From 8cd60e189f306796ec5e1235886c7934b8a01e6f Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 27 Oct 2020 10:58:09 +0100
Subject: [PATCH 01/51] Version 1.12dev bump

---
 CHANGELOG.md | 11 +++++++++++
 setup.py     |  2 +-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d91c1f5cb..617c1f29d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,16 @@
 # nf-core/tools: Changelog
 
+## v1.12dev
+
+### Tools helper code
+
+### Template
+
+### Linting
+
+### Other
+
+
 ## [v1.11 - Iron Tiger](https://github.com/nf-core/tools/releases/tag/1.11) - [2020-10-27]
 
 ### Template
diff --git a/setup.py b/setup.py
index afe3ae7db..16c80531b 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 from setuptools import setup, find_packages
 import sys
 
-version = "1.11"
+version = "1.12dev"
 
 with open("README.md") as f:
     readme = f.read()

From 26dc763495f72e8f1a80c8395c22af4425d8b3cc Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 27 Oct 2020 11:00:34 +0100
Subject: [PATCH 02/51] too many newlines\!

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 617c1f29d..5e07164df 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,6 @@
 
 ### Other
 
-
 ## [v1.11 - Iron Tiger](https://github.com/nf-core/tools/releases/tag/1.11) - [2020-10-27]
 
 ### Template

From 2f4194a2d6a5e3ec26d0bddeeeac15cd87d06f89 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 12:16:58 +0100
Subject: [PATCH 03/51] Logging - force colours if certain env vars are set.

---
 nf_core/__main__.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 6eebbe881..a1d7f726f 100755
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -28,13 +28,18 @@
 # Submodules should all traverse back to this
 log = logging.getLogger()
 
+# Should we force coloured output from Rich?
+rich_force_colors = None
+if os.getenv("GITHUB_ACTIONS") or os.getenv("FORCE_COLOR") or os.getenv("PY_COLORS"):
+    rich_force_colors = True
+
 
 def run_nf_core():
     # Set up the rich traceback
     rich.traceback.install(width=200, word_wrap=True)
 
     # Print nf-core header to STDERR
-    stderr = rich.console.Console(file=sys.stderr)
+    stderr = rich.console.Console(file=sys.stderr, force_terminal=rich_force_colors)
     stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False)
     stderr.print("[blue]          ___     __   __   __   ___     [green]/,-._.--~\\", highlight=False)
     stderr.print("[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {", highlight=False)
@@ -114,7 +119,7 @@ def nf_core_cli(verbose, log_file):
     log.addHandler(
         rich.logging.RichHandler(
             level=logging.DEBUG if verbose else logging.INFO,
-            console=rich.console.Console(file=sys.stderr),
+            console=rich.console.Console(file=sys.stderr, force_terminal=rich_force_colors),
             show_time=False,
             markup=True,
         )

From 29ce8b36c3af82524d5d6a941c7c5167bf4ce739 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 12:23:54 +0100
Subject: [PATCH 04/51] Add to utils function, apply to lint and launch console
 functions

---
 nf_core/__main__.py | 9 ++-------
 nf_core/launch.py   | 2 +-
 nf_core/lint.py     | 2 +-
 nf_core/utils.py    | 9 +++++++++
 4 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index a1d7f726f..ec3c1aa2a 100755
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -28,18 +28,13 @@
 # Submodules should all traverse back to this
 log = logging.getLogger()
 
-# Should we force coloured output from Rich?
-rich_force_colors = None
-if os.getenv("GITHUB_ACTIONS") or os.getenv("FORCE_COLOR") or os.getenv("PY_COLORS"):
-    rich_force_colors = True
-
 
 def run_nf_core():
     # Set up the rich traceback
     rich.traceback.install(width=200, word_wrap=True)
 
     # Print nf-core header to STDERR
-    stderr = rich.console.Console(file=sys.stderr, force_terminal=rich_force_colors)
+    stderr = rich.console.Console(file=sys.stderr, force_terminal=nf_core.utils.rich_force_colors())
     stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False)
     stderr.print("[blue]          ___     __   __   __   ___     [green]/,-._.--~\\", highlight=False)
     stderr.print("[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {", highlight=False)
@@ -119,7 +114,7 @@ def nf_core_cli(verbose, log_file):
     log.addHandler(
         rich.logging.RichHandler(
             level=logging.DEBUG if verbose else logging.INFO,
-            console=rich.console.Console(file=sys.stderr, force_terminal=rich_force_colors),
+            console=rich.console.Console(file=sys.stderr, force_terminal=nf_core.utils.rich_force_colors()),
             show_time=False,
             markup=True,
         )
diff --git a/nf_core/launch.py b/nf_core/launch.py
index 488d19c22..162cf5062 100644
--- a/nf_core/launch.py
+++ b/nf_core/launch.py
@@ -640,7 +640,7 @@ def validate_pattern(val):
     def print_param_header(self, param_id, param_obj):
         if "description" not in param_obj and "help_text" not in param_obj:
             return
-        console = Console()
+        console = Console(nf_core.utils.rich_force_colors())
         console.print("\n")
         console.print(param_obj.get("title", param_id), style="bold")
         if "description" in param_obj:
diff --git a/nf_core/lint.py b/nf_core/lint.py
index 9b62da320..1fb0aeac6 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -1307,7 +1307,7 @@ def check_schema_params(self):
     def print_results(self, show_passed=False):
 
         log.debug("Printing final results")
-        console = Console()
+        console = Console(force_terminal=nf_core.utils.rich_force_colors())
 
         # Helper function to format test links nicely
         def format_result(test_results, table):
diff --git a/nf_core/utils.py b/nf_core/utils.py
index c0eb461e3..f09c4bd3c 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -43,6 +43,15 @@ def check_if_outdated(current_version=None, remote_version=None, source_url="htt
     return (is_outdated, current_version, remote_version)
 
 
+def rich_force_colors():
+    """
+    Check if any environment variables are set to force Rich to use coloured output
+    """
+    if os.getenv("GITHUB_ACTIONS") or os.getenv("FORCE_COLOR") or os.getenv("PY_COLORS"):
+        return True
+    return None
+
+
 def fetch_wf_config(wf_path):
     """Uses Nextflow to retrieve the the configuration variables
     from a Nextflow workflow.

From d2ee7b69fba6b4d47874bed83a9adb17da644762 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 12:26:04 +0100
Subject: [PATCH 05/51] Add tests for new utils function

---
 tests/test_utils.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tests/test_utils.py b/tests/test_utils.py
index 9c73919ad..f4874506b 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -4,6 +4,7 @@
 
 import nf_core.utils
 
+import os
 import unittest
 
 
@@ -39,3 +40,15 @@ def test_check_if_outdated_5(self):
         remote_version = "1.11"
         is_outdated, current, remote = nf_core.utils.check_if_outdated(current_version, remote_version)
         assert is_outdated
+
+    def test_rich_force_colours_false(self):
+        os.environ.pop("GITHUB_ACTIONS", None)
+        os.environ.pop("FORCE_COLOR", None)
+        os.environ.pop("PY_COLORS", None)
+        assert nf_core.utils.rich_force_colors() is None
+
+    def test_rich_force_colours_true(self):
+        os.environ["GITHUB_ACTIONS"] = True
+        os.environ.pop("FORCE_COLOR", None)
+        os.environ.pop("PY_COLORS", None)
+        assert nf_core.utils.rich_force_colors() is True

From e9d7c86cf18ebbec0918b751a1f87beffe282e1c Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 12:33:25 +0100
Subject: [PATCH 06/51] Fix new utils test

---
 tests/test_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_utils.py b/tests/test_utils.py
index f4874506b..b533abb7a 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -48,7 +48,7 @@ def test_rich_force_colours_false(self):
         assert nf_core.utils.rich_force_colors() is None
 
     def test_rich_force_colours_true(self):
-        os.environ["GITHUB_ACTIONS"] = True
+        os.environ["GITHUB_ACTIONS"] = "1"
         os.environ.pop("FORCE_COLOR", None)
         os.environ.pop("PY_COLORS", None)
         assert nf_core.utils.rich_force_colors() is True

From cfe7ce5481329ed8b7a0754d81e596eecc931251 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 13:06:04 +0100
Subject: [PATCH 07/51] Missed a function argument name

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

diff --git a/nf_core/launch.py b/nf_core/launch.py
index 162cf5062..8d64a612b 100644
--- a/nf_core/launch.py
+++ b/nf_core/launch.py
@@ -640,7 +640,7 @@ def validate_pattern(val):
     def print_param_header(self, param_id, param_obj):
         if "description" not in param_obj and "help_text" not in param_obj:
             return
-        console = Console(nf_core.utils.rich_force_colors())
+        console = Console(force_terminal=nf_core.utils.rich_force_colors())
         console.print("\n")
         console.print(param_obj.get("title", param_id), style="bold")
         if "description" in param_obj:

From 99bf59234ddba8591cbeb2b1dc6cb93a48b994ad Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 13:06:40 +0100
Subject: [PATCH 08/51] Changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e07164df..362b1dda6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,8 @@
 
 ### Linting
 
+* Updated code to display colours in GitHub Actions log output
+
 ### Other
 
 ## [v1.11 - Iron Tiger](https://github.com/nf-core/tools/releases/tag/1.11) - [2020-10-27]

From c77ccb3591ed404329cd7ebbef09ac84beffff98 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 13:34:57 +0100
Subject: [PATCH 09/51] Get GitHub issue templates working again

---
 .github/ISSUE_TEMPLATE/bug_report.md          | 44 +++++++++++++++++++
 .github/ISSUE_TEMPLATE/config.yml             |  8 ++++
 .github/ISSUE_TEMPLATE/feature_request.md     | 32 ++++++++++++++
 CHANGELOG.md                                  |  2 +
 .../.github/ISSUE_TEMPLATE/bug_report.md      |  7 ++-
 .../.github/ISSUE_TEMPLATE/config.yml         |  8 ++++
 .../.github/ISSUE_TEMPLATE/feature_request.md |  6 +++
 7 files changed, 106 insertions(+), 1 deletion(-)
 create mode 100644 .github/ISSUE_TEMPLATE/bug_report.md
 create mode 100644 .github/ISSUE_TEMPLATE/config.yml
 create mode 100644 .github/ISSUE_TEMPLATE/feature_request.md
 create mode 100644 nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/config.yml

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
new file mode 100644
index 000000000..9023381e9
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,44 @@
+---
+name: Bug report
+about: Report something that is broken or incorrect
+labels: bug
+---
+
+<!--
+# nf-core/tools bug report
+
+Hi there!
+
+Thanks for telling us about a problem with the nf-core/tools package.
+Please delete this text and anything that's not relevant from the template below:
+-->
+
+## Description of the bug
+
+<!-- A clear and concise description of what the bug is. -->
+
+## Steps to reproduce
+
+Steps to reproduce the behaviour:
+
+1. Command line: <!-- [e.g. `nf-core lint ...`] -->
+2. See error: <!-- [Please provide your error message] -->
+
+## Expected behaviour
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+## System
+
+- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
+- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
+- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
+- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
+
+## Nextflow Installation
+
+- Version: <!-- [e.g. 19.10.0] -->
+
+## Additional context
+
+<!-- Add any other context about the problem here. -->
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 000000000..2a0317913
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #tools channel"
+    url: https://nfcore.slack.com/channels/tools
+    about: Discussion about the nf-core/tools package
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
new file mode 100644
index 000000000..8c4e9237f
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -0,0 +1,32 @@
+---
+name: Feature request
+about: Suggest an idea for the nf-core website
+labels: enhancement
+---
+
+<!--
+# nf-core/tools feature request
+
+Hi there!
+
+Thanks for suggesting a new feature for the nf-core/tools package!
+Please delete this text and anything that's not relevant from the template below:
+-->
+
+## Is your feature request related to a problem? Please describe
+
+<!-- A clear and concise description of what the problem is. -->
+
+<!-- e.g. [I'm always frustrated when ...] -->
+
+## Describe the solution you'd like
+
+<!-- A clear and concise description of what you want to happen. -->
+
+## Describe alternatives you've considered
+
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
+
+## Additional context
+
+<!-- Add any other context about the feature request here. -->
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 362b1dda6..ee558c03c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@
 
 ### Template
 
+* Updated GitHub issue templates, which had stopped working
+
 ### Linting
 
 * Updated code to display colours in GitHub Actions log output
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/bug_report.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/bug_report.md
index 30a5ef8b4..6f384d628 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/bug_report.md
@@ -1,10 +1,15 @@
+---
+name: Bug report
+about: Report something that is broken or incorrect
+labels: bug
+---
+
 <!--
 # {{ cookiecutter.name }} bug report
 
 Hi there!
 
 Thanks for telling us about a problem with the pipeline.
-
 Please delete this text and anything that's not relevant from the template below:
 -->
 
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/config.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 000000000..c812ac10f
--- /dev/null
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #{{ cookiecutter.short_name }} channel"
+    url: https://nfcore.slack.com/channels/{{ cookiecutter.short_name }}
+    about: Discussion about the {{ cookiecutter.name }} pipeline
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/feature_request.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/feature_request.md
index 199fb5d52..27176dcc5 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/feature_request.md
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/feature_request.md
@@ -1,3 +1,9 @@
+---
+name: Feature request
+about: Suggest an idea for the nf-core website
+labels: enhancement
+---
+
 <!--
 # {{ cookiecutter.name }} feature request
 

From 1ed590abd7ffa5f3b31c51d3ff00bcb221d0b4f7 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 21:39:31 +0100
Subject: [PATCH 10/51] Make some lint messages shorter

---
 README.md       |  4 ++--
 nf_core/lint.py | 14 ++++++--------
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 99a8c3257..d40e05c4e 100644
--- a/README.md
+++ b/README.md
@@ -478,8 +478,8 @@ $ nf-core lint .
 │ [!] 3 Test Warnings                                                                                      │
 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────┤
 │ https://nf-co.re/errors#5: GitHub Actions AWS full test should test full datasets: nf-core-testpipeline… │
-│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::fastqc=0.11.8, 0.11.9 avail… │
-│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::multiqc=1.7, 1.9 available   │
+│ https://nf-co.re/errors#8: Conda dep outdated: bioconda::fastqc=0.11.8, 0.11.9 available                 │
+│ https://nf-co.re/errors#8: Conda dep outdated: bioconda::multiqc=1.7, 1.9 available                      │
 ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ╭───────────────────────╮
 │ LINT RESULTS SUMMARY  │
diff --git a/nf_core/lint.py b/nf_core/lint.py
index 1fb0aeac6..280d9ed52 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -1015,9 +1015,9 @@ def check_conda_env_yaml(self):
                 try:
                     assert dep.count("=") in [1, 2]
                 except AssertionError:
-                    self.failed.append((8, "Conda dependency did not have pinned version number: `{}`".format(dep)))
+                    self.failed.append((8, "Conda dep did not have pinned version number: `{}`".format(dep)))
                 else:
-                    self.passed.append((8, "Conda dependency had pinned version number: `{}`".format(dep)))
+                    self.passed.append((8, "Conda dep had pinned version number: `{}`".format(dep)))
 
                     try:
                         depname, depver = dep.split("=")[:2]
@@ -1027,16 +1027,14 @@ def check_conda_env_yaml(self):
                     else:
                         # Check that required version is available at all
                         if depver not in self.conda_package_info[dep].get("versions"):
-                            self.failed.append((8, "Conda dependency had an unknown version: {}".format(dep)))
+                            self.failed.append((8, "Conda dep had unknown version: {}".format(dep)))
                             continue  # No need to test for latest version, continue linting
                         # Check version is latest available
                         last_ver = self.conda_package_info[dep].get("latest_version")
                         if last_ver is not None and last_ver != depver:
-                            self.warned.append(
-                                (8, "Conda package is not latest available: `{}`, `{}` available".format(dep, last_ver))
-                            )
+                            self.warned.append((8, "Conda dep outdated: `{}`, `{}` available".format(dep, last_ver)))
                         else:
-                            self.passed.append((8, "Conda package is latest available: `{}`".format(dep)))
+                            self.passed.append((8, "Conda package is the latest available: `{}`".format(dep)))
 
             elif isinstance(dep, dict):
                 for pip_dep in dep.get("pip", []):
@@ -1203,7 +1201,7 @@ def check_pipeline_todos(self):
                                 .replace("TODO nf-core: ", "")
                                 .strip()
                             )
-                            self.warned.append((10, "TODO string found in `{}`: _{}_".format(fname, l)))
+                            self.warned.append((10, "TODO string in `{}`: _{}_".format(fname, l)))
 
     def check_pipeline_name(self):
         """Check whether pipeline name adheres to lower case/no hyphen naming convention"""

From b1f07cfa251ec1376b28c6240d81c024ad7bf934 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 21:45:34 +0100
Subject: [PATCH 11/51] Don't lint for dockerfile base image if running
 nf-core/tools dev version

---
 nf_core/lint.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/nf_core/lint.py b/nf_core/lint.py
index 1fb0aeac6..eb0bc94f5 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -1165,13 +1165,15 @@ def check_conda_dockerfile(self):
             return
 
         expected_strings = [
-            "FROM nfcore/base:{}".format("dev" if "dev" in self.version else self.version),
             "COPY environment.yml /",
             "RUN conda env create --quiet -f /environment.yml && conda clean -a",
             "RUN conda env export --name {} > {}.yml".format(self.conda_config["name"], self.conda_config["name"]),
             "ENV PATH /opt/conda/envs/{}/bin:$PATH".format(self.conda_config["name"]),
         ]
 
+        if "dev" not in self.version:
+            expected_strings.append("FROM nfcore/base:{}".format(self.version))
+
         difference = set(expected_strings) - set(self.dockerfile)
         if not difference:
             self.passed.append((9, "Found all expected strings in Dockerfile file"))

From 07bc9e0125a16a2a0745f677312be8123d30f0a2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Nov 2020 21:47:35 +0100
Subject: [PATCH 12/51] Changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 362b1dda6..3edba0eeb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@
 ### Linting
 
 * Updated code to display colours in GitHub Actions log output
+* Allow tests to pass with dev version of nf-core/tools (previous failure due to base image version)
 
 ### Other
 

From 0f9cf9210fae9e6f64417d6797ab24f2f9709bf4 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 7 Nov 2020 00:10:44 +0100
Subject: [PATCH 13/51] Use pull_request_target event for branch protection CI

Closes nf-core/tools#765
---
 .github/workflows/branch.yml                           |  9 ++++-----
 .../.github/workflows/branch.yml                       | 10 +++++-----
 2 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 9463a5130..755bd4646 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -2,19 +2,18 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to master branch on the repository
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
-  pull_request:
+  pull_request_target:
     branches: [master]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/tools'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request_target.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -22,9 +21,9 @@ jobs:
         uses: mshick/add-pr-comment@v1
         with:
           message: |
-            Hi @${{ github.event.pull_request.user.login }},
+            Hi @${{ github.event.pull_request_target.user.login }},
 
-            It looks like this pull-request has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch. The `master` branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+            It looks like this pull-request has been made against the ${{github.event.pull_request_target.head.repo.full_name}} `master` branch. The `master` branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request_target.head.repo.full_name}} `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
 
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml
index a561ad54f..7b9c9e5c9 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml
@@ -2,7 +2,7 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to master branch on the repository
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
-  pull_request:
+  pull_request_target:
     branches: [master]
 
 jobs:
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == '{{cookiecutter.name}}'
         run: |
-          { [[ {% raw %}${{github.event.pull_request.head.repo.full_name}}{% endraw %} == {{cookiecutter.name}} ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ {% raw %}${{github.event.pull_request_target.head.repo.full_name}}{% endraw %} == {{cookiecutter.name}} ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
 {% raw %}
       # If the above check failed, post a comment on the PR explaining the failure
@@ -23,11 +23,11 @@ jobs:
         uses: mshick/add-pr-comment@v1
         with:
           message: |
-            Hi @${{ github.event.pull_request.user.login }},
+            Hi @${{ github.event.pull_request_target.user.login }},
 
-            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            It looks like this pull-request is has been made against the ${{github.event.pull_request_target.head.repo.full_name}} `master` branch.
             The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request_target.head.repo.full_name}} `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
 

From f3314119f91557f31c14dbdc02184af07a9c46ac Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 7 Nov 2020 00:12:27 +0100
Subject: [PATCH 14/51] Changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3edba0eeb..922745f58 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@
 
 ### Template
 
+* Make branch-protection CI comments work with PRs from forks [[#765](https://github.com/nf-core/tools/issues/765)]
+
 ### Linting
 
 * Updated code to display colours in GitHub Actions log output

From bbcbcfd0bc46857d53fcb318a62292b3b61ab40b Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 7 Nov 2020 00:14:17 +0100
Subject: [PATCH 15/51] Update linting to check for pull_request_target instead
 of pull_request

---
 nf_core/lint.py                                               | 4 ++--
 .../minimalworkingexample/.github/workflows/branch.yml        | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/lint.py b/nf_core/lint.py
index e285a5fb6..dc49b6470 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -645,7 +645,7 @@ def check_actions_branch_protection(self):
             # Check that the action is turned on for PRs to master
             try:
                 # Yaml 'on' parses as True - super weird
-                assert "master" in branchwf[True]["pull_request"]["branches"]
+                assert "master" in branchwf[True]["pull_request_target"]["branches"]
             except (AssertionError, KeyError):
                 self.failed.append(
                     (5, "GitHub Actions 'branch' workflow should be triggered for PRs to master: `{}`".format(fn))
@@ -665,7 +665,7 @@ def check_actions_branch_protection(self):
                 # Don't use .format() as the squiggly brackets get ridiculous
                 has_run = step.get(
                     "run", ""
-                ).strip() == '{ [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/PIPELINENAME ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]'.replace(
+                ).strip() == '{ [[ ${{github.event.pull_request_target.head.repo.full_name}} == nf-core/PIPELINENAME ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]'.replace(
                     "PIPELINENAME", self.pipeline_name.lower()
                 )
                 if has_name and has_if and has_run:
diff --git a/tests/lint_examples/minimalworkingexample/.github/workflows/branch.yml b/tests/lint_examples/minimalworkingexample/.github/workflows/branch.yml
index 49836c50f..60d8a05d2 100644
--- a/tests/lint_examples/minimalworkingexample/.github/workflows/branch.yml
+++ b/tests/lint_examples/minimalworkingexample/.github/workflows/branch.yml
@@ -2,7 +2,7 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to master branch on the repository
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
-  pull_request:
+  pull_request_target:
     branches: [master]
 
 jobs:
@@ -13,4 +13,4 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/tools'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request_target.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]

From b4f0c4084737ae7a7bc640c32665f1adcef1aecc Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 10 Nov 2020 19:15:33 +0100
Subject: [PATCH 16/51] Change github.event.pull_request_target back to
 github.event.pull_request for branch CI tests

---
 .github/workflows/branch.yml                              | 6 +++---
 nf_core/lint.py                                           | 2 +-
 .../.github/workflows/branch.yml                          | 8 ++++----
 .../minimalworkingexample/.github/workflows/branch.yml    | 2 +-
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 755bd4646..b703dff38 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/tools'
         run: |
-          { [[ ${{github.event.pull_request_target.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -21,9 +21,9 @@ jobs:
         uses: mshick/add-pr-comment@v1
         with:
           message: |
-            Hi @${{ github.event.pull_request_target.user.login }},
+            Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request has been made against the ${{github.event.pull_request_target.head.repo.full_name}} `master` branch. The `master` branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request_target.head.repo.full_name}} `dev` branch.
+            It looks like this pull-request has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch. The `master` branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
 
diff --git a/nf_core/lint.py b/nf_core/lint.py
index dc49b6470..b3571c1ec 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -665,7 +665,7 @@ def check_actions_branch_protection(self):
                 # Don't use .format() as the squiggly brackets get ridiculous
                 has_run = step.get(
                     "run", ""
-                ).strip() == '{ [[ ${{github.event.pull_request_target.head.repo.full_name}} == nf-core/PIPELINENAME ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]'.replace(
+                ).strip() == '{ [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/PIPELINENAME ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]'.replace(
                     "PIPELINENAME", self.pipeline_name.lower()
                 )
                 if has_name and has_if and has_run:
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml
index 7b9c9e5c9..f89d40ba7 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == '{{cookiecutter.name}}'
         run: |
-          { [[ {% raw %}${{github.event.pull_request_target.head.repo.full_name}}{% endraw %} == {{cookiecutter.name}} ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ {% raw %}${{github.event.pull_request.head.repo.full_name}}{% endraw %} == {{cookiecutter.name}} ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
 {% raw %}
       # If the above check failed, post a comment on the PR explaining the failure
@@ -23,11 +23,11 @@ jobs:
         uses: mshick/add-pr-comment@v1
         with:
           message: |
-            Hi @${{ github.event.pull_request_target.user.login }},
+            Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the ${{github.event.pull_request_target.head.repo.full_name}} `master` branch.
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
             The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request_target.head.repo.full_name}} `dev` branch.
+            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
 
diff --git a/tests/lint_examples/minimalworkingexample/.github/workflows/branch.yml b/tests/lint_examples/minimalworkingexample/.github/workflows/branch.yml
index 60d8a05d2..1d1305cab 100644
--- a/tests/lint_examples/minimalworkingexample/.github/workflows/branch.yml
+++ b/tests/lint_examples/minimalworkingexample/.github/workflows/branch.yml
@@ -13,4 +13,4 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/tools'
         run: |
-          { [[ ${{github.event.pull_request_target.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]

From ba2e85334fb4f4097766061d3e5042fc0c0d3b62 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 10 Nov 2020 22:14:38 +0100
Subject: [PATCH 17/51] New GitHub Actions workflow to add lint results to a PR
 as a comment

---
 .../.github/workflows/linting.yml             | 11 ++++++--
 .../.github/workflows/linting_comment.yml     | 27 +++++++++++++++++++
 2 files changed, 36 insertions(+), 2 deletions(-)
 create mode 100644 nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting_comment.yml

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting.yml
index 3298bafb7..aa58239a2 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting.yml
@@ -57,12 +57,19 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE}
+        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE} --markdown lint_results.md
+
+      - name: Save PR number
+        if: ${{ always() }}
+        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v2
         with:
           name: linting-log-file
-          path: lint_log.txt
+          path: |
+            lint_log.txt
+            lint_results.md
+            PR_number.txt
 {% endraw %}
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting_comment.yml
new file mode 100644
index 000000000..0471addcc
--- /dev/null
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting_comment.yml
@@ -0,0 +1,27 @@
+name: nf-core linting comment
+# This workflow is triggered after the linting action is complete
+# It posts an automated comment to the PR, even if the PR is coming from a fork
+
+on:
+  workflow_run:
+    workflows: ["nf-core linting"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download lint results
+        uses: dawidd6/action-download-artifact@v2
+        with:
+          workflow: linting.yml
+
+      - name: Get PR number
+        id: pr_number
+        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+
+      - name: Post PR comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          number: ${{ steps.pr_number.outputs.pr_number }}
+          path: linting-logs/lint_results.md

From 75bd22beed02d521b32d09fcaa5615c9ef341d7d Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 09:12:33 +0100
Subject: [PATCH 18/51] Remove lint code that posts GH PR comments

---
 CHANGELOG.md       |  4 +++-
 nf_core/lint.py    | 57 ----------------------------------------------
 tests/test_lint.py | 31 -------------------------
 3 files changed, 3 insertions(+), 89 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 651f67121..7b541bc7f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,13 +6,15 @@
 
 ### Template
 
-* Make branch-protection CI comments work with PRs from forks [[#765](https://github.com/nf-core/tools/issues/765)]
+* Make CI comments work with PRs from forks [[#765](https://github.com/nf-core/tools/issues/765)]
+  * Branch protection and linting results should now show on all PRs
 * Updated GitHub issue templates, which had stopped working
 
 ### Linting
 
 * Updated code to display colours in GitHub Actions log output
 * Allow tests to pass with dev version of nf-core/tools (previous failure due to base image version)
+* Lint code no longer tries to post GitHub PR comments. This is now done in a GitHub Action only.
 
 ### Other
 
diff --git a/nf_core/lint.py b/nf_core/lint.py
index b3571c1ec..de8d2fa56 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -78,9 +78,6 @@ def run_linting(pipeline_dir, release_mode=False, show_passed=False, md_fn=None,
     if json_fn is not None:
         lint_obj.save_json_results(json_fn)
 
-    # Try to post comment to a GitHub PR
-    lint_obj.github_comment()
-
     # Exit code
     if len(lint_obj.failed) > 0:
         if release_mode:
@@ -1470,60 +1467,6 @@ def save_json_results(self, json_fn):
         with open(json_fn, "w") as fh:
             json.dump(results, fh, indent=4)
 
-    def github_comment(self):
-        """
-        If we are running in a GitHub PR, try to post results as a comment
-        """
-        if os.environ.get("GITHUB_TOKEN", "") == "":
-            log.debug("Environment variable GITHUB_TOKEN not found")
-            return
-        if os.environ.get("GITHUB_COMMENTS_URL", "") == "":
-            log.debug("Environment variable GITHUB_COMMENTS_URL not found")
-            return
-        try:
-            headers = {"Authorization": "token {}".format(os.environ["GITHUB_TOKEN"])}
-            # Get existing comments - GET
-            get_r = requests.get(url=os.environ["GITHUB_COMMENTS_URL"], headers=headers)
-            if get_r.status_code == 200:
-
-                # Look for an existing comment to update
-                update_url = False
-                for comment in get_r.json():
-                    if comment["user"]["login"] == "github-actions[bot]" and comment["body"].startswith(
-                        "\n#### `nf-core lint` overall result"
-                    ):
-                        # Update existing comment - PATCH
-                        log.info("Updating GitHub comment")
-                        update_r = requests.patch(
-                            url=comment["url"],
-                            data=json.dumps({"body": self.get_results_md().replace("Posted", "**Updated**")}),
-                            headers=headers,
-                        )
-                        return
-
-                # Create new comment - POST
-                if len(self.warned) > 0 or len(self.failed) > 0:
-                    r = requests.post(
-                        url=os.environ["GITHUB_COMMENTS_URL"],
-                        data=json.dumps({"body": self.get_results_md()}),
-                        headers=headers,
-                    )
-                    try:
-                        r_json = json.loads(r.content)
-                        response_pp = json.dumps(r_json, indent=4)
-                    except:
-                        r_json = r.content
-                        response_pp = r.content
-
-                    if r.status_code == 201:
-                        log.info("Posted GitHub comment: {}".format(r_json["html_url"]))
-                        log.debug(response_pp)
-                    else:
-                        log.warning("Could not post GitHub comment: '{}'\n{}".format(r.status_code, response_pp))
-
-        except Exception as e:
-            log.warning("Could not post GitHub comment: {}\n{}".format(os.environ["GITHUB_COMMENTS_URL"], e))
-
     def _wrap_quotes(self, files):
         if not isinstance(files, list):
             files = [files]
diff --git a/tests/test_lint.py b/tests/test_lint.py
index c3243018e..ad609389b 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -587,34 +587,3 @@ def json(self):
                     return []
 
         return MockResponse(kwargs["url"])
-
-    @mock.patch("requests.get", side_effect=mock_gh_get_comments)
-    @mock.patch("requests.post")
-    def test_gh_comment_post(self, mock_get, mock_post):
-        """
-        Test updating a Github comment with the lint results
-        """
-        os.environ["GITHUB_COMMENTS_URL"] = "https://github.com"
-        os.environ["GITHUB_TOKEN"] = "testing"
-        os.environ["GITHUB_PR_COMMIT"] = "abcdefg"
-        # Don't run testing, just fake some testing results
-        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
-        lint_obj.failed.append((1, "This test failed"))
-        lint_obj.passed.append((2, "This test also passed"))
-        lint_obj.warned.append((2, "This test gave a warning"))
-        lint_obj.github_comment()
-
-    @mock.patch("requests.get", side_effect=mock_gh_get_comments)
-    @mock.patch("requests.post")
-    def test_gh_comment_update(self, mock_get, mock_post):
-        """
-        Test updating a Github comment with the lint results
-        """
-        os.environ["GITHUB_COMMENTS_URL"] = "existing_comment"
-        os.environ["GITHUB_TOKEN"] = "testing"
-        # Don't run testing, just fake some testing results
-        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
-        lint_obj.failed.append((1, "This test failed"))
-        lint_obj.passed.append((2, "This test also passed"))
-        lint_obj.warned.append((2, "This test gave a warning"))
-        lint_obj.github_comment()

From 975d34e15c6d7acf6a32fa3b650572894ac742e2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 09:15:07 +0100
Subject: [PATCH 19/51] Lint results markdown - only post summary counts if > 0
 tests

---
 nf_core/lint.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/nf_core/lint.py b/nf_core/lint.py
index de8d2fa56..733ff9481 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -1372,8 +1372,10 @@ def get_results_md(self):
             overall_result = "Failed :x:"
 
         # List of tests for details
+        test_failure_count = ""
         test_failures = ""
         if len(self.failed) > 0:
+            test_failure_count = "\n-| ❌ {:3d} tests failed       |-".format(len(self.failed))
             test_failures = "### :x: Test failures:\n\n{}\n\n".format(
                 "\n".join(
                     [
@@ -1383,8 +1385,10 @@ def get_results_md(self):
                 )
             )
 
+        test_warning_count = ""
         test_warnings = ""
         if len(self.warned) > 0:
+            test_warning_count = "\n!| ❗ {:3d} tests had warnings |!".format(len(self.warned))
             test_warnings = "### :heavy_exclamation_mark: Test warnings:\n\n{}\n\n".format(
                 "\n".join(
                     [
@@ -1394,8 +1398,10 @@ def get_results_md(self):
                 )
             )
 
+        test_passe_count = ""
         test_passes = ""
         if len(self.passed) > 0:
+            test_passed_count = "\n+| ✅ {:3d} tests passed       |+".format(len(self.passed))
             test_passes = "### :white_check_mark: Tests passed:\n\n{}\n\n".format(
                 "\n".join(
                     [
@@ -1413,10 +1419,7 @@ def get_results_md(self):
 
         {}
 
-        ```diff
-        +| ✅ {:2d} tests passed       |+
-        !| ❗ {:2d} tests had warnings |!
-        -| ❌ {:2d} tests failed       |-
+        ```diff{}{}{}
         ```
 
         <details>
@@ -1431,9 +1434,9 @@ def get_results_md(self):
         ).format(
             overall_result,
             "Posted for pipeline commit {}".format(self.git_sha[:7]) if self.git_sha is not None else "",
-            len(self.passed),
-            len(self.warned),
-            len(self.failed),
+            test_passed_count,
+            test_warning_count,
+            test_failure_count,
             test_failures,
             test_warnings,
             test_passes,

From 379d3af5639897e9ee5778183131a1ab7b73aa43 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 09:40:50 +0100
Subject: [PATCH 20/51] Don't try to parse linting_comment.yml with
 cookiecutter

---
 .../.github/workflows/linting_comment.yml                       | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting_comment.yml
index 0471addcc..0c718c0d9 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting_comment.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting_comment.yml
@@ -1,3 +1,4 @@
+{% raw %}
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
@@ -25,3 +26,4 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
+{% endraw %}

From 5db86b01f07d47ca63560a5ef836426a5f0ad0f2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 11:12:19 +0100
Subject: [PATCH 21/51] Split docker push GHA workflows, update trigger for AWS
 full test

---
 .../.github/workflows/awsfulltest.yml         |  5 ++--
 .../.github/workflows/push_dockerhub_dev.yml  | 28 +++++++++++++++++++
 ...ckerhub.yml => push_dockerhub_release.yml} | 15 ++--------
 3 files changed, 33 insertions(+), 15 deletions(-)
 create mode 100644 nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub_dev.yml
 rename nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/{push_dockerhub.yml => push_dockerhub_release.yml} (69%)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awsfulltest.yml
index 3054b61db..e44229bae 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awsfulltest.yml
@@ -4,8 +4,9 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  workflow_run:
+    workflows: ["nf-core Docker push (release)"]
+    types: [completed]
   workflow_dispatch:
 
 jobs:
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub_dev.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub_dev.yml
new file mode 100644
index 000000000..0303241f1
--- /dev/null
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub_dev.yml
@@ -0,0 +1,28 @@
+name: nf-core Docker push (dev)
+# This builds the docker image and pushes it to DockerHub
+# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
+on:
+  push:
+    branches:
+      - dev
+
+jobs:
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub (dev)
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: {% raw %}${{{% endraw %} github.repository == '{{ cookiecutter.name }}' {% raw %}}}{% endraw %}
+    env:
+      DOCKERHUB_USERNAME: {% raw %}${{ secrets.DOCKERHUB_USERNAME }}{% endraw %}
+      DOCKERHUB_PASS: {% raw %}${{ secrets.DOCKERHUB_PASS }}{% endraw %}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache . -t {{ cookiecutter.name_docker }}:dev
+
+      - name: Push Docker image to DockerHub (dev)
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push {{ cookiecutter.name_docker }}:dev
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub_release.yml
similarity index 69%
rename from nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub.yml
rename to nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub_release.yml
index 0035185f9..d5e260af9 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/push_dockerhub_release.yml
@@ -1,16 +1,13 @@
-name: nf-core Docker push
+name: nf-core Docker push (release)
 # This builds the docker image and pushes it to DockerHub
 # Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
 on:
-  push:
-    branches:
-      - dev
   release:
     types: [published]
 
 jobs:
   push_dockerhub:
-    name: Push new Docker image to Docker Hub
+    name: Push new Docker image to Docker Hub (release)
     runs-on: ubuntu-latest
     # Only run for the nf-core repo, for releases and merged PRs
     if: {% raw %}${{{% endraw %} github.repository == '{{ cookiecutter.name }}' {% raw %}}}{% endraw %}
@@ -24,15 +21,7 @@ jobs:
       - name: Build new docker image
         run: docker build --no-cache . -t {{ cookiecutter.name_docker }}:latest
 
-      - name: Push Docker image to DockerHub (dev)
-        if: {% raw %}${{ github.event_name == 'push' }}{% endraw %}
-        run: |
-          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker tag {{ cookiecutter.name_docker }}:latest {{ cookiecutter.name_docker }}:dev
-          docker push {{ cookiecutter.name_docker }}:dev
-
       - name: Push Docker image to DockerHub (release)
-        if: {% raw %}${{ github.event_name == 'release' }}{% endraw %}
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
           docker push {{ cookiecutter.name_docker }}:latest

From 28ca63b783bd54651244f0e81cb42c3c7c40bb6b Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 11:15:20 +0100
Subject: [PATCH 22/51] Changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7b541bc7f..ced479859 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@
 * Make CI comments work with PRs from forks [[#765](https://github.com/nf-core/tools/issues/765)]
   * Branch protection and linting results should now show on all PRs
 * Updated GitHub issue templates, which had stopped working
+* Refactored GitHub Actions so that the AWS full-scale tests are triggered after docker build is finished
 
 ### Linting
 

From 68128afd24268710a060811b12f22a9a0b3cf52b Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 11:39:44 +0100
Subject: [PATCH 23/51] Update lint tests to look for new workflow trigger on
 AWS full size tests

---
 nf_core/lint.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/nf_core/lint.py b/nf_core/lint.py
index 733ff9481..261fcd6bd 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -843,11 +843,10 @@ def check_actions_awsfulltest(self):
 
             # Check that the action is only turned on for published releases
             try:
-                assert "release" in wf[True]
-                assert "published" in wf[True]["release"]["types"]
+                assert "workflow_run" in wf[True]
+                assert wf[True]["workflow_run"]["workflows"] == ["nf-core Docker push (release)"]
+                assert wf[True]["workflow_run"]["types"] == ["completed"]
                 assert "workflow_dispatch" in wf[True]
-                assert "push" not in wf[True]
-                assert "pull_request" not in wf[True]
             except (AssertionError, KeyError, TypeError):
                 self.failed.append(
                     (

From e31a6f9c03a006c01de1db2f03510b3872926c38 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 11:42:35 +0100
Subject: [PATCH 24/51] Update docs

---
 docs/lint_errors.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/docs/lint_errors.md b/docs/lint_errors.md
index d42e85acf..8a1ecde7b 100644
--- a/docs/lint_errors.md
+++ b/docs/lint_errors.md
@@ -238,13 +238,14 @@ You can trigger the tests by going to the `Actions` tab on the pipeline GitHub r
 Additionally, we provide the possibility of testing the pipeline on full size datasets on AWS.
 This should ensure that the pipeline runs as expected on AWS and provide a resource estimation.
 The GitHub Actions workflow is `awsfulltest.yml`, and it can be found in the `.github/workflows/` directory.
-This workflow incurrs higher AWS costs, therefore it should only be triggered on `release` and `workflow_dispatch`.
+This workflow incurrs higher AWS costs, therefore it should only be triggered for releases (`workflow_run` - after the docker hub release workflow) and `workflow_dispatch`.
 You can trigger the tests by going to the `Actions` tab on the pipeline GitHub repository and selecting the `nf-core AWS full size tests` workflow on the left.
 For tests on full data prior to release, [Nextflow Tower](https://tower.nf) launch feature can be employed.
 
 `awsfulltest.yml`: Triggers full sized tests run on AWS batch after releasing.
 
-* Must be only turned on for `release` and `workflow_dispatch`.
+* Must be turned on `workflow_dispatch`.
+* Must be turned on for `workflow_run` with `workflows: ["nf-core Docker push (release)"]` and `types: [completed]`
 * Should run the profile `test_full` that should be edited to provide the links to full-size datasets. If it runs the profile `test` a warning is given.
 
 ## Error #6 - Repository `README.md` tests ## {#6}

From 95afd894fa80aa4a0e48a0e6e897deb57e9fc969 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 11:43:52 +0100
Subject: [PATCH 25/51] Update example file for tests

---
 .../.github/workflows/awsfulltest.yml                      | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/lint_examples/minimalworkingexample/.github/workflows/awsfulltest.yml b/tests/lint_examples/minimalworkingexample/.github/workflows/awsfulltest.yml
index ef81b9cd5..2045d5014 100644
--- a/tests/lint_examples/minimalworkingexample/.github/workflows/awsfulltest.yml
+++ b/tests/lint_examples/minimalworkingexample/.github/workflows/awsfulltest.yml
@@ -3,8 +3,9 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  workflow_run:
+    workflows: ["nf-core Docker push (release)"]
+    types: [completed]
   workflow_dispatch:
 
 jobs:
@@ -34,4 +35,4 @@ jobs:
             --job-name nf-core-tools \
             --job-queue $AWS_JOB_QUEUE \
             --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["nf-core/tools", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://nf-core-awsmegatests/tools/results-'"${GITHUB_SHA}"' -w s3://nf-core-awsmegatests/tools/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
\ No newline at end of file
+            --container-overrides '{"command": ["nf-core/tools", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://nf-core-awsmegatests/tools/results-'"${GITHUB_SHA}"' -w s3://nf-core-awsmegatests/tools/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

From bf9dada596ba32f6d7bd7594e530a243dd39fcee Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 11:56:59 +0100
Subject: [PATCH 26/51] Linting: Fail if old push_dockerhub.yml still exists

---
 nf_core/lint.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/nf_core/lint.py b/nf_core/lint.py
index 261fcd6bd..bd1e16a2a 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -274,7 +274,8 @@ def check_files_exist(self):
 
             'Singularity',
             'parameters.settings.json',
-            'bin/markdown_to_html.r'
+            'bin/markdown_to_html.r'.
+            '.github/workflows/push_dockerhub.yml'
 
         Files that *should not* be present::
 
@@ -309,7 +310,12 @@ def check_files_exist(self):
         ]
 
         # List of strings. Dails / warns if any of the strings exist.
-        files_fail_ifexists = ["Singularity", "parameters.settings.json", os.path.join("bin", "markdown_to_html.r")]
+        files_fail_ifexists = [
+            "Singularity",
+            "parameters.settings.json",
+            os.path.join("bin", "markdown_to_html.r"),
+            os.path.join(".github", "workflows", "push_dockerhub.yml"),
+        ]
         files_warn_ifexists = [".travis.yml"]
 
         def pf(file_path):

From cfb506e4dfc26ad4b52ba2f74542e2623d1bcffd Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 11:59:04 +0100
Subject: [PATCH 27/51] Changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ced479859..79ef23c17 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
   * Branch protection and linting results should now show on all PRs
 * Updated GitHub issue templates, which had stopped working
 * Refactored GitHub Actions so that the AWS full-scale tests are triggered after docker build is finished
+  * DockerHub push workflow split into two - one for dev, one for releases
 
 ### Linting
 

From f9307a58ab0722091257f5d3c608286f9829b7b7 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 12:01:09 +0100
Subject: [PATCH 28/51] Update test numbers in pytest

---
 tests/test_lint.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_lint.py b/tests/test_lint.py
index ad609389b..d628d70dc 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -45,7 +45,7 @@ def pf(wd, path):
 ]
 
 # The maximum sum of passed tests currently possible
-MAX_PASS_CHECKS = 84
+MAX_PASS_CHECKS = 85
 # The additional tests passed for releases
 ADD_PASS_RELEASE = 1
 
@@ -114,7 +114,7 @@ def test_failing_missingfiles_example(self):
         """Tests for missing files like Dockerfile or LICENSE"""
         lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE)
         lint_obj.check_files_exist()
-        expectations = {"failed": 6, "warned": 2, "passed": 13}
+        expectations = {"failed": 6, "warned": 2, "passed": 14}
         self.assess_lint_status(lint_obj, **expectations)
 
     def test_mit_licence_example_pass(self):

From 7856729bb81a4d78f34bdd4aae835145fe53c82f Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 11 Nov 2020 12:10:05 +0100
Subject: [PATCH 29/51] Docs

---
 docs/lint_errors.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/lint_errors.md b/docs/lint_errors.md
index 8a1ecde7b..1bc6546a2 100644
--- a/docs/lint_errors.md
+++ b/docs/lint_errors.md
@@ -47,6 +47,8 @@ The following files will cause a failure if the _are_ present (to fix, delete th
     deleted and new `nextflow_schema.json` files created instead.
 * `bin/markdown_to_html.r`
   * The old markdown to HTML conversion script, now replaced by `markdown_to_html.py`
+* `.github/workflows/push_dockerhub.yml`
+  * The old dockerhub build script, now split into `.github/workflows/push_dockerhub_dev.yml` and `.github/workflows/push_dockerhub_release.yml`
 
 ## Error #2 - Docker file check failed ## {#2}
 

From a85f06fbe17390cf94da3f0d86963d56f10401e0 Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Thu, 12 Nov 2020 21:20:39 +0100
Subject: [PATCH 30/51] include test_full pipeline template

---
 CHANGELOG.md                                                     | 1 +
 .../{{cookiecutter.name_noslash}}/nextflow.config                | 1 +
 2 files changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ced479859..9edb1da2f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
   * Branch protection and linting results should now show on all PRs
 * Updated GitHub issue templates, which had stopped working
 * Refactored GitHub Actions so that the AWS full-scale tests are triggered after docker build is finished
+* Added import for test_full in nextflow.config
 
 ### Linting
 
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
index 122a916e2..0085111bb 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -75,6 +75,7 @@ profiles {
     podman.enabled = true
   }
   test { includeConfig 'conf/test.config' }
+  test_full { includeConfig 'conf/test_full.config' }
 }
 
 // Load igenomes.config if required

From 9a9abeb6d51d6b8d10b29377e120fa43178db55b Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Mon, 16 Nov 2020 08:44:58 +0100
Subject: [PATCH 31/51] Updated github actions

---
 .../.github/workflows/awsfulltest.yml                         | 2 +-
 .../.github/workflows/awstest.yml                             | 2 +-
 .../{{cookiecutter.name_noslash}}/.github/workflows/ci.yml    | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awsfulltest.yml
index e44229bae..6cb029ecc 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awsfulltest.yml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awstest.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awstest.yml
index d261c7878..911a9c883 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awstest.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/awstest.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
index ce1d56569..75a3337fb 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
@@ -26,9 +26,9 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Check if Dockerfile or Conda environment changed
-        uses: technote-space/get-diff-action@v1
+        uses: technote-space/get-diff-action@v4
         with:
-          PREFIX_FILTER: |
+          FILES: |
             Dockerfile
             environment.yml
 

From 7d339cc070fbca4083291e4d7d1080e4855e8542 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 18 Nov 2020 13:41:59 +0100
Subject: [PATCH 32/51] CI Docker diffs - use env.MATCHED_FILES

With update to GitHub Actions technote-space/get-diff-action, we need to use env.MATCHED_FILES instead of env.GIT_DIFF to see if any of the files listed under FILES have been changed. env.GIT_DIFF basically always returns true, so currently the Docker image always builds.

Docs: https://github.com/marketplace/actions/get-diff-action#examples-of-env

Original PR: https://github.com/nf-core/tools/pull/774
---
 .../{{cookiecutter.name_noslash}}/.github/workflows/ci.yml    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
index 75a3337fb..6176fbbb9 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
@@ -33,11 +33,11 @@ jobs:
             environment.yml
 
       - name: Build new docker image
-        if: env.GIT_DIFF
+        if: env.MATCHED_FILES
         run: docker build --no-cache . -t {{ cookiecutter.name_docker }}:dev
 
       - name: Pull docker image
-        if: {% raw %}${{ !env.GIT_DIFF }}{% endraw %}
+        if: {% raw %}${{ !env.MATCHED_FILES }}{% endraw %}
         run: |
           docker pull {{ cookiecutter.name_docker }}:dev
           docker tag {{ cookiecutter.name_docker }}:dev {{ cookiecutter.name_docker }}:dev

From 0263de1f083a5c2f28087673cbcfa4daea8a5766 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 18 Nov 2020 19:44:45 +0100
Subject: [PATCH 33/51] Switch baseDir to projectDir

---
 .../assets/sendmail_template.txt                   |  2 +-
 .../{{cookiecutter.name_noslash}}/main.nf          | 14 +++++++-------
 .../{{cookiecutter.name_noslash}}/nextflow.config  |  2 +-
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/assets/sendmail_template.txt b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/assets/sendmail_template.txt
index db7637e28..4314c5c80 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/assets/sendmail_template.txt
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/assets/sendmail_template.txt
@@ -14,7 +14,7 @@ Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
 Content-Disposition: inline; filename="{{ cookiecutter.name_noslash }}_logo.png"
 
-<% out << new File("$baseDir/assets/{{ cookiecutter.name_noslash }}_logo.png").
+<% out << new File("$projectDir/assets/{{ cookiecutter.name_noslash }}_logo.png").
   bytes.
   encodeBase64().
   toString().
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
index b30a6727a..f5c767e31 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
@@ -92,10 +92,10 @@ if (workflow.profile.contains('awsbatch')) {
 }
 
 // Stage config files
-ch_multiqc_config = file("$baseDir/assets/multiqc_config.yaml", checkIfExists: true)
+ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
 ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-ch_output_docs = file("$baseDir/docs/output.md", checkIfExists: true)
-ch_output_docs_images = file("$baseDir/docs/images/", checkIfExists: true)
+ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
+ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
 
 /*
  * Create a channel for input read files
@@ -326,18 +326,18 @@ workflow.onComplete {
 
     // Render the TXT template
     def engine = new groovy.text.GStringTemplateEngine()
-    def tf = new File("$baseDir/assets/email_template.txt")
+    def tf = new File("$projectDir/assets/email_template.txt")
     def txt_template = engine.createTemplate(tf).make(email_fields)
     def email_txt = txt_template.toString()
 
     // Render the HTML template
-    def hf = new File("$baseDir/assets/email_template.html")
+    def hf = new File("$projectDir/assets/email_template.html")
     def html_template = engine.createTemplate(hf).make(email_fields)
     def email_html = html_template.toString()
 
     // Render the sendmail template
-    def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
-    def sf = new File("$baseDir/assets/sendmail_template.txt")
+    def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
+    def sf = new File("$projectDir/assets/sendmail_template.txt")
     def sendmail_template = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html = sendmail_template.toString()
 
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
index 0085111bb..58fb7e09f 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -57,7 +57,7 @@ try {
 }
 
 profiles {
-  conda { process.conda = "$baseDir/environment.yml" }
+  conda { process.conda = "$projectDir/environment.yml" }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   docker {
     docker.enabled = true

From d3d9ec118c8a5078e973011c5664551bbb25a024 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 18 Nov 2020 19:47:37 +0100
Subject: [PATCH 34/51] Changelog

---
 CHANGELOG.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9edb1da2f..5a6160153 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,9 @@
   * Branch protection and linting results should now show on all PRs
 * Updated GitHub issue templates, which had stopped working
 * Refactored GitHub Actions so that the AWS full-scale tests are triggered after docker build is finished
-* Added import for test_full in nextflow.config
+* Updated actions to no longer use `set-env` which is now depreciating [[#739](https://github.com/nf-core/tools/issues/739)]
+* Added config import for `test_full` in `nextflow.config`
+* Switched depreciated `$baseDir` to `$projectDir`
 
 ### Linting
 

From 392d2d29945a0ef26d95b6af48f4914d41f0b58c Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 18 Nov 2020 20:02:21 +0100
Subject: [PATCH 35/51] Update sphinx autodocs

---
 docs/api/_src/conf.py      | 5 +++--
 docs/api/_src/index.rst    | 5 ++++-
 docs/api/_src/launch.rst   | 5 +++++
 docs/api/_src/modules.rst  | 5 +++++
 docs/api/_src/schema.rst   | 5 +++++
 docs/api/_src/sync.rst     | 5 +++++
 docs/api/_src/workflow.rst | 5 -----
 7 files changed, 27 insertions(+), 8 deletions(-)
 create mode 100644 docs/api/_src/launch.rst
 create mode 100644 docs/api/_src/modules.rst
 create mode 100644 docs/api/_src/schema.rst
 create mode 100644 docs/api/_src/sync.rst
 delete mode 100644 docs/api/_src/workflow.rst

diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
index e35007f3f..e96464a16 100644
--- a/docs/api/_src/conf.py
+++ b/docs/api/_src/conf.py
@@ -14,6 +14,7 @@
 #
 import os
 import sys
+import nf_core
 
 sys.path.insert(0, os.path.abspath("../../../nf_core"))
 
@@ -24,9 +25,9 @@
 author = "Phil Ewels, Sven Fillinger"
 
 # The short X.Y version
-version = "1.4"
+version = nf_core.__version__
 # The full version, including alpha/beta/rc tags
-release = "1.4"
+release = nf_core.__version__
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/docs/api/_src/index.rst b/docs/api/_src/index.rst
index 35ee30034..793aba7c6 100644
--- a/docs/api/_src/index.rst
+++ b/docs/api/_src/index.rst
@@ -13,11 +13,14 @@ Welcome to nf-core tools API documentation!
    bump_version
    create
    download
+   launch
    licences
    lint
    list
+   modules
+   schema
+   sync
    utils
-   workflow
 
 
 Indices and tables
diff --git a/docs/api/_src/launch.rst b/docs/api/_src/launch.rst
new file mode 100644
index 000000000..3f9a79cb5
--- /dev/null
+++ b/docs/api/_src/launch.rst
@@ -0,0 +1,5 @@
+nf_core.launch
+============
+
+.. automodule:: nf_core.launch
+    :members:
diff --git a/docs/api/_src/modules.rst b/docs/api/_src/modules.rst
new file mode 100644
index 000000000..3d5c82e03
--- /dev/null
+++ b/docs/api/_src/modules.rst
@@ -0,0 +1,5 @@
+nf_core.modules
+============
+
+.. automodule:: nf_core.modules
+    :members:
diff --git a/docs/api/_src/schema.rst b/docs/api/_src/schema.rst
new file mode 100644
index 000000000..bb2da2421
--- /dev/null
+++ b/docs/api/_src/schema.rst
@@ -0,0 +1,5 @@
+nf_core.schema
+============
+
+.. automodule:: nf_core.schema
+    :members:
diff --git a/docs/api/_src/sync.rst b/docs/api/_src/sync.rst
new file mode 100644
index 000000000..1e1fddbb2
--- /dev/null
+++ b/docs/api/_src/sync.rst
@@ -0,0 +1,5 @@
+nf_core.sync
+==============
+
+.. automodule:: nf_core.sync
+    :members:
diff --git a/docs/api/_src/workflow.rst b/docs/api/_src/workflow.rst
deleted file mode 100644
index 7cf9afc71..000000000
--- a/docs/api/_src/workflow.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-nf_core.list
-============
-
-.. automodule:: nf_core.workflow
-    :members:
\ No newline at end of file

From 4c70fabea984b419926f80be8ec51efcdd604499 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 18 Nov 2020 20:03:07 +0100
Subject: [PATCH 36/51] Changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9edb1da2f..e6794e95c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,8 @@
 
 ### Tools helper code
 
+* Updated `nf_core` documentation generator for building [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/)
+
 ### Template
 
 * Make CI comments work with PRs from forks [[#765](https://github.com/nf-core/tools/issues/765)]

From a404d6f1490e14e3e1013db50ee0c19083f84c76 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 18 Nov 2020 20:14:35 +0100
Subject: [PATCH 37/51] Don't use rnaseq in Python tests for environment.yml
 file as it's now DSL2\!

---
 tests/test_licenses.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_licenses.py b/tests/test_licenses.py
index 5458b6b1c..2c1db3915 100644
--- a/tests/test_licenses.py
+++ b/tests/test_licenses.py
@@ -47,7 +47,7 @@ def test_get_environment_file_local(self):
         assert any(["multiqc" in k for k in self.license_obj.conda_config["dependencies"]])
 
     def test_get_environment_file_remote(self):
-        self.license_obj = nf_core.licences.WorkflowLicences("rnaseq")
+        self.license_obj = nf_core.licences.WorkflowLicences("methylseq")
         self.license_obj.get_environment_file()
         assert any(["multiqc" in k for k in self.license_obj.conda_config["dependencies"]])
 

From 89aa46344de4afdc6379723ae859abcba51b2973 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 18 Nov 2020 19:49:45 +0100
Subject: [PATCH 38/51] Min nextflow version

---
 .../{{cookiecutter.name_noslash}}/.github/workflows/ci.yml      | 2 +-
 .../pipeline-template/{{cookiecutter.name_noslash}}/README.md   | 2 +-
 .../{{cookiecutter.name_noslash}}/nextflow.config               | 2 +-
 tests/lint_examples/minimalworkingexample/nextflow.config       | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
index 6176fbbb9..d295d373a 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['19.10.0', '']
+        nxf_ver: ['20.04.0', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md
index 28a731799..6b8859a53 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md
@@ -4,7 +4,7 @@
 
 [![GitHub Actions CI Status](https://github.com/{{ cookiecutter.name }}/workflows/nf-core%20CI/badge.svg)](https://github.com/{{ cookiecutter.name }}/actions)
 [![GitHub Actions Linting Status](https://github.com/{{ cookiecutter.name }}/workflows/nf-core%20linting/badge.svg)](https://github.com/{{ cookiecutter.name }}/actions)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.04.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/{{ cookiecutter.name_docker }}.svg)](https://hub.docker.com/r/{{ cookiecutter.name_docker }})
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
index 58fb7e09f..d245c9134 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -116,7 +116,7 @@ manifest {
   homePage = 'https://github.com/{{ cookiecutter.name }}'
   description = '{{ cookiecutter.description }}'
   mainScript = 'main.nf'
-  nextflowVersion = '>=19.10.0'
+  nextflowVersion = '>=20.04.0'
   version = '{{ cookiecutter.version }}'
 }
 
diff --git a/tests/lint_examples/minimalworkingexample/nextflow.config b/tests/lint_examples/minimalworkingexample/nextflow.config
index cbe2163a9..5bd148751 100644
--- a/tests/lint_examples/minimalworkingexample/nextflow.config
+++ b/tests/lint_examples/minimalworkingexample/nextflow.config
@@ -37,6 +37,6 @@ manifest {
   homePage = 'https://github.com/nf-core/tools'
   description = 'Minimal working example pipeline'
   mainScript = 'main.nf'
-  nextflowVersion = '>=19.10.0'
+  nextflowVersion = '>=20.04.0'
   version = '0.4'
 }

From 4652226796d2540b70f8497ffbe6aa5af0c5030e Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 18 Nov 2020 21:50:10 +0100
Subject: [PATCH 39/51] Changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5a6160153..f6f0f2975 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@
 * Updated actions to no longer use `set-env` which is now depreciating [[#739](https://github.com/nf-core/tools/issues/739)]
 * Added config import for `test_full` in `nextflow.config`
 * Switched depreciated `$baseDir` to `$projectDir`
+* Updated minimum Nextflow version to `20.04.10`
 
 ### Linting
 

From d66369e9e0cd151f1b40022461f5309cd83aa2fd Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 09:38:12 +0100
Subject: [PATCH 40/51] Quietly install Nextflow in CI

---
 .github/workflows/create-lint-wf.yml                            | 2 ++
 .github/workflows/pytest.yml                                    | 2 ++
 .github/workflows/sync.yml                                      | 2 ++
 .../{{cookiecutter.name_noslash}}/.github/workflows/ci.yml      | 2 ++
 .../{{cookiecutter.name_noslash}}/.github/workflows/linting.yml | 2 ++
 .../minimalworkingexample/.github/workflows/ci.yml              | 2 ++
 .../minimalworkingexample/.github/workflows/linting.yml         | 2 ++
 7 files changed, 14 insertions(+)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index dc19a3c7f..f9656a256 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -19,6 +19,8 @@ jobs:
           pip install .
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           mkdir /tmp/nextflow
           cd /tmp/nextflow
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index c87b3b55f..493fb53c2 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -32,6 +32,8 @@ jobs:
         pip install -e .
 
     - name: Install Nextflow
+      env:
+          CAPSULE_LOG: none
       run: |
         mkdir /tmp/nextflow
         cd /tmp/nextflow
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 9e67087de..6d5bd24c6 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -45,6 +45,8 @@ jobs:
           pip install .
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           mkdir /tmp/nextflow
           cd /tmp/nextflow
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
index d295d373a..1e27cafe6 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
@@ -43,6 +43,8 @@ jobs:
           docker tag {{ cookiecutter.name_docker }}:dev {{ cookiecutter.name_docker }}:dev
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting.yml
index aa58239a2..c56434eee 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/linting.yml
@@ -38,6 +38,8 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
diff --git a/tests/lint_examples/minimalworkingexample/.github/workflows/ci.yml b/tests/lint_examples/minimalworkingexample/.github/workflows/ci.yml
index 43adc25b7..0e9334211 100644
--- a/tests/lint_examples/minimalworkingexample/.github/workflows/ci.yml
+++ b/tests/lint_examples/minimalworkingexample/.github/workflows/ci.yml
@@ -44,6 +44,8 @@ jobs:
           docker tag nfcore/tools:dev nfcore/tools:0.4
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
diff --git a/tests/lint_examples/minimalworkingexample/.github/workflows/linting.yml b/tests/lint_examples/minimalworkingexample/.github/workflows/linting.yml
index 9e261424e..6bf4fccf0 100644
--- a/tests/lint_examples/minimalworkingexample/.github/workflows/linting.yml
+++ b/tests/lint_examples/minimalworkingexample/.github/workflows/linting.yml
@@ -26,6 +26,8 @@ jobs:
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/

From 8b14e19daf536f8aab764438b2970bb3ab8b0b94 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 09:41:50 +0100
Subject: [PATCH 41/51] Changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e56e91e9f..f8a3d86cb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@
 * Added config import for `test_full` in `nextflow.config`
 * Switched depreciated `$baseDir` to `$projectDir`
 * Updated minimum Nextflow version to `20.04.10`
+* Make Nextflow installation less verbose in GitHub Actions [[#780](https://github.com/nf-core/tools/pull/780)]
 
 ### Linting
 

From 6f97cd6062f6181209290a1a6f7c305d26375216 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 10:06:18 +0100
Subject: [PATCH 42/51] Better sphinx autodocs

* Index page - auto ToC for all pages
* Show all methods, including those that are undocumented
* Show intheritance between methods
* Remove disabling of syntax highlighting
---
 docs/api/_src/bump_version.rst |  6 +++++-
 docs/api/_src/conf.py          |  2 +-
 docs/api/_src/create.rst       |  6 +++++-
 docs/api/_src/download.rst     |  6 +++++-
 docs/api/_src/index.rst        | 12 +-----------
 docs/api/_src/launch.rst       |  4 ++++
 docs/api/_src/licences.rst     |  6 +++++-
 docs/api/_src/lint.rst         |  6 +++++-
 docs/api/_src/list.rst         |  6 +++++-
 docs/api/_src/modules.rst      |  4 ++++
 docs/api/_src/schema.rst       |  4 ++++
 docs/api/_src/sync.rst         |  4 ++++
 docs/api/_src/utils.rst        |  6 +++++-
 13 files changed, 53 insertions(+), 19 deletions(-)

diff --git a/docs/api/_src/bump_version.rst b/docs/api/_src/bump_version.rst
index d74430143..5ee0cee93 100644
--- a/docs/api/_src/bump_version.rst
+++ b/docs/api/_src/bump_version.rst
@@ -2,4 +2,8 @@ nf_core.bump_version
 ====================
 
 .. automodule:: nf_core.bump_version
-    :members:
\ No newline at end of file
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
index e96464a16..4766da0c6 100644
--- a/docs/api/_src/conf.py
+++ b/docs/api/_src/conf.py
@@ -66,7 +66,7 @@
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = None
+# pygments_style = None
 
 
 # -- Options for HTML output -------------------------------------------------
diff --git a/docs/api/_src/create.rst b/docs/api/_src/create.rst
index 31e9d8072..220d17874 100644
--- a/docs/api/_src/create.rst
+++ b/docs/api/_src/create.rst
@@ -2,4 +2,8 @@ nf_core.create
 ==============
 
 .. automodule:: nf_core.create
-    :members:
\ No newline at end of file
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/download.rst b/docs/api/_src/download.rst
index 5f98014a0..8243157b8 100644
--- a/docs/api/_src/download.rst
+++ b/docs/api/_src/download.rst
@@ -2,4 +2,8 @@ nf_core.download
 ================
 
 .. automodule:: nf_core.download
-    :members:
\ No newline at end of file
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/index.rst b/docs/api/_src/index.rst
index 793aba7c6..87a1fec66 100644
--- a/docs/api/_src/index.rst
+++ b/docs/api/_src/index.rst
@@ -10,17 +10,7 @@ Welcome to nf-core tools API documentation!
    :maxdepth: 2
    :caption: Contents:
 
-   bump_version
-   create
-   download
-   launch
-   licences
-   lint
-   list
-   modules
-   schema
-   sync
-   utils
+   *
 
 
 Indices and tables
diff --git a/docs/api/_src/launch.rst b/docs/api/_src/launch.rst
index 3f9a79cb5..aa47a2157 100644
--- a/docs/api/_src/launch.rst
+++ b/docs/api/_src/launch.rst
@@ -3,3 +3,7 @@ nf_core.launch
 
 .. automodule:: nf_core.launch
     :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/licences.rst b/docs/api/_src/licences.rst
index f50820881..449b9f4e4 100644
--- a/docs/api/_src/licences.rst
+++ b/docs/api/_src/licences.rst
@@ -2,4 +2,8 @@ nf_core.licences
 ================
 
 .. automodule:: nf_core.licences
-    :members:
\ No newline at end of file
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/lint.rst b/docs/api/_src/lint.rst
index 41add506f..f3d40cd0b 100644
--- a/docs/api/_src/lint.rst
+++ b/docs/api/_src/lint.rst
@@ -2,4 +2,8 @@ nf_core.lint
 ============
 
 .. automodule:: nf_core.lint
-    :members:
\ No newline at end of file
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/list.rst b/docs/api/_src/list.rst
index 632326126..bd0cd33ca 100644
--- a/docs/api/_src/list.rst
+++ b/docs/api/_src/list.rst
@@ -2,4 +2,8 @@ nf_core.list
 ============
 
 .. automodule:: nf_core.list
-    :members:
\ No newline at end of file
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/modules.rst b/docs/api/_src/modules.rst
index 3d5c82e03..af52026a0 100644
--- a/docs/api/_src/modules.rst
+++ b/docs/api/_src/modules.rst
@@ -3,3 +3,7 @@ nf_core.modules
 
 .. automodule:: nf_core.modules
     :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/schema.rst b/docs/api/_src/schema.rst
index bb2da2421..d668e96c2 100644
--- a/docs/api/_src/schema.rst
+++ b/docs/api/_src/schema.rst
@@ -3,3 +3,7 @@ nf_core.schema
 
 .. automodule:: nf_core.schema
     :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/sync.rst b/docs/api/_src/sync.rst
index 1e1fddbb2..c7c813264 100644
--- a/docs/api/_src/sync.rst
+++ b/docs/api/_src/sync.rst
@@ -3,3 +3,7 @@ nf_core.sync
 
 .. automodule:: nf_core.sync
     :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods
diff --git a/docs/api/_src/utils.rst b/docs/api/_src/utils.rst
index 94a1628c2..3cdaead3f 100644
--- a/docs/api/_src/utils.rst
+++ b/docs/api/_src/utils.rst
@@ -2,4 +2,8 @@ nf_core.utils
 =============
 
 .. automodule:: nf_core.utils
-    :members:
\ No newline at end of file
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members: # if you want to document __x attributes
+    :special-members: # if you want to document __xxx__ dunder methods

From fed713978494fee25c85e0ce6830b9a201ab00d9 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 10:25:17 +0100
Subject: [PATCH 43/51] Remove sphinx comment

---
 docs/api/_src/bump_version.rst | 4 ++--
 docs/api/_src/create.rst       | 4 ++--
 docs/api/_src/download.rst     | 4 ++--
 docs/api/_src/launch.rst       | 4 ++--
 docs/api/_src/licences.rst     | 4 ++--
 docs/api/_src/lint.rst         | 4 ++--
 docs/api/_src/list.rst         | 4 ++--
 docs/api/_src/modules.rst      | 4 ++--
 docs/api/_src/schema.rst       | 4 ++--
 docs/api/_src/sync.rst         | 4 ++--
 docs/api/_src/utils.rst        | 4 ++--
 11 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/docs/api/_src/bump_version.rst b/docs/api/_src/bump_version.rst
index 5ee0cee93..9115d7bb7 100644
--- a/docs/api/_src/bump_version.rst
+++ b/docs/api/_src/bump_version.rst
@@ -5,5 +5,5 @@ nf_core.bump_version
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/create.rst b/docs/api/_src/create.rst
index 220d17874..1b64c6666 100644
--- a/docs/api/_src/create.rst
+++ b/docs/api/_src/create.rst
@@ -5,5 +5,5 @@ nf_core.create
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/download.rst b/docs/api/_src/download.rst
index 8243157b8..be57e1b0c 100644
--- a/docs/api/_src/download.rst
+++ b/docs/api/_src/download.rst
@@ -5,5 +5,5 @@ nf_core.download
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/launch.rst b/docs/api/_src/launch.rst
index aa47a2157..63209e69a 100644
--- a/docs/api/_src/launch.rst
+++ b/docs/api/_src/launch.rst
@@ -5,5 +5,5 @@ nf_core.launch
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/licences.rst b/docs/api/_src/licences.rst
index 449b9f4e4..41222ffc3 100644
--- a/docs/api/_src/licences.rst
+++ b/docs/api/_src/licences.rst
@@ -5,5 +5,5 @@ nf_core.licences
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/lint.rst b/docs/api/_src/lint.rst
index f3d40cd0b..4cacfded7 100644
--- a/docs/api/_src/lint.rst
+++ b/docs/api/_src/lint.rst
@@ -5,5 +5,5 @@ nf_core.lint
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/list.rst b/docs/api/_src/list.rst
index bd0cd33ca..3ed74c56d 100644
--- a/docs/api/_src/list.rst
+++ b/docs/api/_src/list.rst
@@ -5,5 +5,5 @@ nf_core.list
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/modules.rst b/docs/api/_src/modules.rst
index af52026a0..a3eb7bdc0 100644
--- a/docs/api/_src/modules.rst
+++ b/docs/api/_src/modules.rst
@@ -5,5 +5,5 @@ nf_core.modules
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/schema.rst b/docs/api/_src/schema.rst
index d668e96c2..458172e01 100644
--- a/docs/api/_src/schema.rst
+++ b/docs/api/_src/schema.rst
@@ -5,5 +5,5 @@ nf_core.schema
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/sync.rst b/docs/api/_src/sync.rst
index c7c813264..eebb0da04 100644
--- a/docs/api/_src/sync.rst
+++ b/docs/api/_src/sync.rst
@@ -5,5 +5,5 @@ nf_core.sync
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:
diff --git a/docs/api/_src/utils.rst b/docs/api/_src/utils.rst
index 3cdaead3f..132317c6b 100644
--- a/docs/api/_src/utils.rst
+++ b/docs/api/_src/utils.rst
@@ -5,5 +5,5 @@ nf_core.utils
     :members:
     :undoc-members:
     :show-inheritance:
-    :private-members: # if you want to document __x attributes
-    :special-members: # if you want to document __xxx__ dunder methods
+    :private-members:
+    :special-members:

From b89e074e0ebc2f87b9e3fb1803185e147925bebc Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 10:42:05 +0100
Subject: [PATCH 44/51] Fix pytests

Left over from https://github.com/nf-core/tools/pull/778 - not sure why they didn't fail in that PR?
---
 .../minimalworkingexample/.github/workflows/ci.yml              | 2 +-
 tests/lint_examples/minimalworkingexample/README.md             | 2 +-
 tests/test_bump_version.py                                      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/lint_examples/minimalworkingexample/.github/workflows/ci.yml b/tests/lint_examples/minimalworkingexample/.github/workflows/ci.yml
index 0e9334211..ea6d955d0 100644
--- a/tests/lint_examples/minimalworkingexample/.github/workflows/ci.yml
+++ b/tests/lint_examples/minimalworkingexample/.github/workflows/ci.yml
@@ -21,7 +21,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['19.10.0', '']
+        nxf_ver: ['20.04.0', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
diff --git a/tests/lint_examples/minimalworkingexample/README.md b/tests/lint_examples/minimalworkingexample/README.md
index fc732ac05..ae26ae11c 100644
--- a/tests/lint_examples/minimalworkingexample/README.md
+++ b/tests/lint_examples/minimalworkingexample/README.md
@@ -1,5 +1,5 @@
 # The pipeline readme file
 
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.04.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
diff --git a/tests/test_bump_version.py b/tests/test_bump_version.py
index 5eca5d239..20a7f44da 100644
--- a/tests/test_bump_version.py
+++ b/tests/test_bump_version.py
@@ -57,7 +57,7 @@ def test_multiple_patterns_found(datafiles):
 def test_successfull_nextflow_version_bump(datafiles):
     lint_obj = nf_core.lint.PipelineLint(str(datafiles))
     lint_obj.pipeline_name = "tools"
-    lint_obj.config["manifest.nextflowVersion"] = "19.10.0"
+    lint_obj.config["manifest.nextflowVersion"] = "20.04.0"
     nf_core.bump_version.bump_nextflow_version(lint_obj, "0.40")
     lint_obj_new = nf_core.lint.PipelineLint(str(datafiles))
     lint_obj_new.check_nextflow_config()

From 0453ef73ba7779959c6c1748b147cc7672e10ac8 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 10:48:54 +0100
Subject: [PATCH 45/51] Fix more tests with version

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

diff --git a/tests/test_lint.py b/tests/test_lint.py
index d628d70dc..468090127 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -170,7 +170,7 @@ def test_actions_wf_branch_fail(self):
     def test_actions_wf_ci_pass(self):
         """Tests that linting for GitHub Actions CI workflow works for a good example"""
         lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
-        lint_obj.minNextflowVersion = "19.10.0"
+        lint_obj.minNextflowVersion = "20.04.0"
         lint_obj.pipeline_name = "tools"
         lint_obj.config["process.container"] = "'nfcore/tools:0.4'"
         lint_obj.check_actions_ci()
@@ -180,7 +180,7 @@ def test_actions_wf_ci_pass(self):
     def test_actions_wf_ci_fail(self):
         """Tests that linting for GitHub Actions CI workflow fails for a bad example"""
         lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE)
-        lint_obj.minNextflowVersion = "19.10.0"
+        lint_obj.minNextflowVersion = "20.04.0"
         lint_obj.pipeline_name = "tools"
         lint_obj.config["process.container"] = "'nfcore/tools:0.4'"
         lint_obj.check_actions_ci()
@@ -257,7 +257,7 @@ def test_missing_license_example(self):
     def test_readme_pass(self):
         """Tests that the pipeline README file checks work with a good example"""
         lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
-        lint_obj.minNextflowVersion = "19.10.0"
+        lint_obj.minNextflowVersion = "20.04.0"
         lint_obj.files = ["environment.yml"]
         lint_obj.check_readme()
         expectations = {"failed": 0, "warned": 0, "passed": 2}

From 1305ac1f8fe5e222815809130ec978aa718b5f91 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 10:50:36 +0100
Subject: [PATCH 46/51] Very minor docs typo

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

diff --git a/nf_core/lint.py b/nf_core/lint.py
index bd1e16a2a..74c5b170a 100755
--- a/nf_core/lint.py
+++ b/nf_core/lint.py
@@ -274,7 +274,7 @@ def check_files_exist(self):
 
             'Singularity',
             'parameters.settings.json',
-            'bin/markdown_to_html.r'.
+            'bin/markdown_to_html.r',
             '.github/workflows/push_dockerhub.yml'
 
         Files that *should not* be present::

From 4c193fc639cbc80eb16ea2ca1e9715ed3dc60e55 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 11:06:09 +0100
Subject: [PATCH 47/51] Fix pytest DeprecationWarning

---
 tests/test_launch.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_launch.py b/tests/test_launch.py
index f33e60043..70acc982a 100644
--- a/tests/test_launch.py
+++ b/tests/test_launch.py
@@ -280,7 +280,7 @@ def test_ob_to_pyinquirer_pattern(self):
         assert result["validate"]("") is True
         assert (
             result["validate"]("not_an_email")
-            == "Must match pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$"
+            == r"Must match pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$"
         )
 
     def test_strip_default_params(self):

From b46149be424ce8cf34b8a53f979d9695386f2838 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 11:23:26 +0100
Subject: [PATCH 48/51] Add missing directive for sphinx homepage toc

---
 docs/api/_src/index.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/api/_src/index.rst b/docs/api/_src/index.rst
index 87a1fec66..facd9f13b 100644
--- a/docs/api/_src/index.rst
+++ b/docs/api/_src/index.rst
@@ -9,6 +9,7 @@ Welcome to nf-core tools API documentation!
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
+   :glob:
 
    *
 

From a5c371a2ebadaf5b9e21a382e94482011e78d000 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 11:23:47 +0100
Subject: [PATCH 49/51] Sphinx docs - remove :special-members:

---
 docs/api/_src/bump_version.rst | 1 -
 docs/api/_src/create.rst       | 1 -
 docs/api/_src/download.rst     | 1 -
 docs/api/_src/launch.rst       | 1 -
 docs/api/_src/licences.rst     | 1 -
 docs/api/_src/lint.rst         | 1 -
 docs/api/_src/list.rst         | 1 -
 docs/api/_src/modules.rst      | 1 -
 docs/api/_src/schema.rst       | 1 -
 docs/api/_src/sync.rst         | 1 -
 docs/api/_src/utils.rst        | 1 -
 11 files changed, 11 deletions(-)

diff --git a/docs/api/_src/bump_version.rst b/docs/api/_src/bump_version.rst
index 9115d7bb7..aca9f7621 100644
--- a/docs/api/_src/bump_version.rst
+++ b/docs/api/_src/bump_version.rst
@@ -6,4 +6,3 @@ nf_core.bump_version
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/create.rst b/docs/api/_src/create.rst
index 1b64c6666..10803a831 100644
--- a/docs/api/_src/create.rst
+++ b/docs/api/_src/create.rst
@@ -6,4 +6,3 @@ nf_core.create
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/download.rst b/docs/api/_src/download.rst
index be57e1b0c..b7f8940f8 100644
--- a/docs/api/_src/download.rst
+++ b/docs/api/_src/download.rst
@@ -6,4 +6,3 @@ nf_core.download
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/launch.rst b/docs/api/_src/launch.rst
index 63209e69a..416c2c99e 100644
--- a/docs/api/_src/launch.rst
+++ b/docs/api/_src/launch.rst
@@ -6,4 +6,3 @@ nf_core.launch
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/licences.rst b/docs/api/_src/licences.rst
index 41222ffc3..8d061741d 100644
--- a/docs/api/_src/licences.rst
+++ b/docs/api/_src/licences.rst
@@ -6,4 +6,3 @@ nf_core.licences
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/lint.rst b/docs/api/_src/lint.rst
index 4cacfded7..532801c55 100644
--- a/docs/api/_src/lint.rst
+++ b/docs/api/_src/lint.rst
@@ -6,4 +6,3 @@ nf_core.lint
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/list.rst b/docs/api/_src/list.rst
index 3ed74c56d..ea4a406ff 100644
--- a/docs/api/_src/list.rst
+++ b/docs/api/_src/list.rst
@@ -6,4 +6,3 @@ nf_core.list
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/modules.rst b/docs/api/_src/modules.rst
index a3eb7bdc0..44c341175 100644
--- a/docs/api/_src/modules.rst
+++ b/docs/api/_src/modules.rst
@@ -6,4 +6,3 @@ nf_core.modules
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/schema.rst b/docs/api/_src/schema.rst
index 458172e01..e1cefb98d 100644
--- a/docs/api/_src/schema.rst
+++ b/docs/api/_src/schema.rst
@@ -6,4 +6,3 @@ nf_core.schema
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/sync.rst b/docs/api/_src/sync.rst
index eebb0da04..edb9c28e3 100644
--- a/docs/api/_src/sync.rst
+++ b/docs/api/_src/sync.rst
@@ -6,4 +6,3 @@ nf_core.sync
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:
diff --git a/docs/api/_src/utils.rst b/docs/api/_src/utils.rst
index 132317c6b..f3077f4cb 100644
--- a/docs/api/_src/utils.rst
+++ b/docs/api/_src/utils.rst
@@ -6,4 +6,3 @@ nf_core.utils
     :undoc-members:
     :show-inheritance:
     :private-members:
-    :special-members:

From 43440c5228432e85d3755dea122ee3e8d4e32a8c Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 13:06:28 +0100
Subject: [PATCH 50/51] Version bump to 1.12

---
 CHANGELOG.md | 6 ++----
 setup.py     | 2 +-
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d36f5b540..e949ddce9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # nf-core/tools: Changelog
 
-## v1.12dev
+## [v1.12 - Mercury Weasel](https://github.com/nf-core/tools/releases/tag/1.12) - [2020-11-19]
 
 ### Tools helper code
 
@@ -22,11 +22,9 @@
 ### Linting
 
 * Updated code to display colours in GitHub Actions log output
-* Allow tests to pass with dev version of nf-core/tools (previous failure due to base image version)
+* Allow tests to pass with `dev` version of nf-core/tools (previous failure due to base image version)
 * Lint code no longer tries to post GitHub PR comments. This is now done in a GitHub Action only.
 
-### Other
-
 ## [v1.11 - Iron Tiger](https://github.com/nf-core/tools/releases/tag/1.11) - [2020-10-27]
 
 ### Template
diff --git a/setup.py b/setup.py
index 16c80531b..de3c45720 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 from setuptools import setup, find_packages
 import sys
 
-version = "1.12dev"
+version = "1.12"
 
 with open("README.md") as f:
     readme = f.read()

From d06c16f511921c728529b1a3366325eece03d62b Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 19 Nov 2020 14:21:40 +0100
Subject: [PATCH 51/51] Update .github/ISSUE_TEMPLATE/bug_report.md

---
 .github/ISSUE_TEMPLATE/bug_report.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index 9023381e9..8f2a1bccf 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -33,7 +33,8 @@ Steps to reproduce the behaviour:
 - Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
 - Executor: <!-- [e.g. slurm, local, awsbatch...] -->
 - OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
-- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
+- Version of nf-core/tools: <!-- [e.g. 1.1, 1.5, 1.8.2...] -->
+- Python version: <!-- [e.g. 3.7, 3.8...] -->
 
 ## Nextflow Installation