Merge branch 'dev' of https://github.com/nf-core/tools into refgenie-…

…config

CHANGELOG.md

@@ -18,6 +18,7 @@
 
 - Fix the syntax of github_output in GitHub actions ([#2114](https://github.com/nf-core/tools/pull/2114))
 - Fix a bug introduced in 2.7 that made pipelines hang ([#2132](https://github.com/nf-core/tools/issues/2132))
+- Explicitly disable `conda` when a container profile ([#2140](https://github.com/nf-core/tools/pull/2140))
 
 ### Linting
 

README.md

@@ -344,6 +344,8 @@ You can run the pipeline by simply providing the directory path for the `workflo
 nextflow run /path/to/download/nf-core-rnaseq-dev/workflow/ --input mydata.csv --outdir results  # usual parameters here
 ```
 
+> Note that if you downloaded singularity images, you will need to use `-profile singularity` or have it enabled in your config file.
+
 ### Downloaded nf-core configs
 
 The pipeline files are automatically updated (`params.custom_config_base` is set to `../configs`), so that the local copy of institutional configs are available when running the pipeline.

nf_core/__main__.py

@@ -1446,8 +1446,7 @@ def docs(schema_path, output, format, force, columns):
     # Assume we're in a pipeline dir root if schema path not set
     schema_obj.get_schema_path(schema_path)
     schema_obj.load_schema()
-    if not output:
-        stdout.print(schema_obj.print_documentation(output, format, force, columns.split(",")))
+    schema_obj.print_documentation(output, format, force, columns.split(","))
 
 
 # nf-core bump-version

nf_core/pipeline-template/nextflow.config

@@ -102,6 +102,7 @@ profiles {
     docker {
         docker.enabled         = true
         docker.userEmulation   = true
+        conda.enabled          = false
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
@@ -113,27 +114,31 @@ profiles {
     singularity {
         singularity.enabled    = true
         singularity.autoMounts = true
+        conda.enabled          = false
         docker.enabled         = false
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
     }
     podman {
         podman.enabled         = true
+        conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
         shifter.enabled        = false
         charliecloud.enabled   = false
     }
     shifter {
         shifter.enabled        = true
+        conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false
         charliecloud.enabled   = false
     }
     charliecloud {
         charliecloud.enabled   = true
+        conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false

nf_core/schema.py

@@ -6,17 +6,20 @@
 import json
 import logging
 import os
+import tempfile
 import webbrowser
 
 import jinja2
 import jsonschema
 import markdown
+import rich.console
 import yaml
 from rich.prompt import Confirm
+from rich.syntax import Syntax
 
 import nf_core.list
 import nf_core.utils
-from nf_core.lint_utils import dump_json_with_prettier
+from nf_core.lint_utils import dump_json_with_prettier, run_prettier_on_file
 
 log = logging.getLogger(__name__)
 
@@ -464,13 +467,21 @@ def print_documentation(
         if format == "html":
             output = self.markdown_to_html(output)
 
-        # Print to file
-        if output_fn:
+        with tempfile.NamedTemporaryFile(mode="w+") as fh:
+            fh.write(output)
+            run_prettier_on_file(fh.name)
+            fh.seek(0)
+            prettified_docs = fh.read()
+
+        if not output_fn:
+            console = rich.console.Console()
+            console.print("\n", Syntax(prettified_docs, format), "\n")
+        else:
             if os.path.exists(output_fn) and not force:
                 log.error(f"File '{output_fn}' exists! Please delete first, or use '--force'")
                 return
-            with open(output_fn, "w") as file:
-                file.write(output)
+            with open(output_fn, "w") as fh:
+                fh.write(prettified_docs)
                 log.info(f"Documentation written to '{output_fn}'")
 
         # Return as a string
@@ -495,9 +506,11 @@ def schema_to_markdown(self, columns):
                     if column == "parameter":
                         out += f"| `{p_key}` "
                     elif column == "description":
-                        out += f"| {param.get('description', '')} "
+                        desc = param.get("description", "").replace("\n", "<br>")
+                        out += f"| {desc} "
                         if param.get("help_text", "") != "":
-                            out += f"<details><summary>Help</summary><small>{param['help_text']}</small></details>"
+                            help_txt = param["help_text"].replace("\n", "<br>")
+                            out += f"<details><summary>Help</summary><small>{help_txt}</small></details>"
                     elif column == "type":
                         out += f"| `{param.get('type', '')}` "
                     else: