Add nf-core configs create sub command

.editorconfig

@@ -20,3 +20,11 @@ indent_style = unset
 
 [**/Makefile]
 indent_style = unset
+
+[tests/__snapshots__/*]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset

.github/actions/create-lint-wf/action.yml

@@ -27,7 +27,7 @@ runs:
       run: |
         mkdir -p create-lint-wf && cd create-lint-wf
         export NXF_WORK=$(pwd)
-        nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+        nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
 
     # Try syncing it before we change anything
     - name: nf-core sync

.github/workflows/create-test-lint-wf-template.yml

@@ -103,7 +103,7 @@ jobs:
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
           cd create-test-lint-wf
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
 
       - name: run the pipeline
         run: |

.github/workflows/create-test-wf.yml

@@ -67,7 +67,7 @@ jobs:
         run: |
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
           nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
 
       - name: Upload log file artifact

.gitignore

@@ -115,3 +115,6 @@ ENV/
 pip-wheel-metadata
 .vscode
 .*.sw?
+
+# Textual
+snapshot_report.html

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.3.1
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -9,6 +9,8 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - [email protected]
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"

CHANGELOG.md

@@ -4,6 +4,8 @@
 
 ### Template
 
+- Update templates to use nf-core/setup-nextflow v2
+
 ### Linting
 
 ### Components
@@ -12,6 +14,7 @@
 
 - Update CI to use nf-core/setup-nextflow v2
 - Changelog bot: handle also patch version before dev suffix ([#2820](https://github.com/nf-core/tools/pull/2820))
+- update prettier to 3.2.5 ([#2830](https://github.com/nf-core/tools/pull/2830))
 - Update GitHub Actions ([#2827](https://github.com/nf-core/tools/pull/2827))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]

MANIFEST.in

@@ -9,3 +9,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-lightbg.png
 include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
 include nf_core/assets/logo/placeholder_logo.svg
 include nf_core/assets/logo/MavenPro-Bold.ttf
+include nf_core/pipelines/create/create.tcss

nf_core/__init__.py

@@ -1,4 +1,4 @@
-""" Main nf_core module file.
+"""Main nf_core module file.
 
 Shouldn't do much, as everything is under subcommands.
 """

nf_core/__main__.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
-""" nf-core: Helper tools for use with nf-core Nextflow pipelines. """
+"""nf-core: Helper tools for use with nf-core Nextflow pipelines."""
+
 import logging
 import os
 import sys
@@ -35,6 +36,7 @@
             "commands": [
                 "list",
                 "launch",
+                "configs",
                 "create-params-file",
                 "download",
                 "licences",
@@ -44,7 +46,7 @@
         {
             "name": "Commands for developers",
             "commands": [
-                "create",
+                "pipelines",
                 "lint",
                 "modules",
                 "subworkflows",
@@ -55,6 +57,18 @@
             ],
         },
     ],
+    "nf-core configs": [
+        {
+            "name": "Config commands",
+            "commands": ["create"],
+        },
+    ],
+    "nf-core pipelines": [
+        {
+            "name": "Pipeline commands",
+            "commands": ["create"],
+        },
+    ],
     "nf-core modules": [
         {
             "name": "For pipelines",
@@ -302,6 +316,35 @@ def launch(
         sys.exit(1)
 
 
+# nf-core configs
+@nf_core_cli.group()
+@click.pass_context
+def configs(ctx):
+    """
+    Commands to manage nf-core pipelines.
+    """
+    # ensure that ctx.obj exists and is a dict (in case `cli()` is called
+    # by means other than the `if` block below)
+    ctx.ensure_object(dict)
+
+
+@configs.command("create")
+def create_configs():
+    """
+    Command to interactively create a nextflow config
+    """
+    from nf_core.configs.create import ConfigsCreateApp
+
+    try:
+        log.info("Launching interactive nf-core configs creation tool.")
+        app = ConfigsCreateApp()
+        app.run()
+        sys.exit(app.return_code or 0)
+    except UserWarning as e:
+        log.error(e)
+        sys.exit(1)
+
+
 # nf-core create-params-file
 @nf_core_cli.command()
 @click.argument("pipeline", required=False, metavar="<pipeline name>")
@@ -466,53 +509,6 @@ def licences(pipeline, json):
         sys.exit(1)
 
 
-# nf-core create
-@nf_core_cli.command()
-@click.option(
-    "-n",
-    "--name",
-    type=str,
-    help="The name of your new pipeline",
-)
-@click.option("-d", "--description", type=str, help="A short description of your pipeline")
-@click.option("-a", "--author", type=str, help="Name of the main author(s)")
-@click.option("--version", type=str, default="1.0dev", help="The initial version number to use")
-@click.option(
-    "-f",
-    "--force",
-    is_flag=True,
-    default=False,
-    help="Overwrite output directory if it already exists",
-)
-@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)")
-@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
-@click.option("--plain", is_flag=True, help="Use the standard nf-core template")
-def create(name, description, author, version, force, outdir, template_yaml, plain):
-    """
-    Create a new pipeline using the nf-core template.
-
-    Uses the nf-core template to make a skeleton Nextflow pipeline with all required
-    files, boilerplate code and best-practices.
-    """
-    from nf_core.create import PipelineCreate
-
-    try:
-        create_obj = PipelineCreate(
-            name,
-            description,
-            author,
-            version=version,
-            force=force,
-            outdir=outdir,
-            template_yaml_path=template_yaml,
-            plain=plain,
-        )
-        create_obj.init_pipeline()
-    except UserWarning as e:
-        log.error(e)
-        sys.exit(1)
-
-
 # nf-core lint
 @nf_core_cli.command()
 @click.option(
@@ -630,6 +626,123 @@ def lint(
         sys.exit(1)
 
 
+# nf-core pipelines subcommands
+@nf_core_cli.group()
+@click.pass_context
+def pipelines(ctx):
+    """
+    Commands to manage nf-core pipelines.
+    """
+    # ensure that ctx.obj exists and is a dict (in case `cli()` is called
+    # by means other than the `if` block below)
+    ctx.ensure_object(dict)
+
+
+# nf-core pipelines create
+@pipelines.command("create")
+@click.pass_context
+@click.option(
+    "-n",
+    "--name",
+    type=str,
+    help="The name of your new pipeline",
+)
+@click.option("-d", "--description", type=str, help="A short description of your pipeline")
+@click.option("-a", "--author", type=str, help="Name of the main author(s)")
+@click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use")
+@click.option(
+    "-f",
+    "--force",
+    is_flag=True,
+    default=False,
+    help="Overwrite output directory if it already exists",
+)
+@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)")
+@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
+@click.option(
+    "--organisation",
+    type=str,
+    default="nf-core",
+    help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)",
+)
+def create_pipeline(ctx, name, description, author, version, force, outdir, template_yaml, organisation):
+    """
+    Create a new pipeline using the nf-core template.
+
+    Uses the nf-core template to make a skeleton Nextflow pipeline with all required
+    files, boilerplate code and best-practices.
+    \n\n
+    Run without any command line arguments to use an interactive interface.
+    """
+    from nf_core.pipelines.create import PipelineCreateApp
+    from nf_core.pipelines.create.create import PipelineCreate
+
+    if (name and description and author) or (template_yaml):
+        # If all command arguments are used, run without the interactive interface
+        try:
+            create_obj = PipelineCreate(
+                name,
+                description,
+                author,
+                version=version,
+                force=force,
+                outdir=outdir,
+                organisation=organisation,
+            )
+            create_obj.init_pipeline()
+        except UserWarning as e:
+            log.error(e)
+            sys.exit(1)
+    elif name or description or author or version != "1.0.0dev" or force or outdir or organisation != "nf-core":
+        log.error(
+            "Command arguments are not accepted in interactive mode.\n"
+            "Run with all command line arguments to avoid using an interactive interface"
+            "or run without any command line arguments to use an interactive interface."
+        )
+        sys.exit(1)
+    else:
+        log.info(
+            "Launching interactive nf-core pipeline creation tool."
+            "\nRun with all command line arguments to avoid using an interactive interface."
+        )
+        app = PipelineCreateApp()
+        app.run()
+        sys.exit(app.return_code or 0)
+
+
+# nf-core create (deprecated)
+@nf_core_cli.command(hidden=True, deprecated=True)
+@click.option(
+    "-n",
+    "--name",
+    type=str,
+    help="The name of your new pipeline",
+)
+@click.option("-d", "--description", type=str, help="A short description of your pipeline")
+@click.option("-a", "--author", type=str, help="Name of the main author(s)")
+@click.option("--version", type=str, help="The initial version number to use")
+@click.option(
+    "-f",
+    "--force",
+    is_flag=True,
+    default=False,
+    help="Overwrite output directory if it already exists",
+)
+@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)")
+@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
+@click.option("--plain", is_flag=True, help="Use the standard nf-core template")
+def create(name, description, author, version, force, outdir, template_yaml, plain):
+    """
+    DEPRECATED
+    Create a new pipeline using the nf-core template.
+
+    Uses the nf-core template to make a skeleton Nextflow pipeline with all required
+    files, boilerplate code and best-practices.
+    """
+    log.error("[bold][green]nf-core create[/] command is deprecated. Use [green]nf-core pipelines create[/].[/]")
+    sys.exit(0)
+
+
 # nf-core modules subcommands
 @nf_core_cli.group()
 @click.option(

nf_core/components/components_test.py

@@ -2,7 +2,6 @@
 The ComponentsTest class handles the generation and testing of nf-test snapshots.
 """
 
-
 import logging
 import os
 import re
@@ -91,9 +90,9 @@ def run(self) -> None:
         """Run build steps"""
         self.check_inputs()
         os.environ["NFT_DIFF"] = "pdiff"  # set nf-test differ to pdiff to get a better diff output
-        os.environ[
-            "NFT_DIFF_ARGS"
-        ] = "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
+        os.environ["NFT_DIFF_ARGS"] = (
+            "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
+        )
         with nf_core.utils.set_wd(Path(self.dir)):
             self.check_snapshot_stability()
         if len(self.errors) > 0:

nf_core/components/create.py

@@ -2,7 +2,6 @@
 The ComponentCreate class handles generating of module and subworkflow templates
 """
 
-
 import glob
 import json
 import logging

nf_core/components/lint/__init__.py

@@ -3,7 +3,6 @@
 in nf-core pipelines
 """
 
-
 import logging
 import operator
 import os

nf_core/components/nfcore_component.py

@@ -1,6 +1,7 @@
 """
 The NFCoreComponent class holds information and utility functions for a single module or subworkflow
 """
+
 import logging
 import re
 from pathlib import Path

nf_core/configs/__init__.py

@@ -0,0 +1 @@
+from .create import ConfigsCreateApp