refactor: move shared functions to ccbr_tools and import them here

.github/workflows/build-nextflow.yml

@@ -0,0 +1,79 @@
+name: build
+# TODO replace tool_name with the name of your tool
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - main
+      - develop
+  workflow_dispatch:
+    inputs:
+      test_run:
+        type: boolean
+        default: false
+        required: true
+
+env:
+  test_run: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.test_run }}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 2
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install nextflow
+        uses: nf-core/setup-nextflow@v1
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install .[dev,test]
+      - name: Check CLI basics
+        run: |
+          which tool_name
+          tool_name --help
+          tool_name --version
+          tool_name --citation
+      - name: Stub run
+        run: |
+          mkdir -p tmp && pushd tmp
+          tool_name init
+          tool_name run -c conf/ci_stub.config -stub
+          popd
+      - name: Test run
+        if: ${{ env.test_run == 'true' }}
+        run: |
+          mkdir -p tmp && pushd tmp
+          tool_name init
+          tool_name run -c conf/ci_stub.config -profile docker
+          popd
+      - name: "Upload Artifact"
+        uses: actions/upload-artifact@v3
+        if: always() # run even if previous steps fail
+        with:
+          name: nextflow-log
+          path: .nextflow.log
+
+  build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
+    runs-on: ubuntu-latest
+    needs: [build]
+    if: always()
+    steps:
+      - name: Successful build
+        if: ${{ !(contains(needs.*.result, 'failure')) }}
+        run: exit 0
+      - name: Failing build
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1

.github/workflows/docs-mkdocs.yml

@@ -0,0 +1,25 @@
+name: docs
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  push:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+      - "**.md"
+      - .github/workflows/docs-mkdocs.yml
+      - mkdocs.yml
+
+jobs:
+  mkdocs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: CCBR/actions/[email protected]
+        with:
+          github-token: ${{ github.token }}

README.md

@@ -2,7 +2,13 @@
 
 CCBR template for creating Nextflow pipelines <!-- TODO: replace this line with the description of TOOL_NAME -->
 
-[![build](https://github.com/CCBR/CCBR_NextflowTemplate/actions/workflows/build.yml/badge.svg)](https://github.com/CCBR/CCBR_NextflowTemplate/actions/workflows/build.yml) <!-- TODO: replace CCBR/CCBR_NextflowTemplate with your OWNER/TOOL_NAME -->
+<!-- TODO: replace CCBR/CCBR_NextflowTemplate in these badge links with your OWNER/TOOL_NAME -->
+
+[![build](https://github.com/CCBR/CCBR_NextflowTemplate/actions/workflows/build-nextflow.yml/badge.svg)](https://github.com/CCBR/CCBR_NextflowTemplate/actions/workflows/build-nextflow.yml)
+[![docs](https://github.com/CCBR/CCBR_NextflowTemplate/actions/workflows/docs-mkdocs.yml/badge.svg)](https://github.com/CCBR/CCBR_NextflowTemplate/actions/workflows/docs-mkdocs.yml)
+
+See the website for detailed information, documentation, and examples:
+<https://ccbr.github.io/TOOL_NAME/>
 
 ## Using this template
 
@@ -77,10 +83,22 @@ Install the tool in edit mode:
 pip3 install -e .
 ```
 
+View CLI options:
+
+```sh
+tool_name --help
+```
+
+Navigate to your project directory and initialize required config files:
+
+```sh
+tool_name init
+```
+
 Run the example
 
 ```sh
-TOOL_NAME run --input "Hello world"
+tool_name run --input "Hello world"
 ```
 
 ![dag](assets/dag.png)

docs/index.md

@@ -3,9 +3,3 @@
 --8<-- "README.md"
 
 <!--- write additional info that you only want to appear in the docs index here -->
-
-Information on who the pipeline was developed for, and a statement if it's only been tested on Biowulf. For example:
-
-It has been developed and tested solely on NIH [HPC Biowulf](https://hpc.nih.gov/).
-
-Also include a workflow image to summarize the pipeline.

pyproject.toml

@@ -31,11 +31,12 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
-    "pyyaml >= 6.0",
+    "ccbr_tools@git+https://github.com/CCBR/Tools",
+    "cffconvert >= 2.0.0",
     "Click >= 8.1.3",
-    "cffconvert >= 2.0.0"
+    "pyyaml >= 6.0"
 ]
 
 [project.optional-dependencies]

src/__main__.py

@@ -4,17 +4,28 @@
 Check out the wiki for a detailed look at customizing this file:
 https://github.com/beardymcjohnface/Snaketool/wiki/Customising-your-Snaketool
 """
-
-import os
+import cffconvert.cli.cli
 import click
-from .util import (
-    nek_base,
-    get_version,
-    copy_config,
-    OrderedCommands,
-    run_nextflow,
-    print_citation,
-)
+import os
+import pathlib
+
+import ccbr_tools.pkg_util
+import ccbr_tools.pipeline.util
+import ccbr_tools.pipeline.nextflow
+
+
+def repo_base(*paths):
+    basedir = pathlib.Path(__file__).absolute().parent.parent
+    return basedir.joinpath(*paths)
+
+
+def print_citation_flag(ctx, param, value):
+    if not value or ctx.resilient_parsing:
+        return
+    ccbr_tools.pkg_util.print_citation(
+        citation_file=repo_base("CITATION.cff"), output_format="bibtex"
+    )
+    ctx.exit()
 
 
 def common_options(func):
@@ -28,15 +39,22 @@ def common_options(func):
 
 
 @click.group(
-    cls=OrderedCommands, context_settings=dict(help_option_names=["-h", "--help"])
+    cls=ccbr_tools.pkg_util.CustomClickGroup,
+    context_settings=dict(help_option_names=["-h", "--help"]),
+)
+@click.version_option(
+    ccbr_tools.pkg_util.get_version(repo_base=repo_base),
+    "-v",
+    "--version",
+    is_flag=True,
 )
-@click.version_option(get_version(), "-v", "--version", is_flag=True)
 @click.option(
+    "-c",
     "--citation",
+    callback=print_citation_flag,
+    is_eager=True,
     is_flag=True,
-    callback=print_citation,
     expose_value=False,
-    is_eager=True,
     help="Print the citation in bibtex format and exit.",
 )
 def cli():
@@ -74,7 +92,7 @@ def cli():
     "main_path",
     help="Path to the tool_name main.nf file or the GitHub repo (CCBR/TOOL_NAME). Defaults to the version installed in the $PATH.",
     type=str,
-    default=nek_base(os.path.join("main.nf")),
+    default=repo_base("main.nf"),
     show_default=True,
 )
 @click.option(
@@ -97,7 +115,7 @@ def run(main_path, _mode, **kwargs):
                 f"Path to the tool_name main.nf file not found: {main_path}"
             )
 
-    run_nextflow(
+    ccbr_tools.pipeline.nextflow.run_nextflow(
         nextfile_path=main_path,
         mode=_mode,
         **kwargs,
@@ -108,13 +126,38 @@ def run(main_path, _mode, **kwargs):
 def init(**kwargs):
     """Initialize the working directory by copying the system default config files"""
     paths = ("nextflow.config", "conf/", "assets/")
-    copy_config(paths)
-    if not os.path.exists("log/"):
-        os.mkdir("log/")
+    ccbr_tools.pipeline.util.copy_config(paths, repo_base=repo_base)
+    os.makedirs("log", exist_ok=True)
+
+
+@click.command()
+@click.argument(
+    "citation_file",
+    type=click.Path(exists=True),
+    required=True,
+    default=repo_base("CITATION.cff"),
+)
+@click.option(
+    "--output-format",
+    "-f",
+    default="bibtex",
+    help="Output format for the citation",
+    type=cffconvert.cli.cli.options["outputformat"]["type"],
+)
+def cite(citation_file, output_format):
+    """
+    Print the citation in the desired format
+
+    citation_file : Path to a file in Citation File Format (CFF) [default: the CFF for ccbr_tools]
+    """
+    ccbr_tools.pkg_util.print_citation(
+        citation_file=citation_file, output_format=output_format
+    )
 
 
 cli.add_command(run)
 cli.add_command(init)
+cli.add_command(cite)
 
 
 def main():