added "auto process" screen and extracted labels/names from nf

nf_core/configs/create/__init__.py

@@ -12,6 +12,8 @@
 from nf_core.configs.create import utils
 
 ## nf-core question page (screen) imports
+from nf_core.configs.create.autoprocesses import AutoProcesses
+from nf_core.configs.create.autoprocessquestion import AutoProcessQuestion
 from nf_core.configs.create.basicdetails import BasicDetails
 from nf_core.configs.create.configtype import ChooseConfigType
 from nf_core.configs.create.final import FinalScreen
@@ -58,6 +60,8 @@ class ConfigsCreateApp(App[utils.ConfigsCreateConfig]):
         "welcome": WelcomeScreen,
         "choose_type": ChooseConfigType,
         "nfcore_question": ChooseNfcoreConfig,
+        "auto_process": AutoProcesses,
+        "auto_process_question": AutoProcessQuestion,
         "basic_details": BasicDetails,
         "final": FinalScreen,
         "hpc_question": ChooseHpc,

nf_core/configs/create/autoprocesses.py

@@ -0,0 +1,107 @@
+"""Run config auto generator"""
+import logging
+import re
+from pathlib import Path
+from textwrap import dedent
+
+from textual import on
+from textual.app import ComposeResult
+from textual.containers import Center, Horizontal
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Label, Markdown, Switch
+
+# from nf_core.configs.create.utils import (
+#     ConfigsCreateConfig,
+#     TextInput,
+#     init_context
+# )
+
+config_exists_warn = """
+> ⚠️  **The config file you are trying to create already exists.**
+>
+> If you continue, you will **overwrite** the existing config.
+> Please change the config name to create a different config!.
+"""
+
+class AutoProcesses(Screen):
+    """Name, description, author, etc."""
+
+    def __init__(self) -> None:
+        super().__init__()
+        self.auto_load_all = False
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            dedent(
+                """
+                # Auto-load your pipeline's process
+                The processes from your pipeline will be loaded based on your previous config 
+                pipeline path.
+                """
+            )
+        )
+        yield Horizontal(
+            Label("Auto-load all processes from pipeline path?", id="toggle_auto_load_all_label", classes="feature_title"),
+            Switch(id="toggle_auto_load_all", value=self.auto_load_all),
+            Label(
+                "Yes" if self.auto_load_all else "No",
+                id="toggle_auto_load_all_state_label"
+            ),
+            classes="custom_grid",
+        )
+
+        yield Center(
+            Button("Back", id="back", variant="default"),
+            Button("Next", id="next", variant="success"),
+            classes="cta",
+        )
+
+    def on_mount(self) -> None:
+        pipeline_path = self.parent.TEMPLATE_CONFIG.config_pipeline_path
+        process_map = self.scan_nextflow_files(pipeline_path)
+        logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
+        logging.info(process_map)
+
+    def scan_nextflow_files(self, pipeline_path: str):
+        process_map = {}
+        for nf_file in Path(pipeline_path).rglob("*.nf"):
+            content = nf_file.read_text()
+            for match in re.finditer(r'process\s+(\w+)\s*\{([^}]*)\}', content, re.DOTALL):
+                process_name = match.group(1)
+                process_code = match.group(2)
+
+                process_code = re.sub(r'//.*', '', process_code)
+
+                labels = re.findall(r'label\s+[\'"](\w+)[\'"]', process_code)
+                process_map[process_name] = labels if labels else []
+
+        return process_map
+
+    @on(Switch.Changed)
+    def on_toggle_switch(self, event: Switch.Changed) -> None:
+        """ Handle toggling the switches that determine whether to auto-load """
+        valid_toggles = {
+            'toggle_auto_load_all': 'auto_load_all',
+        }
+
+        if event.switch.id not in valid_toggles:
+            return
+
+        attr = valid_toggles[event.switch.id]
+        self.__setattr__(attr, event.value)
+
+        # Update the switch label
+        for label in self.query(Label):
+            if label.id == f'{event.switch.id}_state_label':
+                label.update("Yes" if event.value else "No")
+
+    @on(Button.Pressed)
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        if event.button.id == "back":
+            self.app.pop_screen()
+        elif event.button.id == "next" and not self.auto_load_all:
+            self.app.push_screen("pipeline_config_question")
+        elif event.button.id == "next" and self.auto_load_all:
+            self.app.push_screen("auto_process_question")

nf_core/configs/create/autoprocessquestion.py

@@ -0,0 +1,47 @@
+"""Run config auto generator"""
+
+from textual import on
+from textual.app import ComposeResult
+from textual.containers import Center
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Markdown
+
+config_exists_warn = """
+> ⚠️  **The config file you are trying to create already exists.**
+>
+> If you continue, you will **overwrite** the existing config.
+> Please change the config name to create a different config!.
+"""
+
+class AutoProcessQuestion(Screen):
+    """Name, description, author, etc."""
+
+    def __init__(self) -> None:
+        super().__init__()
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            """
+            Please configure your labels 
+            """
+        )
+
+        yield Markdown(
+            """
+            Please configure your processes
+            """
+        )
+        yield Center(
+            Button("Back", id="back", variant="default"),
+            Button("Next", id="next", variant="success"),
+            classes="cta",
+        )
+
+    @on(Button.Pressed)
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        if event.button.id == "back":
+            self.app.pop_screen()
+        elif event.button.id == "next":
+            self.app.push_screen("final")

nf_core/configs/create/basicdetails.py

@@ -110,7 +110,7 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
                 if self.parent.CONFIG_TYPE == "infrastructure":
                     self.parent.push_screen("hpc_question")
                 elif self.parent.CONFIG_TYPE == "pipeline":
-                    self.parent.push_screen("pipeline_config_question")
+                    self.parent.push_screen("auto_process")
         except ValueError:
             pass