Merge branch 'dev' into patch

CHANGELOG.md

@@ -11,9 +11,11 @@
 ### General
 
 - Fix error in tagging GitPod docker images during releases
+- Fix bug when updating modules from old version in old folder structure
 - Don't remove local copy of modules repo, only update it with fetch ([#1881](https://github.com/nf-core/tools/pull/1881))
 - Add subworkflow commands create-test-yml, create and install ([#1897](https://github.com/nf-core/tools/pull/1897))
 - Update subworkflows install so it installs also imported modules and subworkflows ([#1904](https://github.com/nf-core/tools/pull/1904))
+- `check_up_to_date()` function from `modules_json` also checks for subworkflows.
 
 ### Modules
 

README.md

@@ -17,6 +17,7 @@ A python package with helper tools for the nf-core community.
 ## Table of contents <!-- omit in toc -->
 
 - [`nf-core` tools installation](#installation)
+- [`nf-core` tools update](#update-tools)
 - [`nf-core list` - List available pipelines](#listing-pipelines)
 - [`nf-core launch` - Run a pipeline with interactive parameter prompts](#launch-a-pipeline)
 - [`nf-core download` - Download pipeline for offline use](#downloading-pipelines-for-offline-use)
@@ -186,6 +187,22 @@ If you would prefer to skip this check, set the environment variable `NFCORE_NO_
 export NFCORE_NO_VERSION_CHECK=1
 ```
 
+### Update tools
+
+It is advisable to keep nf-core/tools updated to the most recent version. The command to update depends on the system used to install it, for example if you have installed it with conda you can use:
+
+```bash
+conda update nf-core
+```
+
+if you used pip:
+
+```bash
+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).
+
 ## 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).
@@ -216,7 +233,7 @@ Archived pipelines are not returned by default. To include them, use the `--show
 ## Launch a pipeline
 
 Some nextflow pipelines have a considerable number of command line flags that can be used.
-To help with this, you can use the `nf-core launch` command
+To help with this, you can use the `nf-core launch` command.
 You can choose between a web-based graphical interface or an interactive command-line wizard tool to enter the pipeline parameters for your run.
 Both interfaces show documentation alongside each parameter and validate your inputs.
 
@@ -500,7 +517,7 @@ To help developers working with pipeline schema, nf-core tools has three `schema
 Nextflow can take input parameters in a JSON or YAML file when running a pipeline using the `-params-file` option.
 This command validates such a file against the pipeline schema.
 
-`Usage is `nf-core schema validate <pipeline> <parameter file>`. eg with the pipeline downloaded [above](#download-pipeline), you can run:
+Usage is `nf-core schema validate <pipeline> <parameter file>`. eg with the pipeline downloaded [above](#download-pipeline), you can run:
 
 <!-- RICH-CODEX
 working_dir: tmp

nf_core/modules/install.py

@@ -29,7 +29,7 @@ def __init__(
         self.prompt = prompt
         self.sha = sha
 
-    def install(self, module):
+    def install(self, module, silent=False):
         if self.repo_type == "modules":
             log.error("You cannot install a module in a clone of nf-core/modules")
             return False
@@ -87,7 +87,6 @@ def install(self, module):
         # Check that the module is not already installed
         if (current_version is not None and os.path.exists(module_dir)) and not self.force:
             log.info("Module is already installed.")
-            print(f"Module {module} is already installed.")
 
             self.force = questionary.confirm(
                 f"Module {module} is already installed. Do you want to force the reinstallation?",
@@ -143,10 +142,14 @@ def install(self, module):
         if not self.install_module_files(module, version, self.modules_repo, install_folder):
             return False
 
-        # Print include statement
-        module_name = "_".join(module.upper().split("/"))
-        log.info(f"Include statement: include {{ {module_name} }} from '.{os.path.join(install_folder, module)}/main'")
+        if not silent:
+            # Print include statement
+            module_name = "_".join(module.upper().split("/"))
+            log.info(
+                f"Include statement: include {{ {module_name} }} from '.{os.path.join(install_folder, module)}/main'"
+            )
 
         # Update module.json with newly installed module
+        modules_json.load()
         modules_json.update(self.modules_repo, module, version)
         return True