96fcf1deaba2 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 21 Sep 2023 13:48:14 +0100
Subject: [PATCH 2/9] Template fixes

---
 nf_core/pipeline-template/nextflow.config       | 2 +-
 nf_core/pipeline-template/nextflow_schema.json  | 2 +-
 nf_core/pipeline-template/workflows/pipeline.nf | 5 ++++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 31d6d90ccb..eeed49f31c 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -62,7 +62,7 @@ params {
     validationLenientMode            = false
     validationSchemaIgnoreParams     = 'genomes,igenomes_base'
     validationShowHiddenParams       = false
-    validate_params                  = true
+    validate_parameters              = true
 
 }
 
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 080797b4eb..4c6c9beb77 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -237,7 +237,7 @@
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
                 },
-                "validate_params": {
+                "validate_parameters": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",
                     "default": true,
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index fb2ba96404..74fcedfa0a 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -4,7 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+include { paramsSummaryMap } from 'plugin/nf-validation'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -50,6 +50,9 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
 // Info required for completion email and summary
 def multiqc_report = []
 
+// Get map of parameter values
+def summary_params = paramsSummaryMap(workflow)
+
 workflow {{ short_name|upper }} {
 
     ch_versions = Channel.empty()

From cc01dd0ede532fa3f22340ad534b4fc3377653f9 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 21 Sep 2023 16:12:46 +0100
Subject: [PATCH 3/9] Made sure it matches existing template

---
 nf_core/pipeline-template/main.nf              | 2 +-
 nf_core/pipeline-template/modules.json         | 2 +-
 nf_core/pipeline-template/nextflow.config      | 2 +-
 nf_core/pipeline-template/nextflow_schema.json | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index b520d1f815..0a4bad7790 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -44,7 +44,7 @@ include { {{ short_name|upper }} } from './workflows/{{ short_name }}'
 // WORKFLOW: Run main {{ name }} analysis pipeline
 //
 workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
-    INITIALISE()
+    INITIALISE(params.version, params.help, params.validate_params)
     {{ short_name|upper }} ()
 }
 
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 99c00c5dc5..1e893d5c51 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -26,7 +26,7 @@
                 "nf-core": {
                     "initialise": {
                         "branch": "master",
-                        "git_sha": "709d34798f0fd91052be97ebb83f2a76d2174ba0",
+                        "git_sha": "7b55a4631bebd1cf827a448d0b70386681fea475",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index eeed49f31c..31d6d90ccb 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -62,7 +62,7 @@ params {
     validationLenientMode            = false
     validationSchemaIgnoreParams     = 'genomes,igenomes_base'
     validationShowHiddenParams       = false
-    validate_parameters              = true
+    validate_params                  = true
 
 }
 
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 4c6c9beb77..080797b4eb 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -237,7 +237,7 @@
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
                 },
-                "validate_parameters": {
+                "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",
                     "default": true,

From 61fbeb830c192f9b4d2321e66308ac751db34919 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 21 Sep 2023 16:13:07 +0100
Subject: [PATCH 4/9] fixup

---
 .../subworkflows/nf-core/initialise/main.nf   | 99 +++++++++++--------
 1 file changed, 56 insertions(+), 43 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/nf-core/initialise/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/initialise/main.nf
index 85b6cd8e79..0cbd37993b 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/initialise/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/initialise/main.nf
@@ -2,54 +2,67 @@
 // The role of this subworkflow is to check the input parameters and print help messages
 // Use this to start your nf-core pipeline
 
-include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
+include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
 
 workflow INITIALISE {
 
-    // Print workflow version and exit on --version
-    if (params.version) {
-        String version_string = ""
+    take:
+        version         // bool
+        help            // bool
+        validate_params // bool
 
-        if (workflow.manifest.version) {
-            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-            version_string += "${prefix_v}${workflow.manifest.version}"
+    main:
+
+        // Print workflow version and exit on --version
+        if (version) {
+            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${git_shortsha}"
+            }
+            log.info "${workflow.manifest.name} ${version_string}"
+            System.exit(0)
+        }
+
+        // Print citation for nf-core
+        def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+            "* The nf-core framework\n" +
+            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+            "* Software dependencies\n" +
+            "  ${workflow.manifest.homePage}/blob/master/CITATIONS.md"
+        log.info citation
+
+        // Print help message if needed
+        if (params.help) {
+            def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker"
+            log.info paramsHelp(command)
+            System.exit(0)
         }
 
-        if (workflow.commitId) {
-            def git_shortsha = workflow.commitId.substring(0, 7)
-            version_string += "-g${git_shortsha}"
+        if ( params.validate_params != false ){
+            validateParameters()
         }
-        log.info "${workflow.manifest.name} ${version_string}"
-        System.exit(0)
-    }
-
-    // Print citation for nf-core
-    def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  ${workflow.manifest.homePage}/blob/master/CITATIONS.md"
-    log.info citation
-
-    // Print help message if needed
-    if (params.help) {
-        def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker"
-        log.info paramsHelp(command)
-        System.exit(0)
-    }
-
-    if ( params.validate_parameters != false ){
-        validateParameters()
-    }
-
-    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn "[$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 "
-    }
-
-    log.info paramsSummaryLog(workflow)
+
+        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 "
+        }
+
+        log.info paramsSummaryLog(workflow)
+
+        summary_params = paramsSummaryMap(workflow)
+
+    emit:
+        summary_params
+
 }

From 8153dc457591bfd9808b04ec829ab4e361e7b54e Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 21 Sep 2023 16:13:31 +0100
Subject: [PATCH 5/9] Update tests to remove INITIALISE subworkflow before
 testing

---
 tests/subworkflows/remove.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/tests/subworkflows/remove.py b/tests/subworkflows/remove.py
index 53a948778b..d07a0fa336 100644
--- a/tests/subworkflows/remove.py
+++ b/tests/subworkflows/remove.py
@@ -12,6 +12,10 @@ def test_subworkflows_remove_uninstalled_subworkflow(self):
 
 def test_subworkflows_remove_subworkflow(self):
     """Test removing subworkflow and all it's dependencies after installing it"""
+    # Remove initialise subworkflow for clean slate
+    self.subworkflow_remove.remove("initialise")
+
+    # Install subworkflow
     self.subworkflow_install.install("bam_sort_stats_samtools")
 
     subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
@@ -34,6 +38,10 @@ def test_subworkflows_remove_subworkflow(self):
 
 def test_subworkflows_remove_subworkflow_keep_installed_module(self):
     """Test removing subworkflow and all it's dependencies after installing it, except for a separately installed module"""
+    # Remove initialise subworkflow for clean slate
+    self.subworkflow_remove.remove("initialise")
+
+    # Install subworkflow and module
     self.subworkflow_install.install("bam_sort_stats_samtools")
     self.mods_install.install("samtools/index")
 
@@ -44,6 +52,7 @@ def test_subworkflows_remove_subworkflow_keep_installed_module(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

From 7e307e62ae164913ec2d02df12dd8e0b3277e73a Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 21 Sep 2023 16:25:33 +0100
Subject: [PATCH 6/9] CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 02025f19a8..6b97f3c755 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,7 +15,7 @@
 - ([#2415](https://github.com/nf-core/tools/pull/2415#issuecomment-1709847086)) Add autoMounts for apptainer.
 - Remove `igenomes_base` from the schema, so that nf-validation doesn't create a file path and throw errors offline for s3 objects.
 - Update Gitpod profile resources to reflect base environment settings.
-- Use INITIALISE subworkflow to start pipeline and validate parameters etc.
+- ([#2430](https://github.com/nf-core/tools/pull/2430)) - Use INITIALISE subworkflow to start pipeline and validate parameters etc.
 
 ### Download
 

From 83ccc5ed1249226ac52d9f39e485524fac828ba0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 21 Sep 2023 18:03:15 +0100
Subject: [PATCH 7/9] Test for updating modules fixed

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

diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 698086e186..6ff2387096 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -162,6 +162,9 @@ def test_update_with_config_dont_update(self):
 
 def test_update_with_config_fix_all(self):
     """Fix the version of all nf-core subworkflows"""
+    # Remove intialise
+    self.subworkflow_remove.remove("initialise")
+
     # Install subworkflow at the latest version
     assert self.subworkflow_install.install("fastq_align_bowtie2")
 

From eab144261e1070a57a03eebc1777c4bda6f83ee4 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 22 Sep 2023 16:05:01 +0100
Subject: [PATCH 8/9] initialise-subworkflow-update

---
 nf_core/pipeline-template/modules.json        |  2 +-
 .../subworkflows/nf-core/initialise/meta.yml  | 22 ++++++++++++++++++-
 2 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 1e893d5c51..49486fb7f9 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -26,7 +26,7 @@
                 "nf-core": {
                     "initialise": {
                         "branch": "master",
-                        "git_sha": "7b55a4631bebd1cf827a448d0b70386681fea475",
+                        "git_sha": "2a3d1b469385914c4eeca70f36bc378473049d93",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/initialise/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/initialise/meta.yml
index b1ee015df8..1d36484790 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/initialise/meta.yml
+++ b/nf_core/pipeline-template/subworkflows/nf-core/initialise/meta.yml
@@ -6,8 +6,28 @@ keywords:
   - check
   - help
   - version
-modules:
+components: []
 input:
+  - version:
+      type: boolean
+      description: |
+        Structure: val(version)
+        Boolean to show the pipeline version and exit.
+  - help:
+      type: boolean
+      description: |
+        Structure: val(help)
+        Boolean to show the pipeline help message and exit.
+  - validate_params:
+      type: boolean
+      description: |
+        Structure: val(validate_params)
+        Whether to validate the parameters prior to starting the pipeline.
 output:
+  - summary_params:
+      type: value
+      description: |
+        Structure: val(summary_params)
+        A map of the parameters used in the pipeline.
 authors:
   - "@adamrtalbot"

From 31a47a83337561fbb51118f89c324624cee2ee83 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 25 Sep 2023 09:59:14 +0100
Subject: [PATCH 9/9] Re-add nf-core logo back to template

---
 nf_core/pipeline-template/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 0a4bad7790..606c56cd21 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -44,6 +44,7 @@ include { {{ short_name|upper }} } from './workflows/{{ short_name }}'
 // WORKFLOW: Run main {{ name }} analysis pipeline
 //
 workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
+    log.info NfcoreTemplate.logo(workflow, params.monochrome_logs)
     INITIALISE(params.version, params.help, params.validate_params)
     {{ short_name|upper }} ()
 }