Merge pull request #1919 from bjlang/dev

add nf-core subworkflows list and info commands

nf_core/__main__.py

@@ -58,7 +58,7 @@
     "nf-core subworkflows": [
         {
             "name": "For pipelines",
-            "commands": ["list", "install", "update"],
+            "commands": ["list", "info", "install", "update"],
         },
         {
             "name": "Developing new subworkflows",
@@ -958,6 +958,106 @@ def create_test_yml(ctx, subworkflow, run_tests, output, force, no_prompts):
         sys.exit(1)
 
 
+# nf-core subworkflows list subcommands
+@subworkflows.group()
+@click.pass_context
+def list(ctx):
+    """
+    List subworkflows in a local pipeline or remote repository.
+    """
+    pass
+
+
+# nf-core subworkflows list remote
+@list.command()
+@click.pass_context
+@click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
+@click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
+def remote(ctx, keywords, json):
+    """
+    List subworkflows in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/].
+    """
+    try:
+        subworkflows_list = nf_core.subworkflows.SubworkflowList(
+            None,
+            True,
+            ctx.obj["modules_repo_url"],
+            ctx.obj["modules_repo_branch"],
+            ctx.obj["modules_repo_no_pull"],
+        )
+        stdout.print(subworkflows_list.list_subworkflows(keywords, json))
+    except (UserWarning, LookupError) as e:
+        log.critical(e)
+        sys.exit(1)
+
+
+# nf-core subworkflows list local
+@list.command()
+@click.pass_context
+@click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
+@click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
+@click.option(
+    "-d",
+    "--dir",
+    type=click.Path(exists=True),
+    default=".",
+    help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
+)
+def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+    """
+    List subworkflows installed locally in a pipeline
+    """
+    try:
+        subworkflows_list = nf_core.subworkflows.SubworkflowList(
+            dir,
+            False,
+            ctx.obj["modules_repo_url"],
+            ctx.obj["modules_repo_branch"],
+            ctx.obj["modules_repo_no_pull"],
+        )
+        stdout.print(subworkflows_list.list_subworkflows(keywords, json))
+    except (UserWarning, LookupError) as e:
+        log.error(e)
+        sys.exit(1)
+
+
+# nf-core subworkflows info
+@subworkflows.command()
+@click.pass_context
+@click.argument("tool", type=str, required=False, metavar="subworkflow name")
+@click.option(
+    "-d",
+    "--dir",
+    type=click.Path(exists=True),
+    default=".",
+    help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
+)
+def info(ctx, tool, dir):
+    """
+    Show developer usage information about a given subworkflow.
+
+    Parses information from a subworkflow's [i]meta.yml[/] and renders help
+    on the command line. A handy equivalent to searching the
+    [link=https://nf-co.re/modules]nf-core website[/].
+
+    If run from a pipeline and a local copy of the subworkflow is found, the command
+    will print this usage info.
+    If not, usage from the remote subworkflows repo will be shown.
+    """
+    try:
+        subworkflow_info = nf_core.subworkflows.SubworkflowInfo(
+            dir,
+            tool,
+            ctx.obj["modules_repo_url"],
+            ctx.obj["modules_repo_branch"],
+            ctx.obj["modules_repo_no_pull"],
+        )
+        stdout.print(subworkflow_info.get_subworkflow_info())
+    except (UserWarning, LookupError) as e:
+        log.error(e)
+        sys.exit(1)
+
+
 # nf-core subworkflows install
 @subworkflows.command()
 @click.pass_context

nf_core/modules/modules_repo.py

@@ -485,3 +485,21 @@ def get_meta_yml(self, module_name):
         with open(path) as fh:
             contents = fh.read()
         return contents
+
+    def get_subworkflow_meta_yml(self, subworkflow_name):
+        """
+        Returns the contents of the 'meta.yml' file of a subworkflow
+
+        Args:
+            subworkflow_name (str): The name of the subworkflow
+
+        Returns:
+            (str): The contents of the file in text format
+        """
+        self.checkout_branch()
+        path = os.path.join(self.subworkflows_dir, subworkflow_name, "meta.yml")
+        if not os.path.exists(path):
+            return None
+        with open(path) as fh:
+            contents = fh.read()
+        return contents

nf_core/subworkflows/__init__.py

@@ -1,4 +1,5 @@
 from .create import SubworkflowCreate
+from .info import SubworkflowInfo
 from .install import SubworkflowInstall
 from .list import SubworkflowList
 from .subworkflows_test import SubworkflowsTest