Refactor passing of command line arguments to nf-core commands

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

@@ -32,7 +32,7 @@ jobs:
         run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
 
       - name: nf-core lint
-        run: nf-core --log-file log.txt lint nf-core-testpipeline --fail-ignored
+        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored
 
       - name: nf-core list
         run: nf-core --log-file log.txt list
@@ -41,19 +41,19 @@ jobs:
       #   run: nf-core --log-file log.txt licences nf-core-testpipeline
 
       - name: nf-core sync
-        run: nf-core --log-file log.txt sync nf-core-testpipeline/
+        run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
 
       - name: nf-core schema
-        run: nf-core --log-file log.txt schema build nf-core-testpipeline/ --no-prompts
+        run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts
 
       - name: nf-core bump-version
-        run: nf-core --log-file log.txt bump-version nf-core-testpipeline/ 1.1
+        run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
 
       - name: nf-core lint in release mode
-        run: nf-core --log-file log.txt lint nf-core-testpipeline --fail-ignored --release
+        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored --release
 
       - name: nf-core modules install
-        run: nf-core --log-file log.txt modules install nf-core-testpipeline/ --tool fastqc --force --latest
+        run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force --latest
 
       - name: Upload log file artifact
         if: ${{ always() }}

CHANGELOG.md

@@ -28,6 +28,7 @@
 * Updated `nf-core modules list` to show versions of local modules
 * Improved exit behavior by replacing `sys.exit` with exceptions
 * Updated `nf-core modules remove` to remove module entry in `modules.json` if module directory is missing
+* Refactored passing of command line arguments to `nf-core` commands and subcommands
 
 #### Sync
 

nf_core/__main__.py

@@ -295,7 +295,7 @@ def create(name, description, author, version, no_git, force, outdir):
 
 
 @nf_core_cli.command(help_priority=6)
-@click.argument("pipeline_dir", type=click.Path(exists=True), required=True, metavar="<pipeline directory>")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", help="Pipeline directory. Defaults to CWD")
 @click.option(
     "--release",
     is_flag=True,
@@ -312,7 +312,7 @@ def create(name, description, author, version, no_git, force, outdir):
 @click.option("-i", "--fail-ignored", is_flag=True, help="Convert ignored tests to failures")
 @click.option("--markdown", type=str, metavar="<filename>", help="File to write linting results to (Markdown)")
 @click.option("--json", type=str, metavar="<filename>", help="File to write linting results to (JSON)")
-def lint(pipeline_dir, release, fix, key, show_passed, fail_ignored, markdown, json):
+def lint(dir, release, fix, key, show_passed, fail_ignored, markdown, json):
     """
     Check pipeline code against nf-core guidelines.
 
@@ -324,14 +324,24 @@ def lint(pipeline_dir, release, fix, key, show_passed, fail_ignored, markdown, j
     See the documentation for details.
     """
 
+    # Check if pipeline directory is a pipeline
+    try:
+        nf_core.utils.is_pipeline_directory(dir)
+    except UserWarning as e:
+        log.error(e)
+        sys.exit(1)
+
     # Run the lint tests!
     try:
-        lint_obj = nf_core.lint.run_linting(pipeline_dir, release, fix, key, show_passed, fail_ignored, markdown, json)
+        lint_obj = nf_core.lint.run_linting(dir, release, fix, key, show_passed, fail_ignored, markdown, json)
         if len(lint_obj.failed) > 0:
             sys.exit(1)
     except AssertionError as e:
         log.critical(e)
         sys.exit(1)
+    except UserWarning as e:
+        log.error(e)
+        sys.exit(1)
 
 
 ## nf-core module subcommands
@@ -361,9 +371,9 @@ def modules(ctx, repository, branch):
 
 @modules.command(help_priority=1)
 @click.pass_context
-@click.argument("pipeline_dir", type=click.Path(exists=True), required=False, metavar="(<pipeline directory>)")
+@click.option("-i", "--installed", type=click.Path(exists=True), help="List modules installed in local directory")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
-def list(ctx, pipeline_dir, json):
+def list(ctx, installed, json):
     """
     List available software modules.
 
@@ -372,29 +382,29 @@ def list(ctx, pipeline_dir, json):
     If no pipeline directory is given, lists all currently available
     software wrappers in the nf-core/modules repository.
     """
-    module_list = nf_core.modules.ModuleList(pipeline_dir)
+    module_list = nf_core.modules.ModuleList(installed)
     module_list.modules_repo = ctx.obj["modules_repo_obj"]
     print(module_list.list_modules(json))
 
 
 @modules.command(help_priority=2)
 @click.pass_context
-@click.argument("pipeline_dir", type=click.Path(exists=True), required=True, metavar="<pipeline directory>")
-@click.option("-t", "--tool", type=str, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", help="Pipeline directory. Defaults to CWD")
 @click.option("-l", "--latest", is_flag=True, default=False, help="Install the latest version of the module")
 @click.option(
     "-f", "--force", is_flag=True, default=False, help="Force installation of module if module already exists"
 )
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install module at commit SHA")
-def install(ctx, pipeline_dir, tool, latest, force, sha):
+def install(ctx, tool, dir, latest, force, sha):
     """
     Add a DSL2 software wrapper module to a pipeline.
 
     Finds the relevant files in nf-core/modules and copies to the pipeline,
     along with associated metadata.
     """
     try:
-        module_install = nf_core.modules.ModuleInstall(pipeline_dir, force=force, latest=latest, sha=sha)
+        module_install = nf_core.modules.ModuleInstall(dir, force=force, latest=latest, sha=sha)
         module_install.modules_repo = ctx.obj["modules_repo_obj"]
         module_install.install(tool)
     except UserWarning as e:
@@ -404,14 +414,14 @@ def install(ctx, pipeline_dir, tool, latest, force, sha):
 
 @modules.command(help_priority=3)
 @click.pass_context
-@click.argument("pipeline_dir", type=click.Path(exists=True), required=True, metavar="<pipeline directory>")
-@click.option("-t", "--tool", type=str, metavar="<tool> or <tool/subtool>")
-def remove(ctx, pipeline_dir, tool):
+@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", help="Pipeline directory. Defaults to CWD")
+def remove(ctx, dir, tool):
     """
     Remove a software wrapper from a pipeline.
     """
     try:
-        module_remove = nf_core.modules.ModuleRemove(pipeline_dir)
+        module_remove = nf_core.modules.ModuleRemove(dir)
         module_remove.modules_repo = ctx.obj["modules_repo_obj"]
         module_remove.remove(tool)
     except UserWarning as e:
@@ -567,7 +577,7 @@ def validate(pipeline, params):
 
 
 @schema.command(help_priority=2)
-@click.argument("pipeline_dir", type=click.Path(exists=True), required=True, metavar="<pipeline directory>")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", help="Pipeline directory. Defaults to CWD")
 @click.option("--no-prompts", is_flag=True, help="Do not confirm changes, just update parameters and exit")
 @click.option("--web-only", is_flag=True, help="Skip building using Nextflow config, just launch the web tool")
 @click.option(
@@ -576,7 +586,7 @@ def validate(pipeline, params):
     default="https://nf-co.re/pipeline_schema_builder",
     help="Customise the builder URL (for development work)",
 )
-def build(pipeline_dir, no_prompts, web_only, url):
+def build(dir, no_prompts, web_only, url):
     """
     Interactively build a pipeline schema from Nextflow params.
 
@@ -588,8 +598,12 @@ def build(pipeline_dir, no_prompts, web_only, url):
     https://nf-co.re website where you can annotate and organise parameters.
     Listens for this to be completed and saves the updated schema.
     """
-    schema_obj = nf_core.schema.PipelineSchema()
-    if schema_obj.build_schema(pipeline_dir, no_prompts, web_only, url) is False:
+    try:
+        schema_obj = nf_core.schema.PipelineSchema()
+        if schema_obj.build_schema(dir, no_prompts, web_only, url) is False:
+            sys.exit(1)
+    except UserWarning as e:
+        log.error(e)
         sys.exit(1)
 
 
@@ -619,12 +633,12 @@ def lint(schema_path):
 
 
 @nf_core_cli.command("bump-version", help_priority=9)
-@click.argument("pipeline_dir", type=click.Path(exists=True), required=True, metavar="<pipeline directory>")
 @click.argument("new_version", required=True, metavar="<new version>")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", help="Pipeline directory. Defaults to CWD")
 @click.option(
     "-n", "--nextflow", is_flag=True, default=False, help="Bump required nextflow version instead of pipeline version"
 )
-def bump_version(pipeline_dir, new_version, nextflow):
+def bump_version(new_version, dir, nextflow):
     """
     Update nf-core pipeline version number.
 
@@ -637,24 +651,31 @@ def bump_version(pipeline_dir, new_version, nextflow):
 
     As well as the pipeline version, you can also change the required version of Nextflow.
     """
-    # Make a pipeline object and load config etc
-    pipeline_obj = nf_core.utils.Pipeline(pipeline_dir)
-    pipeline_obj._load()
-
-    # Bump the pipeline version number
-    if not nextflow:
-        nf_core.bump_version.bump_pipeline_version(pipeline_obj, new_version)
-    else:
-        nf_core.bump_version.bump_nextflow_version(pipeline_obj, new_version)
+    try:
+        # Check if pipeline directory contain necessary files
+        nf_core.utils.is_pipeline_directory(dir)
+
+        # Make a pipeline object and load config etc
+        pipeline_obj = nf_core.utils.Pipeline(dir)
+        pipeline_obj._load()
+
+        # Bump the pipeline version number
+        if not nextflow:
+            nf_core.bump_version.bump_pipeline_version(pipeline_obj, new_version)
+        else:
+            nf_core.bump_version.bump_nextflow_version(pipeline_obj, new_version)
+    except UserWarning as e:
+        log.error(e)
+        sys.exit(1)
 
 
 @nf_core_cli.command("sync", help_priority=10)
-@click.argument("pipeline_dir", required=True, type=click.Path(exists=True), metavar="<pipeline directory>")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", help="Pipeline directory. Defaults to CWD")
 @click.option("-b", "--from-branch", type=str, help="The git branch to use to fetch workflow vars.")
 @click.option("-p", "--pull-request", is_flag=True, default=False, help="Make a GitHub pull-request with the changes.")
 @click.option("-r", "--repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
-def sync(pipeline_dir, from_branch, pull_request, repository, username):
+def sync(dir, from_branch, pull_request, repository, username):
     """
     Sync a pipeline TEMPLATE branch with the nf-core template.
 
@@ -667,9 +688,14 @@ def sync(pipeline_dir, from_branch, pull_request, repository, username):
     the pipeline. It is run automatically for all pipelines when ever a
     new release of nf-core/tools (and the included template) is made.
     """
+    # Check if pipeline directory contain necessary files
+    try:
+        nf_core.utils.is_pipeline_directory(dir)
+    except UserWarning:
+        raise
 
     # Sync the given pipeline dir
-    sync_obj = nf_core.sync.PipelineSync(pipeline_dir, from_branch, pull_request, repository, username)
+    sync_obj = nf_core.sync.PipelineSync(dir, from_branch, pull_request, repository, username)
     try:
         sync_obj.sync()
     except (nf_core.sync.SyncException, nf_core.sync.PullRequestException) as e:

nf_core/bump_version.py

@@ -29,8 +29,8 @@ def bump_pipeline_version(pipeline_obj, new_version):
         log.warning("Stripping leading 'v' from new version number")
         new_version = new_version[1:]
     if not current_version:
-        log.error("Could not find config variable 'manifest.version'")
-        sys.exit(1)
+        raise UserWarning("Could not find config variable 'manifest.version'")
+
     log.info("Changing version number from '{}' to '{}'".format(current_version, new_version))
 
     # nextflow.config - workflow manifest version
@@ -60,8 +60,7 @@ def bump_nextflow_version(pipeline_obj, new_version):
     current_version = re.sub(r"^[^0-9\.]*", "", current_version)
     new_version = re.sub(r"^[^0-9\.]*", "", new_version)
     if not current_version:
-        log.error("Could not find config variable 'manifest.nextflowVersion'")
-        sys.exit(1)
+        raise UserWarning("Could not find config variable 'manifest.nextflowVersion'")
     log.info("Changing Nextlow version number from '{}' to '{}'".format(current_version, new_version))
 
     # nextflow.config - manifest minimum nextflowVersion

nf_core/lint/__init__.py

@@ -121,7 +121,10 @@ def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=Fal
         """Initialise linting object"""
 
         # Initialise the parent object
-        super().__init__(wf_path)
+        try:
+            super().__init__(wf_path)
+        except UserWarning:
+            raise
 
         self.lint_config = {}
         self.release_mode = release_mode

nf_core/modules/module_utils.py

@@ -309,4 +309,4 @@ def get_repo_type(dir):
     elif os.path.exists(os.path.join(dir, "software")):
         return "modules"
     else:
-        raise LookupError("Could not determine repository type of {}".format(dir))
+        raise LookupError("Could not determine repository type of '{}'".format(dir))

nf_core/modules/modules_command.py

@@ -23,10 +23,13 @@ def __init__(self, dir):
         self.modules_repo = ModulesRepo()
         self.dir = dir
         self.module_names = []
-        if self.dir:
-            self.repo_type = nf_core.modules.module_utils.get_repo_type(self.dir)
-        else:
-            self.repo_type = None
+        try:
+            if self.dir:
+                self.repo_type = nf_core.modules.module_utils.get_repo_type(self.dir)
+            else:
+                self.repo_type = None
+        except LookupError as e:
+            raise UserWarning(e)
 
     def get_pipeline_modules(self):
         """Get list of modules installed in the current directory"""

nf_core/schema.py

@@ -334,6 +334,12 @@ def make_skeleton_schema(self):
     def build_schema(self, pipeline_dir, no_prompts, web_only, url):
         """Interactively build a new pipeline schema for a pipeline"""
 
+        # Check if supplied pipeline directory really is one
+        try:
+            nf_core.utils.is_pipeline_directory(pipeline_dir)
+        except UserWarning:
+            raise
+
         if no_prompts:
             self.no_prompts = True
         if web_only:

nf_core/utils.py

@@ -183,6 +183,23 @@ def _fp(self, fn):
         return os.path.join(self.wf_path, fn)
 
 
+def is_pipeline_directory(wf_path):
+    """
+    Checks if the specified directory have the minimum required files
+    ('main.nf', 'nextflow.config') for a pipeline directory
+
+    Args:
+        wf_path (str): The directory to be inspected
+
+    Raises:
+        UserWarning: If one of the files are missing
+    """
+    for fn in ["main.nf", "nextflow.config"]:
+        path = os.path.join(wf_path, fn)
+        if not os.path.isfile(path):
+            raise UserWarning(f"'{wf_path}' is not a pipeline - '{fn}' is missing")
+
+
 def fetch_wf_config(wf_path):
     """Uses Nextflow to retrieve the the configuration variables
     from a Nextflow workflow.