CHANGELOG.md

@@ -5,11 +5,18 @@
 ### Template
 
 - Fix bug in pipeline readme logo URL
+- Removed retry strategy for AWS tests CI, as Nextflow now handles spot instance retries itself
+- Add `.prettierignore` file to stop Prettier linting tests from running over test files
 
 ### General
 
+- Bumped the minimum version of `rich` from `v10` to `v10.7.0`
+- Add an empty line to `modules.json`, `params.json` and `nextflow-schema.json` when dumping them to avoid prettier errors.
+
 ### Modules
 
+- Escaped test run output before logging it, to avoid a rich ` MarkupError`
+
 ## [v2.3.2 - Mercury Vulture Fixed Formatting](https://github.com/nf-core/tools/releases/tag/2.3.2) - [2022-03-24]
 
 Very minor patch release to fix the full size AWS tests and re-run the template sync, which partially failed due to GitHub pull-requests being down at the time of release.

nf_core/launch.py

@@ -692,6 +692,7 @@ def build_command(self):
             if self.use_params_file:
                 with open(self.params_out, "w") as fp:
                     json.dump(self.schema_obj.input_params, fp, indent=4)
+                    fp.write("\n")
                 self.nextflow_cmd += ' {} "{}"'.format("-params-file", os.path.relpath(self.params_out))
 
             # Call nextflow with a list of command line flags

nf_core/modules/module_utils.py

@@ -188,6 +188,7 @@ def create_modules_json(pipeline_dir):
     modules_json_path = os.path.join(pipeline_dir, "modules.json")
     with open(modules_json_path, "w") as fh:
         json.dump(modules_json, fh, indent=4)
+        fh.write("\n")
 
 
 def find_correct_commit_sha(module_name, module_path, modules_repo):

nf_core/modules/modules_command.py

@@ -301,6 +301,7 @@ def dump_modules_json(self, modules_json):
         modules_json_path = os.path.join(self.dir, "modules.json")
         with open(modules_json_path, "w") as fh:
             json.dump(modules_json, fh, indent=4)
+            fh.write("\n")
 
     def load_lint_config(self):
         """Parse a pipeline lint config file.

nf_core/modules/test_yml_builder.py

@@ -330,12 +330,13 @@ def run_tests_workflow(self, command):
                     "It looks like Nextflow is not installed. It is required for most nf-core functions."
                 )
         except subprocess.CalledProcessError as e:
-            raise UserWarning(f"Error running test workflow (exit code {e.returncode})\n[red]{e.output.decode()}")
+            output = rich.markup.escape(e.output.decode())
+            raise UserWarning(f"Error running test workflow (exit code {e.returncode})\n[red]{output}")
         except Exception as e:
             raise UserWarning(f"Error running test workflow: {e}")
         else:
             log.info("Test workflow finished!")
-            log.debug(nfconfig_raw)
+            log.debug(rich.markup.escape(nfconfig_raw))
 
         return tmp_dir, tmp_dir_repeat
 

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -28,6 +28,3 @@ jobs:
               "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}"
             }
           profiles: test_full,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3

nf_core/pipeline-template/.github/workflows/awstest.yml

@@ -23,6 +23,3 @@ jobs:
               "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-test-${{ github.sha }}{% endraw %}"
             }
           profiles: test,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3

nf_core/pipeline-template/.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == '{{ name }}'
         run: |
-          "{ [[ {% raw %}${{github.event.pull_request.head.repo.full_name }}{% endraw %} == {{ name }} ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
+          { [[ {% raw %}${{github.event.pull_request.head.repo.full_name }}{% endraw %} == {{ name }} ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure {%- raw %}
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
@@ -41,5 +41,4 @@ jobs:
 
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-# {%- endraw %}
+          allow-repeats: false {%- endraw %}

nf_core/pipeline-template/.github/workflows/ci.yml

@@ -47,6 +47,4 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
-# {%- endraw %}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results {%- endraw %}

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -77,6 +77,4 @@ jobs:
           path: |
             lint_log.txt
             lint_results.md
-            PR_number.txt
-
-# {%- endraw %}
+            PR_number.txt {%- endraw %}

nf_core/pipeline-template/.github/workflows/linting_comment.yml

@@ -25,5 +25,4 @@ jobs:
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
-          path: linting-logs/lint_results.md
-# {%- endraw %}
+          path: linting-logs/lint_results.md {%- endraw %}

nf_core/pipeline-template/.prettierignore

@@ -0,0 +1,8 @@
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc

nf_core/schema.py

@@ -171,6 +171,7 @@ def save_schema(self):
         log.info("Writing schema with {} params: '{}'".format(num_params, self.schema_filename))
         with open(self.schema_filename, "w") as fh:
             json.dump(self.schema, fh, indent=4)
+            fh.write("\n")
 
     def load_input_params(self, params_path):
         """Load a given a path to a parameters file (JSON/YAML)

requirements.txt

@@ -11,5 +11,5 @@ questionary>=1.8.0
 requests
 requests_cache
 rich-click>=1.0.0
-rich>=10.0.0
+rich>=10.7.0
 tabulate