Merge branch 'dev' into custom_registry_for_modules

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

@@ -84,6 +84,10 @@ jobs:
       - name: remove TODO
         run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
 
+      # Replace zenodo.XXXXXX to pass readme linting
+      - name: replace zenodo.XXXXXX
+        run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+
       # Run nf-core linting
       - name: nf-core lint
         run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned

CHANGELOG.md

@@ -17,13 +17,15 @@
 - Added support for the apptainer container engine via `-profile apptainer`. ([#2244](https://github.com/nf-core/tools/issues/2244)) [Contributed by @jfy133]
 - Added config `docker.registry` to pipeline template for a configurable default container registry when using Docker containers. Defaults to `quay.io` ([#2133](https://github.com/nf-core/tools/pull/2133))
 - Add tower.yml file to the pipeline template ([#2251](https://github.com/nf-core/tools/pull/2251))
+- Add mastodon badge to README ([#2253](https://github.com/nf-core/tools/pull/2253))
 - Removed `quay.io` from all module Docker container references as this is now supplied at pipeline level. ([#2249](https://github.com/nf-core/tools/pull/2249))
 
 ### Linting
 
 - Update modules lint test to fail if enable_conda is found ([#2213](https://github.com/nf-core/tools/pull/2213))
 - Read module lint configuration from `.nf-core.yml`, not `.nf-core-lint.yml` ([#2221](https://github.com/nf-core/tools/pull/2221))
 - `nf-core schema lint` now defaults to linting `nextflow_schema.json` if no filename is provided ([#2225](https://github.com/nf-core/tools/pull/2225))
+- Warn if `/zenodo.XXXXXX` is present in the Readme ([#2254](https://github.com/nf-core/tools/pull/2254))
 
 ### Modules
 

nf_core/lint/readme.py

@@ -17,16 +17,12 @@ def readme(self):
 
            [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/)
 
-    * Bioconda badge
+    .. note:: This badge are a markdown image ``![alt-text](<image URL>)`` *inside* a markdown link ``[markdown image](<link URL>)``, so a bit fiddly to write.
 
-      * If your pipeline contains a file called ``environment.yml`` in the root directory, a bioconda badge is required
-      * Required badge code:
+    * Zenodo release
 
-        .. code-block:: md
-
-           [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
+        * If pipeline is released but still contains a 'zenodo.XXXXXXX' tag, the test fails
 
-    .. note:: These badges are a markdown image ``![alt-text](<image URL>)`` *inside* a markdown link ``[markdown image](<link URL>)``, so a bit fiddly to write.
     """
     passed = []
     warned = []
@@ -62,4 +58,16 @@ def readme(self):
         else:
             warned.append("README did not have a Nextflow minimum version badge.")
 
+    if "zenodo_doi" not in ignore_configs:
+        # Check that zenodo.XXXXXXX has been replaced with the zendo.DOI
+        zenodo_re = r"/zenodo\.X+"
+        match = re.search(zenodo_re, content)
+        if match:
+            warned.append(
+                "README contains the placeholder `zenodo.XXXXXXX`. "
+                "This should be replaced with the zenodo doi (after the first release)."
+            )
+        else:
+            passed.append("README Zenodo placeholder was replaced with DOI.")
+
     return {"passed": passed, "warned": warned, "failed": failed}

nf_core/module-template/modules/meta.yml

@@ -1,10 +1,14 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "{{ component_name_underscore }}"
 {% if not_empty_template -%}
 ## TODO nf-core: Add a description of the module and list keywords
 {% endif -%}
 description: write your description here
 keywords:
   - sort
+  - example
+  - genomics
 tools:
   - "{{ component }}":
       {% if not_empty_template -%}
@@ -32,9 +36,9 @@ input:
   ## TODO nf-core: Delete / customise this example input
   {%- endif %}
   - {{ 'bam:' if not_empty_template else "input:" }}
-    type: file
-    description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }}
-    pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }}
+      type: file
+      description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }}
+      pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }}
 
 {% if not_empty_template -%}
 ## TODO nf-core: Add a description of all of the variables used as output
@@ -55,9 +59,9 @@ output:
   ## TODO nf-core: Delete / customise this example output
   {%- endif %}
   - {{ 'bam:' if not_empty_template else "output:" }}
-    type: file
-    description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }}
-    pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }}
+      type: file
+      description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }}
+      pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }}
 
 authors:
   - "{{ author }}"

nf_core/modules/lint/main_nf.py

@@ -235,26 +235,9 @@ def check_process_section(self, lines, fix_version, progress_bar):
         self.failed.append(("process_capitals", "Process name is not in capital letters", self.main_nf))
 
     # Check that process labels are correct
-    correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long"]
-    process_label = [l for l in lines if l.lstrip().startswith("label")]
-    if len(process_label) > 0:
-        try:
-            process_label = re.search("process_[A-Za-z]+", process_label[0]).group(0)
-        except AttributeError:
-            process_label = re.search("'([A-Za-z_-]+)'", process_label[0]).group(0)
-        finally:
-            if not process_label in correct_process_labels:
-                self.warned.append(
-                    (
-                        "process_standard_label",
-                        f"Process label ({process_label}) is not among standard labels: `{'`,`'.join(correct_process_labels)}`",
-                        self.main_nf,
-                    )
-                )
-            else:
-                self.passed.append(("process_standard_label", "Correct process label", self.main_nf))
-    else:
-        self.warned.append(("process_standard_label", "Process label unspecified", self.main_nf))
+    check_process_labels(self, lines)
+
+    # Deprecated enable_conda
     for i, l in enumerate(lines):
         url = None
         l = l.strip(" '\"")
@@ -412,6 +395,56 @@ def check_process_section(self, lines, fix_version, progress_bar):
     return docker_tag == singularity_tag
 
 
+def check_process_labels(self, lines):
+    correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long"]
+    all_labels = [l.strip() for l in lines if l.lstrip().startswith("label ")]
+    bad_labels = []
+    good_labels = []
+    if len(all_labels) > 0:
+        for label in all_labels:
+            try:
+                label = re.match("^label\s+([a-zA-Z0-9_-]+)$", label).group(1)
+            except AttributeError:
+                self.warned.append(
+                    (
+                        "process_standard_label",
+                        f"Specified label appears to contain non-alphanumerics: {label}",
+                        self.main_nf,
+                    )
+                )
+                continue
+            if label not in correct_process_labels:
+                bad_labels.append(label)
+            else:
+                good_labels.append(label)
+        if len(good_labels) > 1:
+            self.warned.append(
+                (
+                    "process_standard_label",
+                    f"Conflicting process labels found: `{'`,`'.join(good_labels)}`",
+                    self.main_nf,
+                )
+            )
+        elif len(good_labels) == 1:
+            self.passed.append(("process_standard_label", "Correct process label", self.main_nf))
+        else:
+            self.warned.append(("process_standard_label", "Standard process label not found", self.main_nf))
+        if len(bad_labels) > 0:
+            self.warned.append(
+                ("process_standard_label", f"Non-standard labels found: `{'`,`'.join(bad_labels)}`", self.main_nf)
+            )
+        if len(all_labels) > len(set(all_labels)):
+            self.warned.append(
+                (
+                    "process_standard_label",
+                    f"Duplicate labels found: `{'`,`'.join(sorted(all_labels))}`",
+                    self.main_nf,
+                )
+            )
+    else:
+        self.warned.append(("process_standard_label", "Process label not specified", self.main_nf))
+
+
 def _parse_input(self, line_raw):
     """
     Return list of input channel names from an input line.

nf_core/modules/lint/meta_yml.py

@@ -1,5 +1,7 @@
+import json
 from pathlib import Path
 
+import jsonschema.validators
 import yaml
 
 from nf_core.modules.modules_differ import ModulesDiffer
@@ -10,17 +12,15 @@ def meta_yml(module_lint_object, module):
     Lint a ``meta.yml`` file
 
     The lint test checks that the module has
-    a ``meta.yml`` file and that it contains
-    the required keys: ``name``, input`` and
-    ``output``.
+    a ``meta.yml`` file and that it follows the
+    JSON schema defined in the ``modules/yaml-schema.json``
+    file in the nf-core/modules repository.
 
     In addition it checks that the module name
     and module input is consistent between the
     ``meta.yml`` and the ``main.nf``.
 
     """
-    required_keys = ["name", "output"]
-    required_keys_lists = ["input", "output"]
     # Check if we have a patch file, get original file in that case
     meta_yaml = None
     if module.is_patched:
@@ -42,21 +42,31 @@ def meta_yml(module_lint_object, module):
             module.failed.append(("meta_yml_exists", "Module `meta.yml` does not exist", module.meta_yml))
             return
 
-    # Confirm that all required keys are given
-    contains_required_keys = True
-    all_list_children = True
-    for rk in required_keys:
-        if rk not in meta_yaml.keys():
-            module.failed.append(("meta_required_keys", f"`{rk}` not specified in YAML", module.meta_yml))
-            contains_required_keys = False
-        elif rk in meta_yaml.keys() and not isinstance(meta_yaml[rk], list) and rk in required_keys_lists:
-            module.failed.append(("meta_required_keys", f"`{rk}` is not a list", module.meta_yml))
-            all_list_children = False
-    if contains_required_keys:
-        module.passed.append(("meta_required_keys", "`meta.yml` contains all required keys", module.meta_yml))
+    # Confirm that the meta.yml file is valid according to the JSON schema
+    valid_meta_yml = True
+    try:
+        with open(Path(module_lint_object.modules_repo.local_repo_dir, "modules/yaml-schema.json"), "r") as fh:
+            schema = json.load(fh)
+        jsonschema.validators.validate(instance=meta_yaml, schema=schema)
+        module.passed.append(("meta_yml_valid", "Module `meta.yml` is valid", module.meta_yml))
+    except jsonschema.exceptions.ValidationError as e:
+        valid_meta_yml = False
+        hint = ""
+        if len(e.path) > 0:
+            hint = f"\nCheck the entry for `{e.path[0]}`."
+        if e.message.startswith("None is not of type 'object'") and len(e.path) > 2:
+            hint = f"\nCheck that the child entries of {e.path[0]+'.'+e.path[2]} are indented correctly."
+        module.failed.append(
+            (
+                "meta_yml_valid",
+                f"The `meta.yml` of the module {module.module_name} is not valid: {e.message}.{hint}",
+                module.meta_yml,
+            )
+        )
+        return
 
     # Confirm that all input and output channels are specified
-    if contains_required_keys and all_list_children:
+    if valid_meta_yml:
         if "input" in meta_yaml:
             meta_input = [list(x.keys())[0] for x in meta_yaml["input"]]
             for input in module.inputs:

nf_core/pipeline-template/README.md

@@ -19,6 +19,7 @@
 {% endif -%}
 {%- if branded -%}[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23{{ short_name }}-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/{{ short_name }}){% endif -%}
 {%- if branded -%}[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core){% endif -%}
+{%- if branded -%}[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core){% endif -%}
 {%- if branded -%}[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 {% endif -%}

nf_core/subworkflow-template/subworkflows/meta.yml

@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "{{ subworkflow_name }}"
 ## TODO nf-core: Add a description of the subworkflow and list keywords
 description: Sort SAM/BAM/CRAM file