Merge pull request #2189 from awgymer/template-yml-to-file-on-create

Dump template yml to file in pipeline repo after creation

nf_core/create.py

@@ -56,7 +56,7 @@ def __init__(
         plain=False,
         default_branch=None,
     ):
-        self.template_params, skip_paths_keys = self.create_param_dict(
+        self.template_params, skip_paths_keys, self.template_yaml = self.create_param_dict(
             name, description, author, version, template_yaml_path, plain
         )
 
@@ -178,7 +178,7 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
             if not re.match(r"^[a-z]+$", param_dict["short_name"]):
                 raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
 
-        return param_dict, skip_paths
+        return param_dict, skip_paths, template_yaml
 
     def customize_template(self, template_areas):
         """Customizes the template parameters.
@@ -348,6 +348,11 @@ def render_template(self):
             # Update the .nf-core.yml with linting configurations
             self.fix_linting()
 
+        log.debug("Dumping pipeline template yml to file")
+        if self.template_yaml:
+            with open(self.outdir / "pipeline_template.yml", "w") as fh:
+                yaml.safe_dump(self.template_yaml, fh)
+
     def update_nextflow_schema(self):
         """
         Removes unused parameters from the nextflow schema.

tests/data/pipeline_create_template.yml

@@ -0,0 +1 @@
+prefix: testprefix

tests/test_create.py

@@ -2,24 +2,47 @@
 """
 import os
 import unittest
+from pathlib import Path
+from unittest import mock
 
 import git
 
 import nf_core.create
 
 from .utils import with_temporary_folder
 
+TEST_DATA_DIR = Path(__file__).parent / "data"
+PIPELINE_TEMPLATE_YML = TEST_DATA_DIR / "pipeline_create_template.yml"
+
 
 class NfcoreCreateTest(unittest.TestCase):
-    @with_temporary_folder
-    def setUp(self, tmp_path):
+    def setUp(self):
         self.pipeline_name = "nf-core/test"
         self.pipeline_description = "just for 4w3s0m3 tests"
         self.pipeline_author = "Chuck Norris"
         self.pipeline_version = "1.0.0"
         self.default_branch = "default"
 
-        self.pipeline = nf_core.create.PipelineCreate(
+    def test_pipeline_creation(self):
+        pipeline = nf_core.create.PipelineCreate(
+            name=self.pipeline_name,
+            description=self.pipeline_description,
+            author=self.pipeline_author,
+            version=self.pipeline_version,
+            no_git=False,
+            force=True,
+            plain=True,
+            default_branch=self.default_branch,
+        )
+
+        assert pipeline.template_params["name"] == self.pipeline_name
+        assert pipeline.template_params["description"] == self.pipeline_description
+        assert pipeline.template_params["author"] == self.pipeline_author
+        assert pipeline.template_params["version"] == self.pipeline_version
+
+    @with_temporary_folder
+    def test_pipeline_creation_initiation(self, tmp_path):
+        pipeline = nf_core.create.PipelineCreate(
             name=self.pipeline_name,
             description=self.pipeline_description,
             author=self.pipeline_author,
@@ -30,14 +53,57 @@ def setUp(self, tmp_path):
             plain=True,
             default_branch=self.default_branch,
         )
+        pipeline.init_pipeline()
+        assert os.path.isdir(os.path.join(pipeline.outdir, ".git"))
+        assert f" {self.default_branch}\n" in git.Repo.init(pipeline.outdir).git.branch()
+        assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml"))
 
-    def test_pipeline_creation(self):
-        assert self.pipeline.template_params["name"] == self.pipeline_name
-        assert self.pipeline.template_params["description"] == self.pipeline_description
-        assert self.pipeline.template_params["author"] == self.pipeline_author
-        assert self.pipeline.template_params["version"] == self.pipeline_version
-
-    def test_pipeline_creation_initiation(self):
-        self.pipeline.init_pipeline()
-        assert os.path.isdir(os.path.join(self.pipeline.outdir, ".git"))
-        assert f" {self.default_branch}\n" in git.Repo.init(self.pipeline.outdir).git.branch()
+    @with_temporary_folder
+    def test_pipeline_creation_initiation_with_yml(self, tmp_path):
+        pipeline = nf_core.create.PipelineCreate(
+            name=self.pipeline_name,
+            description=self.pipeline_description,
+            author=self.pipeline_author,
+            version=self.pipeline_version,
+            no_git=False,
+            force=True,
+            outdir=tmp_path,
+            template_yaml_path=PIPELINE_TEMPLATE_YML,
+            plain=True,
+            default_branch=self.default_branch,
+        )
+        pipeline.init_pipeline()
+        assert os.path.isdir(os.path.join(pipeline.outdir, ".git"))
+        assert f" {self.default_branch}\n" in git.Repo.init(pipeline.outdir).git.branch()
+
+        # Check pipeline yml has been dumped and matches input
+        pipeline_template = os.path.join(pipeline.outdir, "pipeline_template.yml")
+        assert os.path.exists(pipeline_template)
+        with open(pipeline_template) as fh:
+            assert fh.read() == PIPELINE_TEMPLATE_YML.read_text()
+
+    @mock.patch.object(nf_core.create.PipelineCreate, "customize_template")
+    @mock.patch.object(nf_core.create.questionary, "confirm")
+    @with_temporary_folder
+    def test_pipeline_creation_initiation_customize_template(self, mock_questionary, mock_customize, tmp_path):
+        mock_questionary.unsafe_ask.return_value = True
+        mock_customize.return_value = {"prefix": "testprefix"}
+        pipeline = nf_core.create.PipelineCreate(
+            name=self.pipeline_name,
+            description=self.pipeline_description,
+            author=self.pipeline_author,
+            version=self.pipeline_version,
+            no_git=False,
+            force=True,
+            outdir=tmp_path,
+            default_branch=self.default_branch,
+        )
+        pipeline.init_pipeline()
+        assert os.path.isdir(os.path.join(pipeline.outdir, ".git"))
+        assert f" {self.default_branch}\n" in git.Repo.init(pipeline.outdir).git.branch()
+
+        # Check pipeline yml has been dumped and matches input
+        pipeline_template = os.path.join(pipeline.outdir, "pipeline_template.yml")
+        assert os.path.exists(pipeline_template)
+        with open(pipeline_template) as fh:
+            assert fh.read() == PIPELINE_TEMPLATE_YML.read_text()