Merge pull request #1551 from robsyme/nonamer

Make nf-core branding optional to help users create non-nf-core pipelines that can still leverage nf-core standards.

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

@@ -48,7 +48,7 @@ jobs:
 
       # Build a pipeline from the template
       - name: nf-core create
-        run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
+        run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
 
       # Try syncing it before we change anything
       - name: nf-core sync

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

@@ -35,7 +35,7 @@ jobs:
 
       - name: Run nf-core/tools
         run: |
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
+          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
           nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
 
       - name: Upload log file artifact

CHANGELOG.md

@@ -23,6 +23,7 @@
 - Fix and improve broken test for Singularity container download ([#1622](https://github.com/nf-core/tools/pull/1622))
 - Use [`$XDG_CACHE_HOME`](https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html) or `~/.cache` instead of `$XDG_CONFIG_HOME` or `~/config/` as base directory for API cache
 - Switch CI to use [setup-nextflow](https://github.com/nf-core/setup-nextflow) action to install Nextflow ([#1650](https://github.com/nf-core/tools/pull/1650))
+- Allow customization of the `nf-core` pipeline template when using `nf-core create` ([#1548](https://github.com/nf-core/tools/issues/1548))
 
 ### Modules
 

README.md

@@ -593,6 +593,29 @@ Please see the [nf-core documentation](https://nf-co.re/developers/adding_pipeli
 
 Note that if the required arguments for `nf-core create` are not given, it will interactively prompt for them. If you prefer, you can supply them as command line arguments. See `nf-core create --help` for more information.
 
+### Customizing the creation of a pipeline
+
+The `nf-core create` command comes with a number of options that allow you to customize the creation of a pipeline if you intend to not publish it as an
+nf-core pipeline. This can be done in two ways: by using interactive prompts, or by supplying a `template.yml` file using the `--template-yaml <file>` option.
+Both options allow you to specify a custom pipeline prefix, as well as selecting parts of the template to be excluded during pipeline creation.
+The interactive prompts will guide you through the pipeline creation process. An example of a `template.yml` file is shown below.
+
+```yaml
+name: cool-pipe
+description: A cool pipeline
+author: me
+prefix: cool-pipes-company
+skip:
+  - ci
+  - github_badges
+  - igenomes
+  - nf_core_configs
+```
+
+This will create a pipeline called `cool-pipe` in the directory `cool-pipes-company-cool-pipe` with `me` as the author. It will exclude the GitHub CI from the pipeline, remove GitHub badges from the `README.md` file, remove pipeline options related to iGenomes and exclude `nf_core/configs` options.
+
+To run the pipeline creation silently (i.e. without any prompts) with the nf-core template, you can use the `--plain` option.
+
 ## Linting a workflow
 
 The `lint` subcommand checks a given pipeline for all nf-core community guidelines.

nf_core/__main__.py

@@ -260,25 +260,27 @@ def validate_wf_name_prompt(ctx, opts, value):
 @click.option(
     "-n",
     "--name",
-    prompt="Workflow Name",
-    callback=validate_wf_name_prompt,
     type=str,
     help="The name of your new pipeline",
 )
-@click.option("-d", "--description", prompt=True, type=str, help="A short description of your pipeline")
-@click.option("-a", "--author", prompt=True, type=str, help="Name of the main author(s)")
+@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("--no-git", is_flag=True, default=False, help="Do not initialise pipeline as new git repository")
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists")
-@click.option("-o", "--outdir", type=str, help="Output directory for new pipeline (default: pipeline name)")
-def create(name, description, author, version, no_git, force, outdir):
+@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, no_git, 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 bfest-practices.
+    files, boilerplate code and best-practices.
     """
-    create_obj = nf_core.create.PipelineCreate(name, description, author, version, no_git, force, outdir)
+    create_obj = nf_core.create.PipelineCreate(
+        name, description, author, version, no_git, force, outdir, template_yaml, plain
+    )
     create_obj.init_pipeline()