Merge pull request #2136 from nf-core/dev

Dev -> Master for v2.7.2

CHANGELOG.md

@@ -1,5 +1,23 @@
 # nf-core/tools: Changelog
 
+## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]
+
+### Template
+
+- 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))
+
+### Linting
+
+- Allow specifying containers in less than three lines ([#2121](https://github.com/nf-core/tools/pull/2121))
+- Run prettier after dumping a json schema file ([#2124](https://github.com/nf-core/tools/pull/2124))
+
+### General
+
+- Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
+- Deprecate `--enable_conda` parameter. Use `conda.enable` instead ([#2131](https://github.com/nf-core/tools/pull/2131))
+- Handle `json.load()` exceptions ([#2134](https://github.com/nf-core/tools/pull/2134))
+
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 
 - Patch release to fix pipeline sync ([#2110](https://github.com/nf-core/tools/pull/2110))

README.md

@@ -217,11 +217,12 @@ Please refer to the respective documentation for further details to manage packa
 ### 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)`
+
+| 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.
 

nf_core/components/components_create.py

@@ -173,3 +173,5 @@ def get_username(author):
             f"[violet]GitHub Username:[/]{' (@author)' if author_default is None else ''}",
             default=author_default,
         )
+
+    return author

nf_core/create.py

@@ -166,16 +166,17 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
         param_dict["logo_dark"] = f"{param_dict['name_noslash']}_logo_dark.png"
         param_dict["version"] = version
 
-        config_yml = nf_core.utils.load_tools_config()
+        _, config_yml = nf_core.utils.load_tools_config()
         if (
             "lint" in config_yml
             and "nextflow_config" in config_yml["lint"]
             and "manifest.name" in config_yml["lint"]["nextflow_config"]
         ):
             return param_dict, skip_paths
-        # Check that the pipeline name matches the requirements
-        if not re.match(r"^[a-z]+$", param_dict["short_name"]):
-            raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
+        if param_dict["prefix"] == "nf-core":
+            # Check that the pipeline name matches the requirements
+            if not re.match(r"^[a-z]+$", param_dict["short_name"]):
+                raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
 
         return param_dict, skip_paths
 

nf_core/launch.py

@@ -17,6 +17,7 @@
 
 import nf_core.schema
 import nf_core.utils
+from nf_core.lint_utils import dump_json_with_prettier
 
 log = logging.getLogger(__name__)
 
@@ -700,9 +701,7 @@ def build_command(self):
 
             # Write the user selection to a file and run nextflow with that
             if self.use_params_file:
-                with open(self.params_out, "w") as fp:
-                    json.dump(self.schema_obj.input_params, fp, indent=4)
-                    fp.write("\n")
+                dump_json_with_prettier(self.params_out, self.schema_obj.input_params)
                 self.nextflow_cmd += f' -params-file "{os.path.relpath(self.params_out)}"'
 
             # Call nextflow with a list of command line flags

nf_core/lint/nextflow_config.py

@@ -146,6 +146,7 @@ def nextflow_config(self):
         "params.singleEnd",
         "params.igenomesIgnore",
         "params.name",
+        "params.enable_conda",
     ]
 
     # Remove field that should be ignored according to the linting config

nf_core/lint_utils.py

@@ -1,3 +1,4 @@
+import json
 import logging
 import subprocess
 from pathlib import Path
@@ -82,3 +83,14 @@ def run_prettier_on_file(file):
                 "There was an error running the prettier pre-commit hook.\n"
                 f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"
             )
+
+
+def dump_json_with_prettier(file_name, file_content):
+    """Dump a JSON file and run prettier on it.
+    Args:
+        file_name (Path | str): A file identifier as a string or pathlib.Path.
+        file_content (dict): Content to dump into the JSON file
+    """
+    with open(file_name, "w") as fh:
+        json.dump(file_content, fh, indent=4)
+    run_prettier_on_file(file_name)

nf_core/module-template/modules/main.nf

@@ -23,7 +23,7 @@ process {{ tool_name_underscore|upper }} {
     //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda (params.enable_conda ? "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}" : null)
+    conda "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         '{{ singularity_container if singularity_container else 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE' }}':
         '{{ docker_container if docker_container else 'quay.io/biocontainers/YOUR-TOOL-HERE' }}' }"

nf_core/modules/create.py

@@ -123,7 +123,7 @@ def create(self):
         self._get_bioconda_tool()
 
         # Prompt for GitHub username
-        nf_core.components.components_create.get_username(self.author)
+        self.author = nf_core.components.components_create.get_username(self.author)
 
         self._get_module_structure_components()
 

nf_core/modules/lint/main_nf.py

@@ -271,6 +271,15 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 self.failed.append(("singularity_tag", "Unable to parse singularity tag", self.main_nf))
                 singularity_tag = None
             url = urlparse(l.split("'")[0])
+            # lint double quotes
+            if l.count('"') > 2:
+                self.failed.append(
+                    (
+                        "container_links",
+                        "Too many double quotes found when specifying singularity container",
+                        self.main_nf,
+                    )
+                )
         if _container_type(l) == "docker":
             # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
             # e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
@@ -282,13 +291,26 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
                 docker_tag = None
             url = urlparse(l.split("'")[0])
+            # lint double quotes
+            if l.count('"') > 2:
+                self.failed.append(
+                    ("container_links", "Too many double quotes found when specifying docker container", self.main_nf)
+                )
         # lint double quotes
         if l.startswith("container"):
-            container_section = l + lines[i + 1] + lines[i + 2]
-            if container_section.count('"') > 2:
+            if l.count('"') > 2:
                 self.failed.append(
                     ("container_links", "Too many double quotes found when specifying containers", self.main_nf)
                 )
+        # lint more than one container in the same line
+        if ("https://containers" in l or "https://depot" in l) and ("biocontainers/" in l or "quay.io/" in l):
+            self.warned.append(
+                (
+                    "container_links",
+                    "Docker and Singularity containers specified in the same line. Only first one checked.",
+                    self.main_nf,
+                )
+            )
         # Try to connect to container URLs
         if url is None:
             continue

nf_core/modules/modules_json.py

@@ -13,7 +13,7 @@
 
 import nf_core.utils
 from nf_core.components.components_utils import get_components_to_install
-from nf_core.lint_utils import run_prettier_on_file
+from nf_core.lint_utils import dump_json_with_prettier
 from nf_core.modules.modules_repo import (
     NF_CORE_MODULES_NAME,
     NF_CORE_MODULES_REMOTE,
@@ -618,7 +618,11 @@ def load(self):
         """
         try:
             with open(self.modules_json_path, "r") as fh:
-                self.modules_json = json.load(fh)
+                try:
+                    self.modules_json = json.load(fh)
+                except json.JSONDecodeError as e:
+                    raise UserWarning(f"Unable to load JSON file '{self.modules_json_path}' due to error {e}")
+
         except FileNotFoundError:
             raise UserWarning("File 'modules.json' is missing")
 
@@ -1023,10 +1027,7 @@ def dump(self):
         """
         # Sort the modules.json
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
-        with open(self.modules_json_path, "w") as fh:
-            json.dump(self.modules_json, fh, indent=4)
-            fh.write("\n")
-        run_prettier_on_file(self.modules_json_path)
+        dump_json_with_prettier(self.modules_json_path, self.modules_json)
 
     def resolve_missing_installation(self, missing_installation, component_type):
         missing_but_in_mod_json = [

nf_core/pipeline-template/.github/workflows/fix-linting.yml

@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "name=result::pass" >> $GITHUB_OUTPUT
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "name=result::fail" >> $GITHUB_OUTPUT
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

nf_core/pipeline-template/.github/workflows/linting_comment.yml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

nf_core/pipeline-template/lib/WorkflowMain.groovy

@@ -76,7 +76,7 @@ class WorkflowMain {
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
         // Check that conda channels are set-up correctly
-        if (params.enable_conda) {
+        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
             Utils.checkCondaChannels(log)
         }
 

nf_core/pipeline-template/modules.json

@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     }
                 }

nf_core/pipeline-template/modules/local/samplesheet_check.nf

@@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3' :
         'quay.io/biocontainers/python:3.8.3' }"