Add shell completion for nf-core tools commands

README.md

@@ -214,6 +214,22 @@ pip install --upgrade nf-core
 
 Please refer to the respective documentation for further details to manage packages, as for example [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-pkgs.html#updating-packages) or [pip](https://packaging.python.org/en/latest/tutorials/installing-packages/#upgrading-packages).
 
+### Activate shell completions for nf-core/tools
+
+Auto-completion for the `nf-core` command is available for bash, zsh and fish. To activate it, add the following lines to the respective shell config files.
+shell | shell config file | command
+--- | --- | ---
+bash | ~/.bashrc | `eval "$(_NF_CORE_COMPLETE=bash_source nf-core)"`
+Zsh | ~/.zshrc | `eval "$(_NF_CORE_COMPLETE=zsh_source nf-core)"`
+fish | ~/.config/fish/completions/nf-core.fish | `eval (env _NF_CORE_COMPLETE=fish_source nf-core)`
+
+After a restart of the shell session you should have auto-completion for the `nf-core` command and all its sub-commands and options.
+
+> **NB:** The added line will run the command `nf-core` (which will also slow down startup time of your shell). You should therefore either have the nf-core/tools installed globally.
+> You can also wrap it inside `if type nf-core > /dev/null; then ` \<YOUR EVAL CODE LINE\> `fi` for bash and zsh or `if command -v nf-core &> /dev/null eval (env _NF_CORE_COMPLETE=fish_source nf-core) end` for fish. You need to then source the config in your environment for the completions to be activated.
+
+> **NB:** If you see the error `command not found compdef` , be sure that your config file contains the line `autoload -Uz compinit && compinit` before the eval line.
+
 ## Listing pipelines
 
 The command `nf-core list` shows all available nf-core pipelines along with their latest version, when that was published and how recently the pipeline code was pulled to your local system (if at all).

nf_core/__main__.py

@@ -79,27 +79,28 @@
 
 
 def run_nf_core():
-    # Print nf-core header
-    stderr.print(f"\n[green]{' ' * 42},--.[grey39]/[green],-.", highlight=False)
-    stderr.print("[blue]          ___     __   __   __   ___     [green]/,-._.--~\\", highlight=False)
-    stderr.print(r"[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {", highlight=False)
-    stderr.print(r"[blue]    | \| |       \__, \__/ |  \ |___     [green]\`-._,-`-,", highlight=False)
-    stderr.print("[green]                                          `._,._,'\n", highlight=False)
-    stderr.print(
-        f"[grey39]    nf-core/tools version {nf_core.__version__} - [link=https://nf-co.re]https://nf-co.re[/]",
-        highlight=False,
-    )
-    try:
-        is_outdated, _, remote_vers = nf_core.utils.check_if_outdated()
-        if is_outdated:
-            stderr.print(
-                f"[bold bright_yellow]    There is a new version of nf-core/tools available! ({remote_vers})",
-                highlight=False,
-            )
-    except Exception as e:
-        log.debug(f"Could not check latest version: {e}")
-    stderr.print("\n")
-
+    # print nf-core header if environment variable is not set
+    if os.environ.get("_NF_CORE_COMPLETE") is None:
+        # Print nf-core header
+        stderr.print(f"\n[green]{' ' * 42},--.[grey39]/[green],-.", highlight=False)
+        stderr.print("[blue]          ___     __   __   __   ___     [green]/,-._.--~\\", highlight=False)
+        stderr.print(r"[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {", highlight=False)
+        stderr.print(r"[blue]    | \| |       \__, \__/ |  \ |___     [green]\`-._,-`-,", highlight=False)
+        stderr.print("[green]                                          `._,._,'\n", highlight=False)
+        stderr.print(
+            f"[grey39]    nf-core/tools version {nf_core.__version__} - [link=https://nf-co.re]https://nf-co.re[/]",
+            highlight=False,
+        )
+        try:
+            is_outdated, _, remote_vers = nf_core.utils.check_if_outdated()
+            if is_outdated:
+                stderr.print(
+                    f"[bold bright_yellow]    There is a new version of nf-core/tools available! ({remote_vers})",
+                    highlight=False,
+                )
+        except Exception as e:
+            log.debug(f"Could not check latest version: {e}")
+        stderr.print("\n")
     # Launch the click cli
     nf_core_cli(auto_envvar_prefix="NFCORE")