From 7a1c333a480f7ad9d6184e20933fe3b449d365a4 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 23 Mar 2021 13:31:17 +0100
Subject: [PATCH 1/4] Copy file if any exception with jinja in pipeline create

---
 nf_core/create.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/nf_core/create.py b/nf_core/create.py
index bf4271b6d3..85c60b7bc4 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -132,7 +132,11 @@ def render_template(self):
             except (AttributeError, UnicodeDecodeError) as e:
                 log.debug(f"Copying file without Jinja: '{output_path}' - {e}")
                 shutil.copy(template_fn_path, output_path)
-                continue
+
+            # Something else went wrong
+            except Exception as e:
+                log.error(f"Copying raw file as error rendering with Jinja: '{output_path}' - {e}")
+                shutil.copy(template_fn_path, output_path)
 
             # Mirror file permissions
             template_stat = os.stat(template_fn_path)

From 719d22d4666378e2dcaa02b2c0f41994f79d7a07 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 23 Mar 2021 13:31:37 +0100
Subject: [PATCH 2/4] Make lint summary table coloured according to overall
 status

---
 nf_core/lint/__init__.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
index 338c908bbb..4d9c5de35d 100644
--- a/nf_core/lint/__init__.py
+++ b/nf_core/lint/__init__.py
@@ -318,14 +318,15 @@ def _s(some_list):
             console.print(table)
 
         # Summary table
-        table = Table(box=rich.box.ROUNDED)
-        table.add_column("[bold green]LINT RESULTS SUMMARY".format(len(self.passed)), no_wrap=True)
-        table.add_row(r"[✔] {:>3} Test{} Passed".format(len(self.passed), _s(self.passed)), style="green")
+        summary_colour = "red" if len(self.failed) > 0 else "green"
+        table = Table(box=rich.box.ROUNDED, style=summary_colour)
+        table.add_column(f"LINT RESULTS SUMMARY".format(len(self.passed)), no_wrap=True)
+        table.add_row(r"[green][✔] {:>3} Test{} Passed".format(len(self.passed), _s(self.passed)))
         if len(self.fix):
-            table.add_row(r"[?] {:>3} Test{} Fixed".format(len(self.fixed), _s(self.fixed)), style="bright_blue")
-        table.add_row(r"[?] {:>3} Test{} Ignored".format(len(self.ignored), _s(self.ignored)), style="grey58")
-        table.add_row(r"[!] {:>3} Test Warning{}".format(len(self.warned), _s(self.warned)), style="yellow")
-        table.add_row(r"[✗] {:>3} Test{} Failed".format(len(self.failed), _s(self.failed)), style="red")
+            table.add_row(r"[bright blue][?] {:>3} Test{} Fixed".format(len(self.fixed), _s(self.fixed)))
+        table.add_row(r"[grey58][?] {:>3} Test{} Ignored".format(len(self.ignored), _s(self.ignored)))
+        table.add_row(r"[yellow][!] {:>3} Test Warning{}".format(len(self.warned), _s(self.warned)))
+        table.add_row(r"[red][✗] {:>3} Test{} Failed".format(len(self.failed), _s(self.failed)))
         console.print(table)
 
         if len(self.could_fix):

From 6084456892e7457d8f5bb971861ef9590a373ed5 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 23 Mar 2021 13:33:10 +0100
Subject: [PATCH 3/4] Changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 64b50dc04d..ff7a7847af 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
 * Fixed template creation error regarding file permissions [[#932](https://github.com/nf-core/tools/issues/932)]
 * Split the `create-lint-wf` tests up into separate steps in GitHub Actions to make the CI results easier to read
 * Added automated PR comments to the Markdownlint and Python Black lint CI tests to explain failures
+* Make `nf-core lint` summary table borders coloured according to overall pass / fail status
 
 ## [v1.13.1 - Copper Crocodile Patch :crocodile: :pirate_flag:](https://github.com/nf-core/tools/releases/tag/1.13.1) - [2021-03-19]
 

From 17fbcf8de2104aefc769850dc57e626ebb8bc4e5 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 23 Mar 2021 13:44:56 +0100
Subject: [PATCH 4/4] Use '21.03.0-edge' in bump-versions code

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

diff --git a/nf_core/bump_version.py b/nf_core/bump_version.py
index 28e3f9eeaa..b770cb2e65 100644
--- a/nf_core/bump_version.py
+++ b/nf_core/bump_version.py
@@ -145,8 +145,8 @@ def bump_nextflow_version(pipeline_obj, new_version):
         pipeline_obj,
         [
             (
-                r"nxf_ver: \[[\'\"]?{}[\'\"]?, ''\]".format(current_version.replace(".", r"\.")),
-                "nxf_ver: ['{}', '']".format(new_version),
+                r"nxf_ver: \[[\'\"]?{}[\'\"]?, '21.03.0-edge'\]".format(current_version.replace(".", r"\.")),
+                "nxf_ver: ['{}', '21.03.0-edge']".format(new_version),
             )
         ],
     )