From 51587c06811f113d2352f5d941bca1e355b6507c Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 8 Dec 2022 14:13:46 +0100
Subject: [PATCH 01/32] bump to v2.8dev

---
 CHANGELOG.md | 12 ++++++++++++
 setup.py     |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a96b0db398..7894ed3d65 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,17 @@
 # nf-core/tools: Changelog
 
+# v2.8dev
+
+### Template
+
+### Linting
+
+### Modules
+
+### Subworkflows
+
+### General
+
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 
 - Patch release to fix pipeline sync ([#2110](https://github.com/nf-core/tools/pull/2110))
diff --git a/setup.py b/setup.py
index 046f5ddf76..38f36810b7 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "2.7.1"
+version = "2.8dev"
 
 with open("README.md") as f:
     readme = f.read()

From 46317bdcacd3321c23ed43e45345ee2e770d7f20 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 8 Dec 2022 17:52:37 +0100
Subject: [PATCH 02/32] fix github_output syntax

---
 nf_core/pipeline-template/.github/workflows/fix-linting.yml   | 4 ++--
 .../pipeline-template/.github/workflows/linting_comment.yml   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
index 4c586a0929..f3dc3e50fe 100644
--- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "name=result::pass" >> $GITHUB_OUTPUT
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "name=result::fail" >> $GITHUB_OUTPUT
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'
diff --git a/nf_core/pipeline-template/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/.github/workflows/linting_comment.yml
index 585b933f1c..09f8c423e5 100644
--- a/nf_core/pipeline-template/.github/workflows/linting_comment.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting_comment.yml
@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

From 78d4a25ee2d48c9177a3155c779a2699aa07d378 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 8 Dec 2022 17:55:42 +0100
Subject: [PATCH 03/32] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7894ed3d65..fd09bbde70 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,8 @@
 
 ### Template
 
+- Fix the syntax of github_output in GitHub actions ([#2114](https://github.com/nf-core/tools/pull/2114))
+
 ### Linting
 
 ### Modules

From 0d7925bc1e7e0084b7956a0386b1cf7316d05f44 Mon Sep 17 00:00:00 2001
From: Arthur Gymer <24782660+awgymer@users.noreply.github.com>
Date: Fri, 9 Dec 2022 14:35:19 +0000
Subject: [PATCH 04/32] Return from get_username and make sure it is assigned
 back to self.author

---
 nf_core/components/components_create.py | 2 ++
 nf_core/modules/create.py               | 2 +-
 nf_core/subworkflows/create.py          | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/nf_core/components/components_create.py b/nf_core/components/components_create.py
index a8d56411ba..86c42c0373 100644
--- a/nf_core/components/components_create.py
+++ b/nf_core/components/components_create.py
@@ -173,3 +173,5 @@ def get_username(author):
             f"[violet]GitHub Username:[/]{' (@author)' if author_default is None else ''}",
             default=author_default,
         )
+
+    return author
diff --git a/nf_core/modules/create.py b/nf_core/modules/create.py
index b4899750d7..019a77c71f 100644
--- a/nf_core/modules/create.py
+++ b/nf_core/modules/create.py
@@ -123,7 +123,7 @@ def create(self):
         self._get_bioconda_tool()
 
         # Prompt for GitHub username
-        nf_core.components.components_create.get_username(self.author)
+        self.author = nf_core.components.components_create.get_username(self.author)
 
         self._get_module_structure_components()
 
diff --git a/nf_core/subworkflows/create.py b/nf_core/subworkflows/create.py
index d5f9a5efbb..e61f0c6c8d 100644
--- a/nf_core/subworkflows/create.py
+++ b/nf_core/subworkflows/create.py
@@ -88,7 +88,7 @@ def create(self):
         )
 
         # Prompt for GitHub username
-        nf_core.components.components_create.get_username(self.author)
+        self.author = nf_core.components.components_create.get_username(self.author)
 
         # Create subworkflow template with jinja2
         nf_core.components.components_create.render_template(self.component_type, vars(self), self.file_paths)

From 2cd002c218f81368a2789d61c171f148a66b4609 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 9 Dec 2022 16:50:53 +0100
Subject: [PATCH 05/32] allow specifying only one container

---
 nf_core/modules/lint/main_nf.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index c4f4bf9bc8..52aa30f7c3 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -271,6 +271,15 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 self.failed.append(("singularity_tag", "Unable to parse singularity tag", self.main_nf))
                 singularity_tag = None
             url = urlparse(l.split("'")[0])
+            # lint double quotes
+            if l.count('"') > 2:
+                self.failed.append(
+                    (
+                        "container_links",
+                        "Too many double quotes found when specifying singularity container",
+                        self.main_nf,
+                    )
+                )
         if _container_type(l) == "docker":
             # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
             # e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
@@ -282,10 +291,14 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
                 docker_tag = None
             url = urlparse(l.split("'")[0])
+            # lint double quotes
+            if l.count('"') > 2:
+                self.failed.append(
+                    ("container_links", "Too many double quotes found when specifying docker container", self.main_nf)
+                )
         # lint double quotes
         if l.startswith("container"):
-            container_section = l + lines[i + 1] + lines[i + 2]
-            if container_section.count('"') > 2:
+            if l.count('"') > 2:
                 self.failed.append(
                     ("container_links", "Too many double quotes found when specifying containers", self.main_nf)
                 )

From 96826eb00e832d51d543ddf78d805e7babb13cde Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 9 Dec 2022 16:53:37 +0100
Subject: [PATCH 06/32] modify changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd09bbde70..f5584a9235 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,8 @@
 
 ### Linting
 
+- Allow specifying containers in less than three lines ([#2121](https://github.com/nf-core/tools/pull/2121))
+
 ### Modules
 
 ### Subworkflows

From a8cc7d9a10e01307c89e2f59af1cbba09c03ec69 Mon Sep 17 00:00:00 2001
From: Arthur Gymer <24782660+awgymer@users.noreply.github.com>
Date: Fri, 9 Dec 2022 22:21:44 +0000
Subject: [PATCH 07/32] Ensure call to load_tools_config expects tuple return

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

diff --git a/nf_core/create.py b/nf_core/create.py
index 3a5f1a502b..0bad1bec32 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -166,7 +166,7 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
         param_dict["logo_dark"] = f"{param_dict['name_noslash']}_logo_dark.png"
         param_dict["version"] = version
 
-        config_yml = nf_core.utils.load_tools_config()
+        _, config_yml = nf_core.utils.load_tools_config()
         if (
             "lint" in config_yml
             and "nextflow_config" in config_yml["lint"]

From a85b8962b94bd5854424cc2d08d9c97ebf1a3982 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Mon, 12 Dec 2022 13:41:09 +0000
Subject: [PATCH 08/32] check only one container per line

---
 nf_core/modules/lint/main_nf.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 52aa30f7c3..d44fe90f1e 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -302,6 +302,15 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 self.failed.append(
                     ("container_links", "Too many double quotes found when specifying containers", self.main_nf)
                 )
+        # lint more than one container in the same line
+        if ("https://containers" in l or "https://depot" in l) and ("biocontainers/" in l or "quay.io/" in l):
+            self.warned.append(
+                (
+                    "container_links",
+                    "Docker and Singularity containers specified in the same line. Only first one checked.",
+                    self.main_nf,
+                )
+            )
         # Try to connect to container URLs
         if url is None:
             continue

From 6a7da79962da64c2e675a3efef012960a3299033 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Dec 2022 16:30:28 +0100
Subject: [PATCH 09/32] only check pipeline name without dashes if the name is
 provided by prompt

---
 nf_core/create.py | 7 ++++---
 nf_core/sync.py   | 5 +++--
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/nf_core/create.py b/nf_core/create.py
index 0bad1bec32..045c35d1b4 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -173,9 +173,10 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
             and "manifest.name" in config_yml["lint"]["nextflow_config"]
         ):
             return param_dict, skip_paths
-        # Check that the pipeline name matches the requirements
-        if not re.match(r"^[a-z]+$", param_dict["short_name"]):
-            raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
+        if param_dict["prefix"] == "nf-core":
+            # Check that the pipeline name matches the requirements
+            if not re.match(r"^[a-z]+$", param_dict["short_name"]):
+                raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
 
         return param_dict, skip_paths
 
diff --git a/nf_core/sync.py b/nf_core/sync.py
index 4d0e1e88ba..332b524cbb 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -252,8 +252,9 @@ def make_template_pipeline(self):
                 plain=True,
             ).init_pipeline()
         except Exception as err:
-            # If sync fails, remove template_yaml_path before raising error.
-            os.remove(self.template_yaml_path)
+            if self.template_yaml_path:
+                # If sync fails, remove template_yaml_path before raising error.
+                os.remove(self.template_yaml_path)
             # Reset to where you were to prevent git getting messed up.
             self.repo.git.reset("--hard")
             raise SyncException(f"Failed to rebuild pipeline from template with error:\n{err}")

From f05b06e6f10bc7b971830aedeec2c827c5bd99ba Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Dec 2022 17:12:25 +0100
Subject: [PATCH 10/32] run prettier after dumping a json schema file

---
 nf_core/launch.py | 2 ++
 nf_core/schema.py | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/nf_core/launch.py b/nf_core/launch.py
index d03e112c3e..ae4bb174ac 100644
--- a/nf_core/launch.py
+++ b/nf_core/launch.py
@@ -17,6 +17,7 @@
 
 import nf_core.schema
 import nf_core.utils
+from nf_core.lint_utils import run_prettier_on_file
 
 log = logging.getLogger(__name__)
 
@@ -703,6 +704,7 @@ def build_command(self):
                 with open(self.params_out, "w") as fp:
                     json.dump(self.schema_obj.input_params, fp, indent=4)
                     fp.write("\n")
+                run_prettier_on_file(self.params_out)
                 self.nextflow_cmd += f' -params-file "{os.path.relpath(self.params_out)}"'
 
             # Call nextflow with a list of command line flags
diff --git a/nf_core/schema.py b/nf_core/schema.py
index d566f2b519..ee4a275c59 100644
--- a/nf_core/schema.py
+++ b/nf_core/schema.py
@@ -16,6 +16,7 @@
 
 import nf_core.list
 import nf_core.utils
+from nf_core.lint_utils import run_prettier_on_file
 
 log = logging.getLogger(__name__)
 
@@ -173,6 +174,7 @@ def save_schema(self, suppress_logging=False):
         with open(self.schema_filename, "w") as fh:
             json.dump(self.schema, fh, indent=4)
             fh.write("\n")
+        run_prettier_on_file(self.schema_filename)
 
     def load_input_params(self, params_path):
         """Load a given a path to a parameters file (JSON/YAML)

From a0f5d568ce01c6f7ac6fa0f3dba9dad42afeab4d Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Dec 2022 17:14:17 +0100
Subject: [PATCH 11/32] modify changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f5584a9235..82acae6845 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@
 ### Linting
 
 - Allow specifying containers in less than three lines ([#2121](https://github.com/nf-core/tools/pull/2121))
+- Run prettier after dumping a json schema file ([#2124](https://github.com/nf-core/tools/pull/2124))
 
 ### Modules
 

From 5ccbae835e6b536a4d5490f6904bead1f971395a Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Dec 2022 17:15:36 +0100
Subject: [PATCH 12/32] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f5584a9235..ef0cc5e053 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,8 @@
 
 ### General
 
+- Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
+
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 
 - Patch release to fix pipeline sync ([#2110](https://github.com/nf-core/tools/pull/2110))

From e9e039a2679f487a861169caab147c5240c61b3d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 13 Dec 2022 15:55:08 +0100
Subject: [PATCH 13/32] =?UTF-8?q?add=20newline=20before=20table=20?=
 =?UTF-8?q?=F0=9F=A4=9E=F0=9F=8F=BB?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 README.md | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 0ea83c3cca..8874837bc8 100644
--- a/README.md
+++ b/README.md
@@ -217,11 +217,12 @@ Please refer to the respective documentation for further details to manage packa
 ### Activate shell completions for nf-core/tools
 
 Auto-completion for the `nf-core` command is available for bash, zsh and fish. To activate it, add the following lines to the respective shell config files.
-shell | shell config file | command
---- | --- | ---
-bash | ~/.bashrc | `eval "$(_NF_CORE_COMPLETE=bash_source nf-core)"`
-Zsh | ~/.zshrc | `eval "$(_NF_CORE_COMPLETE=zsh_source nf-core)"`
-fish | ~/.config/fish/completions/nf-core.fish | `eval (env _NF_CORE_COMPLETE=fish_source nf-core)`
+
+| shell | shell config file                       | command                                            |
+| ----- | --------------------------------------- | -------------------------------------------------- |
+| bash  | ~/.bashrc                               | `eval "$(_NF_CORE_COMPLETE=bash_source nf-core)"`  |
+| Zsh   | ~/.zshrc                                | `eval "$(_NF_CORE_COMPLETE=zsh_source nf-core)"`   |
+| fish  | ~/.config/fish/completions/nf-core.fish | `eval (env _NF_CORE_COMPLETE=fish_source nf-core)` |
 
 After a restart of the shell session you should have auto-completion for the `nf-core` command and all its sub-commands and options.
 

From e3d987e2afaf76a0edc89c9a0ffb7e8fa970a220 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?=
 <mashehu@users.noreply.github.com>
Date: Tue, 13 Dec 2022 16:04:08 +0100
Subject: [PATCH 14/32] Update README.md

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 8874837bc8..35a06028c9 100644
--- a/README.md
+++ b/README.md
@@ -220,9 +220,9 @@ Auto-completion for the `nf-core` command is available for bash, zsh and fish. T
 
 | shell | shell config file                       | command                                            |
 | ----- | --------------------------------------- | -------------------------------------------------- |
-| bash  | ~/.bashrc                               | `eval "$(_NF_CORE_COMPLETE=bash_source nf-core)"`  |
-| Zsh   | ~/.zshrc                                | `eval "$(_NF_CORE_COMPLETE=zsh_source nf-core)"`   |
-| fish  | ~/.config/fish/completions/nf-core.fish | `eval (env _NF_CORE_COMPLETE=fish_source nf-core)` |
+| bash  | `~/.bashrc`                               | `eval "$(_NF_CORE_COMPLETE=bash_source nf-core)"`  |
+| Zsh   | `~/.zshrc`                                | `eval "$(_NF_CORE_COMPLETE=zsh_source nf-core)"`   |
+| fish  | `~/.config/fish/completions/nf-core.fish` | `eval (env _NF_CORE_COMPLETE=fish_source nf-core)` |
 
 After a restart of the shell session you should have auto-completion for the `nf-core` command and all its sub-commands and options.
 

From 5338afbb3a6e27f01a4a344eb3c566691a89ae73 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 13 Dec 2022 15:10:23 +0000
Subject: [PATCH 15/32] [automated] Fix code linting

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 35a06028c9..480b966f92 100644
--- a/README.md
+++ b/README.md
@@ -218,8 +218,8 @@ Please refer to the respective documentation for further details to manage packa
 
 Auto-completion for the `nf-core` command is available for bash, zsh and fish. To activate it, add the following lines to the respective shell config files.
 
-| shell | shell config file                       | command                                            |
-| ----- | --------------------------------------- | -------------------------------------------------- |
+| shell | shell config file                         | command                                            |
+| ----- | ----------------------------------------- | -------------------------------------------------- |
 | bash  | `~/.bashrc`                               | `eval "$(_NF_CORE_COMPLETE=bash_source nf-core)"`  |
 | Zsh   | `~/.zshrc`                                | `eval "$(_NF_CORE_COMPLETE=zsh_source nf-core)"`   |
 | fish  | `~/.config/fish/completions/nf-core.fish` | `eval (env _NF_CORE_COMPLETE=fish_source nf-core)` |

From 6e7f87aae535110a0c29beadbca007418b9cd9c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?=
 <mashehu@users.noreply.github.com>
Date: Tue, 13 Dec 2022 16:46:31 +0100
Subject: [PATCH 16/32] Update README.md

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

diff --git a/README.md b/README.md
index 480b966f92..73d868bb32 100644
--- a/README.md
+++ b/README.md
@@ -221,7 +221,7 @@ Auto-completion for the `nf-core` command is available for bash, zsh and fish. T
 | shell | shell config file                         | command                                            |
 | ----- | ----------------------------------------- | -------------------------------------------------- |
 | bash  | `~/.bashrc`                               | `eval "$(_NF_CORE_COMPLETE=bash_source nf-core)"`  |
-| Zsh   | `~/.zshrc`                                | `eval "$(_NF_CORE_COMPLETE=zsh_source nf-core)"`   |
+| zsh   | `~/.zshrc`                                | `eval "$(_NF_CORE_COMPLETE=zsh_source nf-core)"`   |
 | fish  | `~/.config/fish/completions/nf-core.fish` | `eval (env _NF_CORE_COMPLETE=fish_source nf-core)` |
 
 After a restart of the shell session you should have auto-completion for the `nf-core` command and all its sub-commands and options.

From 47b4252840817a1f2b77e26c816c6151157fd263 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Tue, 13 Dec 2022 17:31:19 +0100
Subject: [PATCH 17/32] Apply suggestions from code review

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
---
 nf_core/launch.py | 1 -
 nf_core/schema.py | 1 -
 2 files changed, 2 deletions(-)

diff --git a/nf_core/launch.py b/nf_core/launch.py
index ae4bb174ac..0facca72dc 100644
--- a/nf_core/launch.py
+++ b/nf_core/launch.py
@@ -703,7 +703,6 @@ def build_command(self):
             if self.use_params_file:
                 with open(self.params_out, "w") as fp:
                     json.dump(self.schema_obj.input_params, fp, indent=4)
-                    fp.write("\n")
                 run_prettier_on_file(self.params_out)
                 self.nextflow_cmd += f' -params-file "{os.path.relpath(self.params_out)}"'
 
diff --git a/nf_core/schema.py b/nf_core/schema.py
index ee4a275c59..92cbac852d 100644
--- a/nf_core/schema.py
+++ b/nf_core/schema.py
@@ -173,7 +173,6 @@ def save_schema(self, suppress_logging=False):
             log.info(f"Writing schema with {num_params} params: '{self.schema_filename}'")
         with open(self.schema_filename, "w") as fh:
             json.dump(self.schema, fh, indent=4)
-            fh.write("\n")
         run_prettier_on_file(self.schema_filename)
 
     def load_input_params(self, params_path):

From 6eb466428600db57fa132ebfe28ffe0a0fe3f97c Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Dec 2022 10:41:10 +0100
Subject: [PATCH 18/32] add json.dump into a helper function

---
 nf_core/launch.py               |  6 ++----
 nf_core/lint_utils.py           | 12 ++++++++++++
 nf_core/modules/modules_json.py |  7 ++-----
 nf_core/schema.py               |  6 ++----
 4 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/nf_core/launch.py b/nf_core/launch.py
index 0facca72dc..87150172f7 100644
--- a/nf_core/launch.py
+++ b/nf_core/launch.py
@@ -17,7 +17,7 @@
 
 import nf_core.schema
 import nf_core.utils
-from nf_core.lint_utils import run_prettier_on_file
+from nf_core.lint_utils import dump_json_with_prettier
 
 log = logging.getLogger(__name__)
 
@@ -701,9 +701,7 @@ def build_command(self):
 
             # Write the user selection to a file and run nextflow with that
             if self.use_params_file:
-                with open(self.params_out, "w") as fp:
-                    json.dump(self.schema_obj.input_params, fp, indent=4)
-                run_prettier_on_file(self.params_out)
+                dump_json_with_prettier(self.params_out, self.schema_obj.input_params)
                 self.nextflow_cmd += f' -params-file "{os.path.relpath(self.params_out)}"'
 
             # Call nextflow with a list of command line flags
diff --git a/nf_core/lint_utils.py b/nf_core/lint_utils.py
index f8ca563b00..c2fd75d375 100644
--- a/nf_core/lint_utils.py
+++ b/nf_core/lint_utils.py
@@ -1,3 +1,4 @@
+import json
 import logging
 import subprocess
 from pathlib import Path
@@ -82,3 +83,14 @@ def run_prettier_on_file(file):
                 "There was an error running the prettier pre-commit hook.\n"
                 f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"
             )
+
+
+def dump_json_with_prettier(file_name, file_content):
+    """Dump a JSON file and run prettier on it.
+    Args:
+        file_name (Path | str): A file identifier as a string or pathlib.Path.
+        file_content (dict): Content to dump into the JSON file
+    """
+    with open(file_name, "w") as fh:
+        json.dump(file_content, fh, indent=4)
+    run_prettier_on_file(file_name)
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index cda7c827dc..a1609e5fee 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -13,7 +13,7 @@
 
 import nf_core.utils
 from nf_core.components.components_utils import get_components_to_install
-from nf_core.lint_utils import run_prettier_on_file
+from nf_core.lint_utils import dump_json_with_prettier
 from nf_core.modules.modules_repo import (
     NF_CORE_MODULES_NAME,
     NF_CORE_MODULES_REMOTE,
@@ -1023,10 +1023,7 @@ def dump(self):
         """
         # Sort the modules.json
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
-        with open(self.modules_json_path, "w") as fh:
-            json.dump(self.modules_json, fh, indent=4)
-            fh.write("\n")
-        run_prettier_on_file(self.modules_json_path)
+        dump_json_with_prettier(self.modules_json_path, self.modules_json)
 
     def resolve_missing_installation(self, missing_installation, component_type):
         missing_but_in_mod_json = [
diff --git a/nf_core/schema.py b/nf_core/schema.py
index 92cbac852d..04b17a9045 100644
--- a/nf_core/schema.py
+++ b/nf_core/schema.py
@@ -16,7 +16,7 @@
 
 import nf_core.list
 import nf_core.utils
-from nf_core.lint_utils import run_prettier_on_file
+from nf_core.lint_utils import dump_json_with_prettier
 
 log = logging.getLogger(__name__)
 
@@ -171,9 +171,7 @@ def save_schema(self, suppress_logging=False):
         num_params += sum(len(d.get("properties", {})) for d in self.schema.get("definitions", {}).values())
         if not suppress_logging:
             log.info(f"Writing schema with {num_params} params: '{self.schema_filename}'")
-        with open(self.schema_filename, "w") as fh:
-            json.dump(self.schema, fh, indent=4)
-        run_prettier_on_file(self.schema_filename)
+        dump_json_with_prettier(self.schema_filename, self.schema)
 
     def load_input_params(self, params_path):
         """Load a given a path to a parameters file (JSON/YAML)

From 433e5b2a9b532ccff164cf5e189bb32bf70a4a60 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 15 Dec 2022 14:28:35 +0100
Subject: [PATCH 19/32] remove params.enable_conda

---
 nf_core/pipeline-template/lib/WorkflowMain.groovy | 5 -----
 nf_core/pipeline-template/nextflow.config         | 3 ---
 nf_core/pipeline-template/nextflow_schema.json    | 6 ------
 3 files changed, 14 deletions(-)

diff --git a/nf_core/pipeline-template/lib/WorkflowMain.groovy b/nf_core/pipeline-template/lib/WorkflowMain.groovy
index 714e659de9..c9c944b34a 100755
--- a/nf_core/pipeline-template/lib/WorkflowMain.groovy
+++ b/nf_core/pipeline-template/lib/WorkflowMain.groovy
@@ -75,11 +75,6 @@ class WorkflowMain {
         // 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 (params.enable_conda) {
-            Utils.checkCondaChannels(log)
-        }
-
         // Check AWS batch settings
         NfcoreTemplate.awsBatch(workflow, params)
 
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 2a7df54878..5cbb076b46 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -41,7 +41,6 @@ params {
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'
-    enable_conda               = false
 {% if nf_core_configs %}
 
     // Config options
@@ -84,7 +83,6 @@ try {
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
-        params.enable_conda    = true
         conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
@@ -93,7 +91,6 @@ profiles {
         charliecloud.enabled   = false
     }
     mamba {
-        params.enable_conda    = true
         conda.enabled          = true
         conda.useMamba         = true
         docker.enabled         = false
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 72c4e163a9..2743562d6c 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -263,12 +263,6 @@
                     "description": "Show all params when using `--help`",
                     "hidden": true,
                     "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "enable_conda": {
-                    "type": "boolean",
-                    "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-bacon"
                 }
             }
         }

From 547076bb0c16261a980e2d3abaacccd013e4e7df Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 15 Dec 2022 14:50:46 +0100
Subject: [PATCH 20/32] add params.enable_conda to deprecated vars

---
 nf_core/lint/nextflow_config.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py
index 0cf98a5b39..79bce3e7f1 100644
--- a/nf_core/lint/nextflow_config.py
+++ b/nf_core/lint/nextflow_config.py
@@ -146,6 +146,7 @@ def nextflow_config(self):
         "params.singleEnd",
         "params.igenomesIgnore",
         "params.name",
+        "params.enable_conda",
     ]
 
     # Remove field that should be ignored according to the linting config

From d9be489acc55d40b419cb29670c731be376ba04a Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 15 Dec 2022 15:06:32 +0100
Subject: [PATCH 21/32] update CHANGELOG

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c40fb3a035..28a49b70b9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@
 ### General
 
 - Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
+- Deprecate `--enable_conda` parameter. Use `conda.enable` instead ([#2131](https://github.com/nf-core/tools/pull/2131))
 
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 

From 4cf1fdc3dcb59a0b67c35a17c8e47f586fb1cb70 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 15 Dec 2022 15:25:10 +0100
Subject: [PATCH 22/32] update pipeline template modules

---
 nf_core/pipeline-template/modules.json        |  6 +-
 .../custom/dumpsoftwareversions/main.nf       |  2 +-
 .../templates/dumpsoftwareversions.py         | 99 ++++++++++---------
 .../modules/nf-core/fastqc/main.nf            | 40 +++-----
 .../modules/nf-core/multiqc/main.nf           |  2 +-
 5 files changed, 76 insertions(+), 73 deletions(-)
 mode change 100644 => 100755 nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 8618bacab6..08116ecbac 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
index cebb6e0589..3df21765b9 100644
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    conda "bioconda::multiqc=1.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
old mode 100644
new mode 100755
index 787bdb7b1b..e55b8d43a9
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -1,5 +1,9 @@
 #!/usr/bin/env python
 
+
+"""Provide functions to merge multiple versions.yml files."""
+
+
 import platform
 from textwrap import dedent
 
@@ -7,6 +11,7 @@
 
 
 def _make_versions_html(versions):
+    """Generate a tabular HTML output of all versions for MultiQC."""
     html = [
         dedent(
             """\\
@@ -45,47 +50,53 @@ def _make_versions_html(versions):
     return "\\n".join(html)
 
 
-versions_this_module = {}
-versions_this_module["${task.process}"] = {
-    "python": platform.python_version(),
-    "yaml": yaml.__version__,
-}
-
-with open("$versions") as f:
-    versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-# aggregate versions by the module name (derived from fully-qualified process name)
-versions_by_module = {}
-for process, process_versions in versions_by_process.items():
-    module = process.split(":")[-1]
-    try:
-        if versions_by_module[module] != process_versions:
-            raise AssertionError(
-                "We assume that software versions are the same between all modules. "
-                "If you see this error-message it means you discovered an edge-case "
-                "and should open an issue in nf-core/tools. "
-            )
-    except KeyError:
-        versions_by_module[module] = process_versions
-
-versions_by_module["Workflow"] = {
-    "Nextflow": "$workflow.nextflow.version",
-    "$workflow.manifest.name": "$workflow.manifest.version",
-}
-
-versions_mqc = {
-    "id": "software_versions",
-    "section_name": "${workflow.manifest.name} Software Versions",
-    "section_href": "https://github.com/${workflow.manifest.name}",
-    "plot_type": "html",
-    "description": "are collected at run time from the software output.",
-    "data": _make_versions_html(versions_by_module),
-}
-
-with open("software_versions.yml", "w") as f:
-    yaml.dump(versions_by_module, f, default_flow_style=False)
-with open("software_versions_mqc.yml", "w") as f:
-    yaml.dump(versions_mqc, f, default_flow_style=False)
-
-with open("versions.yml", "w") as f:
-    yaml.dump(versions_this_module, f, default_flow_style=False)
+def main():
+    """Load all version files and generate merged output."""
+    versions_this_module = {}
+    versions_this_module["${task.process}"] = {
+        "python": platform.python_version(),
+        "yaml": yaml.__version__,
+    }
+
+    with open("$versions") as f:
+        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+
+    # aggregate versions by the module name (derived from fully-qualified process name)
+    versions_by_module = {}
+    for process, process_versions in versions_by_process.items():
+        module = process.split(":")[-1]
+        try:
+            if versions_by_module[module] != process_versions:
+                raise AssertionError(
+                    "We assume that software versions are the same between all modules. "
+                    "If you see this error-message it means you discovered an edge-case "
+                    "and should open an issue in nf-core/tools. "
+                )
+        except KeyError:
+            versions_by_module[module] = process_versions
+
+    versions_by_module["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
+        "$workflow.manifest.name": "$workflow.manifest.version",
+    }
+
+    versions_mqc = {
+        "id": "software_versions",
+        "section_name": "${workflow.manifest.name} Software Versions",
+        "section_href": "https://github.com/${workflow.manifest.name}",
+        "plot_type": "html",
+        "description": "are collected at run time from the software output.",
+        "data": _make_versions_html(versions_by_module),
+    }
+
+    with open("software_versions.yml", "w") as f:
+        yaml.dump(versions_by_module, f, default_flow_style=False)
+    with open("software_versions_mqc.yml", "w") as f:
+        yaml.dump(versions_mqc, f, default_flow_style=False)
+
+    with open("versions.yml", "w") as f:
+        yaml.dump(versions_this_module, f, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf
index 05730368b2..9ae5838158 100644
--- a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf
@@ -2,7 +2,7 @@ process FASTQC {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    conda "bioconda::fastqc=0.11.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
         'quay.io/biocontainers/fastqc:0.11.9--0' }"
@@ -20,30 +20,22 @@ process FASTQC {
 
     script:
     def args = task.ext.args ?: ''
-    // Add soft-links to original FastQs for consistent naming in pipeline
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    }
+    // Make list of old name and new name pairs to use for renaming in the bash while loop
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    """
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+    done
+    fastqc $args --threads $task.cpus $renamed_files
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
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 a8159a57bf..68f66bea74 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
@@ -1,7 +1,7 @@
 process MULTIQC {
     label 'process_single'
 
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    conda "bioconda::multiqc=1.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"

From c83965db55cf6a793c3525919b0fff05470af4c7 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 15 Dec 2022 15:49:55 +0100
Subject: [PATCH 23/32] fix test

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

diff --git a/tests/modules/update.py b/tests/modules/update.py
index 19b53717fd..9729ef2975 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -329,6 +329,12 @@ def test_update_only_show_differences_when_patch(self, mock_prompt):
     modules_json = ModulesJson(self.pipeline_dir)
     update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
 
+    # Update modules to a fixed old SHA
+    update_old = ModuleUpdate(
+        self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+    )
+    update_old.update()
+
     # Modify fastqc module, it will have a patch which will be applied during update
     # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions)
     module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc")

From 3b2f53d1f6477ddef588ca6bdcc287253b7df626 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 15 Dec 2022 16:29:17 +0100
Subject: [PATCH 24/32] fix test

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

diff --git a/tests/modules/update.py b/tests/modules/update.py
index 9729ef2975..fcfd92fc39 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -303,6 +303,12 @@ def test_update_only_show_differences(self, mock_prompt):
     modules_json = ModulesJson(self.pipeline_dir)
     update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
 
+    # Update modules to a fixed old SHA
+    update_old = ModuleUpdate(
+        self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+    )
+    update_old.update()
+
     tmpdir = tempfile.mkdtemp()
     shutil.rmtree(tmpdir)
     shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir)

From 8acc9d67922180486749175c193ccabfcb57c03d Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Thu, 15 Dec 2022 23:42:46 +0100
Subject: [PATCH 25/32] Revert unique() syntax change. Closes #2132

---
 CHANGELOG.md                                    | 1 +
 nf_core/pipeline-template/workflows/pipeline.nf | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c40fb3a035..47bf9e8f4e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Template
 
 - Fix the syntax of github_output in GitHub actions ([#2114](https://github.com/nf-core/tools/pull/2114))
+- Fix a bug introduced in 2.7 that made pipelines hang ([#2132](https://github.com/nf-core/tools/issues/2132))
 
 ### Linting
 
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 2b54789101..9bcc0086b5 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -82,7 +82,7 @@ workflow {{ short_name|upper }} {
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml')
+        ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 
     //

From 8ce4d17bf3f24fff7175b0842ce5a2dca7b85884 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 16 Dec 2022 09:49:00 +0100
Subject: [PATCH 26/32] handle json exception

---
 nf_core/utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nf_core/utils.py b/nf_core/utils.py
index b2431b3337..b60f61fff0 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -248,7 +248,10 @@ def fetch_wf_config(wf_path, cache_config=True):
         if os.path.isfile(cache_path):
             log.debug(f"Found a config cache, loading: {cache_path}")
             with open(cache_path, "r") as fh:
-                config = json.load(fh)
+                try:
+                    config = json.load(fh)
+                except json.JSONDecodeError as e:
+                    raise UserWarning(f"Unable to load JSON file '{cache_path}' due to error {e}")
             return config
     log.debug("No config cache found")
 

From 67c3656b60fd82c80a809198c0c621feb90d88bc Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 16 Dec 2022 09:52:54 +0100
Subject: [PATCH 27/32] handle all json-load exceptions

---
 nf_core/modules/modules_json.py |  6 +++++-
 nf_core/schema.py               | 10 ++++++++--
 tests/modules/modules_json.py   | 10 ++++++++--
 tests/test_launch.py            |  6 +++++-
 tests/test_lint.py              |  5 ++++-
 5 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index a1609e5fee..2d95afd10c 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -618,7 +618,11 @@ def load(self):
         """
         try:
             with open(self.modules_json_path, "r") as fh:
-                self.modules_json = json.load(fh)
+                try:
+                    self.modules_json = json.load(fh)
+                except json.JSONDecodeError as e:
+                    raise UserWarning(f"Unable to load JSON file '{self.modules_json_path}' due to error {e}")
+
         except FileNotFoundError:
             raise UserWarning("File 'modules.json' is missing")
 
diff --git a/nf_core/schema.py b/nf_core/schema.py
index 04b17a9045..7ea9b972c0 100644
--- a/nf_core/schema.py
+++ b/nf_core/schema.py
@@ -105,7 +105,10 @@ def load_lint_schema(self):
     def load_schema(self):
         """Load a pipeline schema from a file"""
         with open(self.schema_filename, "r") as fh:
-            self.schema = json.load(fh)
+            try:
+                self.schema = json.load(fh)
+            except json.JSONDecodeError as e:
+                raise UserWarning(f"Unable to load JSON file '{self.schema_filename}' due to error {e}")
         self.schema_defaults = {}
         self.schema_params = []
         log.debug(f"JSON file loaded: {self.schema_filename}")
@@ -182,7 +185,10 @@ def load_input_params(self, params_path):
         # First, try to load as JSON
         try:
             with open(params_path, "r") as fh:
-                params = json.load(fh)
+                try:
+                    params = json.load(fh)
+                except json.JSONDecodeError as e:
+                    raise UserWarning(f"Unable to load JSON file '{params_path}' due to error {e}")
                 self.input_params.update(params)
             log.debug(f"Loaded JSON input params: {params_path}")
         except Exception as json_e:
diff --git a/tests/modules/modules_json.py b/tests/modules/modules_json.py
index 67ee44f973..63ee4e743d 100644
--- a/tests/modules/modules_json.py
+++ b/tests/modules/modules_json.py
@@ -18,7 +18,10 @@ def test_get_modules_json(self):
     """Checks that the get_modules_json function returns the correct result"""
     mod_json_path = os.path.join(self.pipeline_dir, "modules.json")
     with open(mod_json_path, "r") as fh:
-        mod_json_sb = json.load(fh)
+        try:
+            mod_json_sb = json.load(fh)
+        except json.JSONDecodeError as e:
+            raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
 
     mod_json_obj = ModulesJson(self.pipeline_dir)
     mod_json = mod_json_obj.get_modules_json()
@@ -212,7 +215,10 @@ def test_mod_json_dump(self):
 
     # Check that the dump function writes the correct content
     with open(mod_json_path, "r") as f:
-        mod_json_new = json.load(f)
+        try:
+            mod_json_new = json.load(f)
+        except json.JSONDecodeError as e:
+            raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
     assert mod_json == mod_json_new
 
 
diff --git a/tests/test_launch.py b/tests/test_launch.py
index de597127a2..d830311ba3 100644
--- a/tests/test_launch.py
+++ b/tests/test_launch.py
@@ -327,7 +327,11 @@ def test_build_command_params(self):
         )
         # Check saved parameters file
         with open(self.nf_params_fn, "r") as fh:
-            saved_json = json.load(fh)
+            try:
+                saved_json = json.load(fh)
+            except json.JSONDecodeError as e:
+                raise UserWarning(f"Unable to load JSON file '{self.nf_params_fn}' due to error {e}")
+
         assert saved_json == {"input": "custom_input"}
 
     def test_build_command_params_cl(self):
diff --git a/tests/test_lint.py b/tests/test_lint.py
index 8160de9fbc..e4e93bd1f4 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -134,7 +134,10 @@ def test_json_output(self, tmp_dir):
 
         # Load created JSON file and check its contents
         with open(json_fn, "r") as fh:
-            saved_json = json.load(fh)
+            try:
+                saved_json = json.load(fh)
+            except json.JSONDecodeError as e:
+                raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}")
         assert saved_json["num_tests_pass"] > 0
         assert saved_json["num_tests_warned"] > 0
         assert saved_json["num_tests_ignored"] == 0

From 1625014620fd1202219369fa65b9daf6b8a49bad Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 16 Dec 2022 09:54:36 +0100
Subject: [PATCH 28/32] update CHANGELOG

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6842c3ffaa..ac0f8a6f6a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@
 
 - Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
 - Deprecate `--enable_conda` parameter. Use `conda.enable` instead ([#2131](https://github.com/nf-core/tools/pull/2131))
+- Handle `json.load()` exceptions ([#2134](https://github.com/nf-core/tools/pull/2134))
 
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 

From 632b675c15eed7c99fe9061c13be695347cf1c5f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 16 Dec 2022 10:18:28 +0100
Subject: [PATCH 29/32] remove handling from linting as it's already handled
 later

---
 nf_core/schema.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/nf_core/schema.py b/nf_core/schema.py
index 7ea9b972c0..a50a1ed789 100644
--- a/nf_core/schema.py
+++ b/nf_core/schema.py
@@ -105,10 +105,7 @@ def load_lint_schema(self):
     def load_schema(self):
         """Load a pipeline schema from a file"""
         with open(self.schema_filename, "r") as fh:
-            try:
-                self.schema = json.load(fh)
-            except json.JSONDecodeError as e:
-                raise UserWarning(f"Unable to load JSON file '{self.schema_filename}' due to error {e}")
+            self.schema = json.load(fh)
         self.schema_defaults = {}
         self.schema_params = []
         log.debug(f"JSON file loaded: {self.schema_filename}")

From 0cb35e64dbec3ab94d7207ecad221f4072cade92 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 16 Dec 2022 10:48:09 +0100
Subject: [PATCH 30/32] check conda channels as it's done in rnaseq

---
 nf_core/pipeline-template/lib/WorkflowMain.groovy | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/nf_core/pipeline-template/lib/WorkflowMain.groovy b/nf_core/pipeline-template/lib/WorkflowMain.groovy
index c9c944b34a..05db418b2d 100755
--- a/nf_core/pipeline-template/lib/WorkflowMain.groovy
+++ b/nf_core/pipeline-template/lib/WorkflowMain.groovy
@@ -75,6 +75,11 @@ class WorkflowMain {
         // 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)
 

From 81fc96627bdc0af31bc186d2ef6acde7677e97fd Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 16 Dec 2022 10:50:07 +0100
Subject: [PATCH 31/32] remove params.enable_conda from modules template

---
 nf_core/module-template/modules/main.nf                      | 2 +-
 nf_core/pipeline-template/modules/local/samplesheet_check.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/module-template/modules/main.nf b/nf_core/module-template/modules/main.nf
index 6cfd5af2d5..e8f043f083 100644
--- a/nf_core/module-template/modules/main.nf
+++ b/nf_core/module-template/modules/main.nf
@@ -23,7 +23,7 @@ process {{ tool_name_underscore|upper }} {
     //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda (params.enable_conda ? "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}" : null)
+    conda "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         '{{ singularity_container if singularity_container else 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE' }}':
         '{{ docker_container if docker_container else 'quay.io/biocontainers/YOUR-TOOL-HERE' }}' }"
diff --git a/nf_core/pipeline-template/modules/local/samplesheet_check.nf b/nf_core/pipeline-template/modules/local/samplesheet_check.nf
index 03a50c1040..5d25800775 100644
--- a/nf_core/pipeline-template/modules/local/samplesheet_check.nf
+++ b/nf_core/pipeline-template/modules/local/samplesheet_check.nf
@@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3' :
         'quay.io/biocontainers/python:3.8.3' }"

From 02acf6561aae7a9b40d4bcd5ffb3fdc9da818dd5 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 19 Dec 2022 09:45:03 +0100
Subject: [PATCH 32/32] bump to 2.7.2 for patch release

---
 CHANGELOG.md | 6 +-----
 setup.py     | 2 +-
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ac0f8a6f6a..923a6c1ca4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # nf-core/tools: Changelog
 
-# v2.8dev
+## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]
 
 ### Template
 
@@ -12,10 +12,6 @@
 - Allow specifying containers in less than three lines ([#2121](https://github.com/nf-core/tools/pull/2121))
 - Run prettier after dumping a json schema file ([#2124](https://github.com/nf-core/tools/pull/2124))
 
-### Modules
-
-### Subworkflows
-
 ### General
 
 - Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
diff --git a/setup.py b/setup.py
index 38f36810b7..cc83e90eed 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "2.8dev"
+version = "2.7.2"
 
 with open("README.md") as f:
     readme = f.read()