Textual create

.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/workflows/create-lint-wf.yml

@@ -59,7 +59,7 @@ jobs:
         run: |
           mkdir 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

@@ -91,7 +91,7 @@ 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

@@ -54,7 +54,7 @@ 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

nf_core/__main__.py

@@ -367,47 +367,6 @@ 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(
@@ -488,6 +447,151 @@ def lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, ma
         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="1.0dev", 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 != "1.0dev" 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):
+    """
+    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.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,
+            )
+            create_obj.init_pipeline()
+        except UserWarning as e:
+            log.error(e)
+            sys.exit(1)
+    elif name or description or author or version or force or outdir or plain:
+        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:
+        if rich.prompt.Confirm.ask(
+            "[blue bold]?[/] [bold] [green]nf-core create[/] command is deprecated in favor of [green]nf-core pipelines create[/].[/]\n"
+            "[bold]Will launch an interactive interface. Do you want to continue?[/]"
+        ):
+            log.info(
+                "Launching interactive nf-core pipeline creation tool."
+                "\nRun with all command line arguments to avoid using an interactive interface."
+            )
+            app = PipelineCreateApp()
+            try:
+                app.run()
+                sys.exit(app.return_code or 0)
+            except UserWarning as e:
+                log.error(e)
+                sys.exit(1)
+        else:
+            sys.exit(0)
+
+
 # nf-core modules subcommands
 @nf_core_cli.group()
 @click.option(

nf_core/lint/files_unchanged.py

@@ -6,7 +6,7 @@
 
 import yaml
 
-import nf_core.create
+import nf_core.pipelines.create.create
 
 log = logging.getLogger(__name__)
 
@@ -111,7 +111,7 @@ def files_unchanged(self):
     ]
 
     # Only show error messages from pipeline creation
-    logging.getLogger("nf_core.create").setLevel(logging.ERROR)
+    logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
 
     # Generate a new pipeline with nf-core create that we can compare to
     tmp_dir = tempfile.mkdtemp()
@@ -129,8 +129,8 @@ def files_unchanged(self):
         yaml.dump(template_yaml, fh, default_flow_style=False)
 
     test_pipeline_dir = os.path.join(tmp_dir, f"{prefix}-{short_name}")
-    create_obj = nf_core.create.PipelineCreate(
-        None, None, None, no_git=True, outdir=test_pipeline_dir, template_yaml_path=template_yaml_path
+    create_obj = nf_core.pipelines.create.create.PipelineCreate(
+        None, None, None, no_git=True, outdir=test_pipeline_dir, template_config=template_yaml_path
     )
     create_obj.init_pipeline()
 

nf_core/pipeline-template/.github/CONTRIBUTING.md

@@ -9,7 +9,7 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 :::info
 If you need help using or modifying {{ name }} then the best place to ask is on the nf-core Slack [#{{ short_name }}](https://nfcore.slack.com/channels/{{ short_name }}) channel ([join our Slack here](https://nf-co.re/join/slack)).
@@ -61,7 +61,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 - Fix the bug, and bump version (X.Y.Z+1).
 - A PR should be made on `master` from patch to directly this particular bug.
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 ## Getting help
 

nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md

@@ -16,7 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/{{ name }}/tree/master/.github/CONTRIBUTING.md)
-      {%- if branded %}
+      {%- if is_nfcore %}
 - [ ] If necessary, also make a PR on the {{ name }} _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
       {%- endif %}
 - [ ] Make sure your code lints (`nf-core lint`).

nf_core/pipeline-template/README.md

@@ -1,12 +1,12 @@
-{% if branded -%}
+{% if is_nfcore -%}
 
 # ![{{ name }}](docs/images/{{ logo_light }}#gh-light-mode-only) ![{{ name }}](docs/images/{{ logo_dark }}#gh-dark-mode-only)
 
 {% endif -%}
 {% if github_badges -%}
 [![GitHub Actions CI Status](https://github.com/{{ name }}/workflows/nf-core%20CI/badge.svg)](https://github.com/{{ name }}/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/{{ name }}/workflows/nf-core%20linting/badge.svg)](https://github.com/{{ name }}/actions?query=workflow%3A%22nf-core+linting%22){% endif -%}
-{% if branded -%}[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/{{ short_name }}/results){% endif -%}
+{% if is_nfcore -%}[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/{{ short_name }}/results){% endif -%}
 {%- if github_badges -%}
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
@@ -17,10 +17,10 @@
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/{{ name }})
 
 {% endif -%}
-{%- if branded -%}[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23{{ short_name }}-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/{{ short_name }}){% endif -%}
-{%- if branded -%}[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core){% endif -%}
-{%- if branded -%}[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core){% endif -%}
-{%- if branded -%}[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+{%- if is_nfcore -%}[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23{{ short_name }}-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/{{ short_name }}){% endif -%}
+{%- if is_nfcore -%}[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core){% endif -%}
+{%- if is_nfcore -%}[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core){% endif -%}
+{%- if is_nfcore -%}[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 {% endif -%}
 
@@ -77,7 +77,7 @@ nextflow run {{ name }} \
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
 > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/{{ short_name }}/usage) and the [parameter documentation](https://nf-co.re/{{ short_name }}/parameters).
 
@@ -101,7 +101,7 @@ We thank the following people for their extensive assistance in the development
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-{% if branded -%}
+{% if is_nfcore -%}
 For further information or help, don't hesitate to get in touch on the [Slack `#{{ short_name }}` channel](https://nfcore.slack.com/channels/{{ short_name }}) (you can join with [this invite](https://nf-co.re/join/slack)).
 
 {% endif -%}
@@ -115,7 +115,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
-{% if branded -%}
+{% if is_nfcore -%}
 You can cite the `nf-core` publication as follows:
 
 {% else -%}

nf_core/pipeline-template/assets/email_template.txt

@@ -1,4 +1,4 @@
-{% if branded -%}
+{% if is_nfcore -%}
 ----------------------------------------------------
                                         ,--./,-.
         ___     __   __   __   ___     /,-._.--~\\

nf_core/pipeline-template/docs/README.md

@@ -6,7 +6,7 @@ The {{ name }} documentation is split into the following pages:
   - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
 - [Output](output.md)
   - An overview of the different results produced by the pipeline and how to interpret them.
-    {%- if branded %}
+    {%- if is_nfcore %}
 
 You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)
 {% else %}

nf_core/pipeline-template/docs/usage.md

@@ -1,6 +1,6 @@
 # {{ name }}: Usage
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 ## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/{{ short_name }}/usage](https://nf-co.re/{{ short_name }}/usage)
 

nf_core/pipeline-template/lib/NfcoreTemplate.groovy

@@ -342,7 +342,7 @@ class NfcoreTemplate {
         String workflow_version = NfcoreTemplate.version(workflow)
         String.format(
             """\n
-            ${dashedLine(monochrome_logs)}{% if branded %}
+            ${dashedLine(monochrome_logs)}{% if is_nfcore %}
                                                     ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
             ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
             ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}

nf_core/pipeline-template/main.nf

@@ -4,7 +4,7 @@
     {{ name }}
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Github : https://github.com/{{ name }}
-{%- if branded %}
+{%- if is_nfcore %}
     Website: https://nf-co.re/{{ short_name }}
     Slack  : https://nfcore.slack.com/channels/{{ short_name }}
 {%- endif %}