From 7c1ba22b458a833b02b3852298e09d83448fea50 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 8 Oct 2024 13:37:19 +0000
Subject: [PATCH 01/28] Fix comment section headers so they don't give phantom
 merge conflict warnings

---
 .../local/utils_nfcore_pipeline_pipeline/main.nf     | 12 ++++++------
 .../nf-core/utils_nextflow_pipeline/main.nf          |  8 ++++----
 .../nf-core/utils_nfcore_pipeline/main.nf            |  8 ++++----
 3 files changed, 14 insertions(+), 14 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 9a58e489e..bcf2f4a9a 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
@@ -22,9 +22,9 @@ include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_INITIALISATION {
@@ -111,9 +111,9 @@ workflow PIPELINE_INITIALISATION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -169,9 +169,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 {%- if igenomes %}
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
index 28e32b200..e03052c5c 100644
--- 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
@@ -3,9 +3,9 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
@@ -45,9 +45,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
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 cbd8495bb..49df430a6 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
@@ -3,9 +3,9 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
@@ -22,9 +22,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //

From 6e0ec01cb6a3b4c20126898e0619ca170bbe0b08 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 8 Oct 2024 15:46:05 +0200
Subject: [PATCH 02/28] Fix a typo in the linting action

---
 nf_core/pipeline-template/.github/workflows/linting.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index dbba830ec..0eee862f9 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -42,10 +42,10 @@ jobs:
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: pietrobolcato/action-read-yaml@1.1.0
         id: read_yml
         with:
-          config: ${{ github.workspace }}/.nf-core.yaml
+          config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
         run: |

From abc50bca5eb354e15738b7192cd43337649c9332 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 8 Oct 2024 15:49:53 +0200
Subject: [PATCH 03/28] Update CHANGELOG.md

---
 CHANGELOG.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9d62a9ab6..ec45b06db 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # nf-core/tools: Changelog
 
+## v3.1.0dev
+
+### Bug fixes
+- Fixed an issue where the linting CI action didn't read the correct file
+
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 
 **Highlights**

From 20c23ce7d35d1b169251f50ed6c01bd32b4b947d Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 8 Oct 2024 13:52:52 +0000
Subject: [PATCH 04/28] [automated] Fix code linting

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ec45b06db..84a48be54 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
 ## v3.1.0dev
 
 ### Bug fixes
+
 - Fixed an issue where the linting CI action didn't read the correct file
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]

From 27e6f49b464ee5500d0d61c69bb7d4a198f0d79c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 8 Oct 2024 15:56:20 +0200
Subject: [PATCH 05/28] Update CHANGELOG.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 84a48be54..709e7b6ea 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # nf-core/tools: Changelog
 
-## v3.1.0dev
+## v3.0.1dev
 
 ### Bug fixes
 

From 83eb32a8a07ad0dcadfc2b3cd30e991bb7f7773a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 8 Oct 2024 16:02:58 +0200
Subject: [PATCH 06/28] Update .gitpod.yml

---
 .gitpod.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitpod.yml b/.gitpod.yml
index f92457278..efe193f35 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -1,4 +1,4 @@
-image: nfcore/gitpod:latest
+image: nfcore/gitpod:dev
 tasks:
   - name: install current state of nf-core/tools and setup pre-commit
     command: |

From 87f0dfdfb0c0d752982df3fcd0da82f4bc13ab77 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 8 Oct 2024 16:03:53 +0200
Subject: [PATCH 07/28] Update setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 95a465530..37aa62a4d 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "3.0.0"
+version = "3.0.1dev"
 
 with open("README.md") as f:
     readme = f.read()

From 0bbaeadcededbb91b8037e84e5330fbbd407487e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 8 Oct 2024 17:30:35 +0200
Subject: [PATCH 08/28] Template: run awsfulltest only when target branch is
 `master`

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index dc0450be4..dc220125e 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -14,7 +14,8 @@ on:
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == '{{ name }}' && github.event.review.state == 'approved'
+    # run only if the PR is approved by at least 2 reviewers and against the master branch
+    if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master'
     runs-on: ubuntu-latest
     steps:
       - uses: octokit/request-action@v2.x

From c20122fcdcd0a4d25fd91f4605ef31350f4074d3 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 8 Oct 2024 17:37:14 +0200
Subject: [PATCH 09/28] fix github variable

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index dc220125e..061f2dee0 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -21,7 +21,7 @@ jobs:
       - uses: octokit/request-action@v2.x
         id: check_approvals
         with:
-          route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+          route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - id: test_variables

From a995dbc4081bbec496673b30d17c5f58c1f8b056 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 8 Oct 2024 17:41:01 +0200
Subject: [PATCH 10/28] still allow manual dispatch

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 061f2dee0..3aa2f7de8 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -14,8 +14,8 @@ on:
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch
-    if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master'
+    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
+    if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: octokit/request-action@v2.x

From d00d36b62f2844df471a78fcae445fa05eebf611 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 8 Oct 2024 17:46:54 +0200
Subject: [PATCH 11/28] update changelog, fix if condition

---
 CHANGELOG.md                                                | 5 +++--
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 1 +
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 709e7b6ea..8c13e54f7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,9 +2,10 @@
 
 ## v3.0.1dev
 
-### Bug fixes
+### Template
 
-- Fixed an issue where the linting CI action didn't read the correct file
+- Fixed an issue where the linting CI action didn't read the correct file ([#3202](https://github.com/nf-core/tools/pull/3202))
+- Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 3aa2f7de8..d8987330d 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -25,6 +25,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'{% endraw %}
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')

From d409c85e0f9625169097deda52b1b7e2eb7eb1c2 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 9 Oct 2024 08:49:53 +0200
Subject: [PATCH 12/28] fix too many empty lines added to .editorconfig file

---
 nf_core/pipeline-template/.editorconfig | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index 1db986f5b..c78ec8e96 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -11,7 +11,7 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-{% if modules %}
+{% if modules -%}
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -25,12 +25,12 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-{% endif %}
+{%- endif %}
 
-{% if email %}
+{% if email -%}
 [/assets/email*]
 indent_size = unset
-{% endif %}
+{%- endif %}
 
 # ignore python and markdown
 [*.{py,md}]

From f27f79608c4397270e4fb8b65085b59c54717abc Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 9 Oct 2024 08:51:37 +0200
Subject: [PATCH 13/28] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 709e7b6ea..a953a539e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Bug fixes
 
 - Fixed an issue where the linting CI action didn't read the correct file
+- Fix too many empty lines added to .editorconfig file ([#3204](https://github.com/nf-core/tools/pull/3204))
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 

From 005eaec876469ad37834c1b180eba8b8147039e8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 9 Oct 2024 10:12:06 +0200
Subject: [PATCH 14/28] use correct key for defaultIgnoreParams

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

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 3aec815c7..37ba4feaf 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -97,7 +97,7 @@ def _update_validation_plugin_from_config(self) -> None:
                 conf.get("validation.help.fullParameter", "helpFull"),
                 conf.get("validation.help.showHiddenParameter", "showHidden"),
             ]  # Help parameter should be ignored by default
-            ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", [])
+            ignored_params_config = conf.get("validation.defaultIgnoreParams", [])
             if len(ignored_params_config) > 0:
                 ignored_params.extend(ignored_params_config)
             self.ignored_params = ignored_params

From bf2c6bb7169afb040630c387bac0a1036fec9b77 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 9 Oct 2024 10:12:23 +0200
Subject: [PATCH 15/28] add more debugging

---
 nf_core/modules/lint/main_nf.py | 1 +
 nf_core/pipelines/schema.py     | 1 +
 2 files changed, 2 insertions(+)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index dbc1bed73..54a69b113 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -342,6 +342,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
             continue
         try:
             container_url = "https://" + urlunparse(url) if not url.scheme == "https" else urlunparse(url)
+            log.debug(f"Trying to connect to URL: {container_url}")
             response = requests.head(
                 container_url,
                 stream=True,
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 37ba4feaf..1f0b4d5e3 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -99,6 +99,7 @@ def _update_validation_plugin_from_config(self) -> None:
             ]  # Help parameter should be ignored by default
             ignored_params_config = conf.get("validation.defaultIgnoreParams", [])
             if len(ignored_params_config) > 0:
+                log.debug(f"Ignoring parameters from config: {ignored_params_config}")
                 ignored_params.extend(ignored_params_config)
             self.ignored_params = ignored_params
             self.schema_draft = "https://json-schema.org/draft/2020-12/schema"

From 61e14c9e34316a4f258f5e7b55040cb2b64afb19 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 9 Oct 2024 08:19:39 +0000
Subject: [PATCH 16/28] Revert nf-core module level subworkflow changes

---
 .../subworkflows/nf-core/utils_nextflow_pipeline/main.nf  | 8 ++++----
 .../subworkflows/nf-core/utils_nfcore_pipeline/main.nf    | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

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
index e03052c5c..28e32b200 100644
--- 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
@@ -3,9 +3,9 @@
 //
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
@@ -45,9 +45,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
 
 //
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 49df430a6..cbd8495bb 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
@@ -3,9 +3,9 @@
 //
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
 
 workflow UTILS_NFCORE_PIPELINE {
@@ -22,9 +22,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
 
 //

From 0840f24ce826378aff28b578383d2a05b8b48ad2 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 9 Oct 2024 08:20:46 +0000
Subject: [PATCH 17/28] Update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7f7ce2ea6..969f54636 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
 - Fixed an issue where the linting CI action didn't read the correct file ([#3202](https://github.com/nf-core/tools/pull/3202))
 - Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
 - Fix too many empty lines added to .editorconfig file ([#3204](https://github.com/nf-core/tools/pull/3204))
+- Fix header blocks in local subworkflow including git merge marker-like strings ([#3201](https://github.com/nf-core/tools/pull/3201))
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 

From 86a9b65daed94aa4dd22cffcbfed4998c8284f3f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 9 Oct 2024 10:51:43 +0200
Subject: [PATCH 18/28] fix more jinja newlines

---
 CHANGELOG.md                                  |  2 +-
 .../pipeline-template/.github/CONTRIBUTING.md |  4 +--
 nf_core/pipeline-template/.prettierignore     |  2 +-
 nf_core/pipeline-template/nextflow.config     | 33 ++++++++++---------
 4 files changed, 22 insertions(+), 19 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 969f54636..bee878636 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,7 @@
 
 - Fixed an issue where the linting CI action didn't read the correct file ([#3202](https://github.com/nf-core/tools/pull/3202))
 - Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
-- Fix too many empty lines added to .editorconfig file ([#3204](https://github.com/nf-core/tools/pull/3204))
+- Fix too many empty lines added by jinja ([#3204](https://github.com/nf-core/tools/pull/3204) and [#3205](https://github.com/nf-core/tools/pull/3205))
 - Fix header blocks in local subworkflow including git merge marker-like strings ([#3201](https://github.com/nf-core/tools/pull/3201))
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md
index d02cad6f1..0200ea26c 100644
--- a/nf_core/pipeline-template/.github/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md
@@ -30,7 +30,7 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-{%- if test_config %}
+{% if test_config -%}
 You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
 
 ```bash
@@ -139,4 +139,4 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-  {% endif %}
+  {%- endif %}
diff --git a/nf_core/pipeline-template/.prettierignore b/nf_core/pipeline-template/.prettierignore
index c8e8ad9e1..7ecc9b61c 100644
--- a/nf_core/pipeline-template/.prettierignore
+++ b/nf_core/pipeline-template/.prettierignore
@@ -1,4 +1,4 @@
-{%- if email %}
+{% if email -%}
 email_template.html
 {%- endif %}
 {%- if adaptivecard %}
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 4c816a2a2..f2bcda097 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -13,14 +13,14 @@ params {
     // Input options
     input                      = null
 
-    {%- if igenomes %}
+    {% if igenomes -%}
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
     {%- endif %}
 
-    {%- if multiqc %}
+    {% if multiqc -%}
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -45,7 +45,7 @@ params {
     version                      = false
     {% if test_config %}pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
 
-    {%- if nf_core_configs %}
+    {% if nf_core_configs -%}
     // Config options
     config_profile_name        = null
     config_profile_description = null
@@ -56,15 +56,17 @@ params {
     config_profile_url         = null
     {%- endif %}
 
-    {%- if nf_schema %}
+    {% if nf_schema -%}
     // Schema validation default options
     validate_params            = true
-    {% endif %}
+    {%- endif %}
 }
-{% if modules %}
+
+{% if modules -%}
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 {%- else %}
+
 process {
     // TODO nf-core: Check the defaults for all processes
     cpus   = { 1    * task.attempt }
@@ -75,7 +77,7 @@ process {
     maxRetries    = 1
     maxErrors     = '-1'
 }
-{% endif %}
+{%- endif %}
 
 profiles {
     debug {
@@ -171,14 +173,14 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
-    {%- if gitpod %}
+    {% if gitpod -%}
     gitpod {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
     {%- endif %}
-    {%- if test_config %}
+    {% if test_config -%}
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
     {%- endif %}
@@ -191,7 +193,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 // Load {{ name }} custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
 // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
-{% endif -%}
+{%- endif %}
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -205,7 +207,7 @@ charliecloud.registry = 'quay.io'
 {% if igenomes -%}
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
-{% endif -%}
+{%- endif %}
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
@@ -273,7 +275,7 @@ validation {
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
-        {%- if is_nfcore %}
+        {% if is_nfcore -%}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -297,8 +299,9 @@ validation {
         afterText = validation.help.afterText
     }{% endif %}
 }
-{% endif -%}
-{%- if modules %}
+{%- endif %}
+
+{% if modules -%}
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-{% endif %}
+{%- endif %}

From 011354948ba0180f0af1b4d7920c19d5aa0f042b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Wed, 9 Oct 2024 10:53:20 +0200
Subject: [PATCH 19/28] Update CHANGELOG.md

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bee878636..dfe97f4fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,7 @@
 
 - Fixed an issue where the linting CI action didn't read the correct file ([#3202](https://github.com/nf-core/tools/pull/3202))
 - Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
-- Fix too many empty lines added by jinja ([#3204](https://github.com/nf-core/tools/pull/3204) and [#3205](https://github.com/nf-core/tools/pull/3205))
+- Fix too many empty lines added by jinja ([#3204](https://github.com/nf-core/tools/pull/3204) and [#3206](https://github.com/nf-core/tools/pull/3206))
 - Fix header blocks in local subworkflow including git merge marker-like strings ([#3201](https://github.com/nf-core/tools/pull/3201))
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]

From 16a36093880398d36fdf87a7595bb8424ac9c2e0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 9 Oct 2024 10:53:47 +0200
Subject: [PATCH 20/28] Bump version to 3.0.1

---
 .gitpod.yml  | 2 +-
 CHANGELOG.md | 2 +-
 setup.py     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitpod.yml b/.gitpod.yml
index efe193f35..f92457278 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -1,4 +1,4 @@
-image: nfcore/gitpod:dev
+image: nfcore/gitpod:latest
 tasks:
   - name: install current state of nf-core/tools and setup pre-commit
     command: |
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 969f54636..bf33dc4a1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # nf-core/tools: Changelog
 
-## v3.0.1dev
+## [v3.0.1 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.1) - [2024-10-09]
 
 ### Template
 
diff --git a/setup.py b/setup.py
index 37aa62a4d..364372f57 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "3.0.1dev"
+version = "3.0.1"
 
 with open("README.md") as f:
     readme = f.read()

From fb952ddc642607609fdc63dc5157e8d34c5ab009 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 9 Oct 2024 10:56:35 +0200
Subject: [PATCH 21/28] update nf-core subworkflows

---
 nf_core/pipeline-template/modules.json        |   4 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   |  46 ++-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 279 ++++++++++--------
 3 files changed, 172 insertions(+), 157 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 9bc344e7d..f694c0443 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -23,12 +23,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
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
index 28e32b200..2b0dc67a6 100644
--- 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
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
-
     take:
     print_version        // boolean: print version
     dump_parameters      // boolean: dump parameters
@@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     // Print workflow version and exit on --version
     //
     if (print_version) {
-        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
         System.exit(0)
     }
 
@@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -72,11 +71,11 @@ def getWorkflowVersion() {
 // Dump pipeline parameters to a JSON file
 //
 def dumpParametersToJSON(outdir) {
-    def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-    def filename   = "params_${timestamp}.json"
-    def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = groovy.json.JsonOutput.toJson(params)
-    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
+    def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
+    def filename  = "params_${timestamp}.json"
+    def temp_pf   = new File(workflow.launchDir.toString(), ".${filename}")
+    def jsonStr   = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text  = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
     nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
@@ -91,9 +90,14 @@ def checkCondaChannels() {
     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
+    }
+    catch (NullPointerException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
+    }
+    catch (IOException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
     }
 
     // Check that all channels are present
@@ -106,19 +110,13 @@ def checkCondaChannels() {
 
     required_channels_in_order.eachWithIndex { channel, index ->
         if (index < required_channels_in_order.size() - 1) {
-            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 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" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        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_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index cbd8495bb..8cda47bcf 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
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
-
     take:
     nextflow_cli_args
 
@@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE {
 def checkConfigProvided() {
     def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-            "Please refer to the quick start section and usage docs for the pipeline.\n "
+        log.warn(
+            "[${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
@@ -49,12 +45,14 @@ def checkConfigProvided() {
 //
 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"
+        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 `${nextflow_cli_args[0]}` has been detected.\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        log.warn(
+            "nf-core pipelines do not accept positional arguments. The positional argument `${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"
+        )
     }
 }
 
@@ -70,13 +68,7 @@ def workflowCitation() {
     manifest_doi.each { doi_ref ->
         temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     }
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
 }
 
 //
@@ -102,7 +94,7 @@ def getWorkflowVersion() {
 //
 def processVersionsFromYAML(yaml_file) {
     def yaml = new org.yaml.snakeyaml.Yaml()
-    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -112,8 +104,8 @@ def processVersionsFromYAML(yaml_file) {
 def workflowVersionToYAML() {
     return """
     Workflow:
-        $workflow.manifest.name: ${getWorkflowVersion()}
-        Nextflow: $workflow.nextflow.version
+        ${workflow.manifest.name}: ${getWorkflowVersion()}
+        Nextflow: ${workflow.nextflow.version}
     """.stripIndent().trim()
 }
 
@@ -121,11 +113,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions
-                .unique()
-                .map { version -> processVersionsFromYAML(version) }
-                .unique()
-                .mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
 }
 
 //
@@ -133,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    summary_params.keySet().each { group ->
-        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
-        if (group_params) {
-            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
-            summary_section += "    <dl class=\"dl-horizontal\">\n"
-            group_params.keySet().sort().each { param ->
-                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class="dl-horizontal">\n"
+                group_params
+                    .keySet()
+                    .sort()
+                    .each { param ->
+                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style="color:#999999;">N/A</a>'}</samp></dd>\n"
+                    }
+                summary_section += "    </dl>\n"
             }
-            summary_section += "    </dl>\n"
         }
-    }
 
-    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
-    yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
-    yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-    yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text        += "plot_type: 'html'\n"
-    yaml_file_text        += "data: |\n"
-    yaml_file_text        += "${summary_section}"
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
+    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${summary_section}"
 
     return yaml_file_text
 }
@@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) {
     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"
+    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"
+    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"
+    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"
+    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"
+    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
 }
@@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) {
             mqc_report = multiqc_report.getVal()
             if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
                 if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
                 }
                 mqc_report = mqc_report[0]
             }
         }
-    } catch (all) {
+    }
+    catch (Exception all) {
         if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
         }
     }
     return mqc_report
@@ -280,26 +275,35 @@ def attachMultiqcReport(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: $workflow.runName"
+    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
     if (!workflow.success) {
-        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
     }
 
     def summary = [:]
-    summary_params.keySet().sort().each { group ->
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
     misc_fields['Date Started']              = workflow.start
     misc_fields['Date Completed']            = workflow.complete
     misc_fields['Pipeline script file path'] = workflow.scriptFile
     misc_fields['Pipeline script hash ID']   = workflow.scriptId
-    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-    misc_fields['Nextflow Version']           = workflow.nextflow.version
-    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    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 = [:]
@@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 
     // 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: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html          = sendmail_template.toString()
@@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) {
+new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-        } catch (all) {
+            ['sendmail', '-t'].execute() << sendmail_html
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
+        }
+        catch (Exception all) {
             // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-")
         }
     }
 
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html")
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt")
     output_tf.delete()
 }
 
@@ -380,12 +386,14 @@ def completionSummary(monochrome_logs=true) {
     def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            log.info("-${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${colors.reset}-"
+    }
+    else {
+        log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
 
@@ -394,21 +402,30 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    summary_params.keySet().sort().each { group ->
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
-    misc_fields['start']                                = workflow.start
-    misc_fields['complete']                             = workflow.complete
-    misc_fields['scriptfile']                           = workflow.scriptFile
-    misc_fields['scriptid']                             = workflow.scriptId
-    if (workflow.repository) misc_fields['repository']  = workflow.repository
-    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-    if (workflow.revision)   misc_fields['revision']    = workflow.revision
-    misc_fields['nxf_version']                          = workflow.nextflow.version
-    misc_fields['nxf_build']                            = workflow.nextflow.build
-    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+    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()
@@ -433,13 +450,13 @@ def imNotification(summary_params, hook_url) {
     def json_message  = json_template.toString()
 
     // POST
-    def post = new URL(hook_url).openConnection();
+    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());
+    post.getOutputStream().write(json_message.getBytes("UTF-8"))
+    def postRC = post.getResponseCode()
+    if (!postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText())
     }
 }

From a4b727adad8a81257b67d348a6ec79568c0ef9d4 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 9 Oct 2024 10:57:46 +0200
Subject: [PATCH 22/28] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 969f54636..b14b7b76f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@
 - Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
 - Fix too many empty lines added to .editorconfig file ([#3204](https://github.com/nf-core/tools/pull/3204))
 - Fix header blocks in local subworkflow including git merge marker-like strings ([#3201](https://github.com/nf-core/tools/pull/3201))
+- Update nf-core subworkflows with fixed header blocks ([#3208](https://github.com/nf-core/tools/pull/3208))
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 

From ad32bb2a57a46442c7ff454e4a1535f545198f74 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 9 Oct 2024 09:00:53 +0000
Subject: [PATCH 23/28] [automated] Update CHANGELOG.md

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b14b7b76f..969f54636 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,6 @@
 - Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
 - Fix too many empty lines added to .editorconfig file ([#3204](https://github.com/nf-core/tools/pull/3204))
 - Fix header blocks in local subworkflow including git merge marker-like strings ([#3201](https://github.com/nf-core/tools/pull/3201))
-- Update nf-core subworkflows with fixed header blocks ([#3208](https://github.com/nf-core/tools/pull/3208))
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 

From 1ce2250d95f1eb68c893fcebab7c087beede4378 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 9 Oct 2024 11:08:58 +0200
Subject: [PATCH 24/28] fix jinja newlines in output.md

---
 nf_core/pipeline-template/docs/output.md | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
index 083c46ecd..1becf24b6 100644
--- a/nf_core/pipeline-template/docs/output.md
+++ b/nf_core/pipeline-template/docs/output.md
@@ -12,12 +12,16 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-{% if fastqc %}- [FastQC](#fastqc) - Raw read QC{% endif %}
-{% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %}
+{% if fastqc -%}
 
+- [FastQC](#fastqc) - Raw read QC
+  {%- endif %}
+  {%- if multiqc %}
+- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+  {%- endif %}
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
-{%- if fastqc %}
+{% if fastqc -%}
 
 ### FastQC
 
@@ -32,7 +36,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 {%- endif %}
-{%- if multiqc %}
+
+{% if multiqc -%}
 
 ### MultiQC
 
@@ -49,7 +54,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
-{% endif %}
+{%- endif %}
 
 ### Pipeline information
 

From 058391dcf8cec7f981564dde03a9b0363616a322 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 9 Oct 2024 11:13:38 +0200
Subject: [PATCH 25/28] CI: fix artifact upload of snapshot report

---
 .github/workflows/pytest.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 325efb91f..ae2df47e6 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -142,18 +142,18 @@ jobs:
             exit 1
           fi
 
+      - name: remove slashes from test name
+        run: |
+          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
+          echo "test=${test}" >> $GITHUB_ENV
+
       - name: Store snapshot report
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         if: always()
         with:
-          name: Snapshot Report ${{ matrix.test }}
+          name: Snapshot Report ${{ env.test }}
           path: ./snapshot_report.html
 
-      - name: remove slashes from test name
-        run: |
-          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
-          echo "test=${test}" >> $GITHUB_ENV
-
       - name: Upload coverage
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:

From 92e2b6e9c743e8dc851d105f52d2b020c21393cc Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 9 Oct 2024 11:28:46 +0200
Subject: [PATCH 26/28] update multiqc

---
 nf_core/pipeline-template/modules.json        |  2 +-
 .../modules/nf-core/multiqc/environment.yml   |  2 +-
 .../modules/nf-core/multiqc/main.nf           |  4 +--
 .../nf-core/multiqc/tests/main.nf.test.snap   | 26 +++++++++----------
 4 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index f694c0443..bc5b7bd4d 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -13,7 +13,7 @@
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
index f1cd99b07..6f5b867b7 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.24.1
+  - bioconda::multiqc=1.25.1
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
index b9ccebdbb..9724d2f34 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
index b779e4692..2fcbb5ff7 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T12:41:34.562023"
+        "timestamp": "2024-10-02T17:51:46.317523"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:27:11.933869532"
+        "timestamp": "2024-10-02T17:52:20.680978"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:26:56.709849369"
+        "timestamp": "2024-10-02T17:52:09.185842"
     }
-}
+}
\ No newline at end of file

From 0aa1c6058f6419588ee8df66677deb6458ae4405 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 9 Oct 2024 11:28:57 +0200
Subject: [PATCH 27/28] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 969f54636..ca7709aa3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@
 - Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
 - Fix too many empty lines added to .editorconfig file ([#3204](https://github.com/nf-core/tools/pull/3204))
 - Fix header blocks in local subworkflow including git merge marker-like strings ([#3201](https://github.com/nf-core/tools/pull/3201))
+- Update included subworkflows and modules ([#3208](https://github.com/nf-core/tools/pull/3208))
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 

From f0fb3d6ed2fccd30e25f670dbda684134beb61a4 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 9 Oct 2024 12:03:00 +0200
Subject: [PATCH 28/28] update utils_nfcore_pipeline subworkflow

---
 nf_core/pipeline-template/modules.json                        | 2 +-
 .../subworkflows/nf-core/utils_nfcore_pipeline/main.nf        | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index bc5b7bd4d..fa4651ee1 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -28,7 +28,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
+                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_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 8cda47bcf..b78273ca4 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
@@ -128,12 +128,12 @@ def paramsSummaryMultiqc(summary_params) {
             // This gets the parameters of that particular group
             if (group_params) {
                 summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
-                summary_section += "    <dl class="dl-horizontal">\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
                 group_params
                     .keySet()
                     .sort()
                     .each { param ->
-                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style="color:#999999;">N/A</a>'}</samp></dd>\n"
+                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
                     }
                 summary_section += "    </dl>\n"
             }