Add Nextflow support

.gitignore

@@ -73,6 +73,7 @@ ipython_config.py
 
 # pyenv
 .python-version
+.data
 
 # workdir for judge
 /workdir/
@@ -82,3 +83,9 @@ venv-*/
 .venv/
 node_modules/
 result/
+
+# Nextflow
+.nextflow*
+
+# .NET
+obj/

dependencies.md

@@ -84,13 +84,13 @@ $ cabal v1-install aeson
 
 | Name                    | Versions | Installation |
 |-------------------------|----------|--------------|
-| `eslint`                | 8.57     | npm package  |
+| `eslint`                | 9.10     | npm package  |
 | `abstract-syntax-tree`  | 2.22     | npm package  |
 
 Install npm packages as follows:
 
 ```shell
-$ npm install eslint@8.57 [email protected]
+$ npm install eslint@9.10 [email protected]
 ```
 
 ## Kotlin

flake.nix

@@ -9,7 +9,7 @@
       inputs.nixpkgs.follows = "nixpkgs";
     };
     poetry2nix = {
-      url = "github:nix-community/poetry2nix?ref=refs/tags/2024.5.939250";
+      url = "github:nix-community/poetry2nix?ref=refs/tags/2024.10.1637698";
       inputs.nixpkgs.follows = "nixpkgs";
     };
   };
@@ -70,20 +70,45 @@
           };
         };
 
+        nextflow-linter = let
+          codenarc = pkgs.fetchurl {
+            url = "https://repo1.maven.org/maven2/org/codenarc/CodeNarc/3.5.0/CodeNarc-3.5.0-all.jar";
+            hash = "sha256-wTGPxP5sjMPPake3WM6Fcz551WIe8C+c6AtCtjBa3jI=";
+          };
+          linter-rules = pkgs.fetchurl {
+            url = "https://github.com/awslabs/linter-rules-for-nextflow/releases/download/v0.1.0/linter-rules-0.1.jar";
+            hash = "sha256-IHl2jAtZyloZLXybLNBELnTyld+ZA9q5Srta7LeUeHs=";
+          };
+          slf4j-api = pkgs.fetchurl {
+            url = "https://repo1.maven.org/maven2/org/slf4j/slf4j-api/1.7.36/slf4j-api-1.7.36.jar";
+            hash = "sha256-0+9XXj5JeWeNwBvx3M5RAhSTtNEft/G+itmCh3wWocA=";
+          };
+          slf4j-simple = pkgs.fetchurl {
+            url = "https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/1.7.36/slf4j-simple-1.7.36.jar";
+            hash = "sha256-Lzm+2UPWJN+o9BAtBXEoOhCHC2qjbxl6ilBvFHAQwQ8=";
+          };
+        in pkgs.writeScriptBin "nextflow-linter" ''
+            ${pkgs.jre_minimal}/bin/java \
+              -Dorg.slf4j.simpleLogger.defaultLogLevel=error \
+              -classpath "${linter-rules}/linter-rules-0.1.jar:${codenarc}/CodeNarc-3.5.0-all.jar:${slf4j-api}/slf4j-api-1.7.36.jar:${slf4j-simple}/slf4j-simple-1.7.36.jar" \
+              "org.codenarc.CodeNarc"
+        '';
+
         # General dependencies for other languages
         haskell-deps = [
           (pkgs.haskell.packages.ghc96.ghcWithPackages (p: [ p.aeson ]))
           pkgs.hlint
         ];
-        node-deps = [ nodejs_base pkgs.nodePackages.eslint ast ];
+        node-deps = [ nodejs_base pkgs.eslint ast ];
         bash-deps = [ pkgs.shellcheck ];
         c-deps = [ pkgs.cppcheck pkgs.gcc13 ];
         java-deps = [ pkgs.openjdk21 pkgs.checkstyle ];
         kotlin-deps = [ pkgs.kotlin pkgs.ktlint ];
         csharp-deps = [ pkgs.dotnetCorePackages.sdk_8_0 ];
+        nextflow-deps = [ pkgs.nextflow pkgs.groovy nextflow-linter ];
 
         all-other-dependencies = haskell-deps ++ node-deps ++ bash-deps
-          ++ c-deps ++ java-deps ++ kotlin-deps ++ csharp-deps
+          ++ c-deps ++ java-deps ++ kotlin-deps ++ csharp-deps ++ nextflow-deps
           ++ [ pkgs.coreutils ];
 
         python-base-env = {
@@ -124,6 +149,8 @@
               export DOTNET_CLI_HOME
               NODE_PATH=${ast}/lib/node_modules
               export NODE_PATH
+              ESLINT_USE_FLAT_CONFIG=false
+              export ESLINT_USE_FLAT_CONFIG
               poetry run pytest -n auto --cov=tested --cov-report=xml tests/
             '';
             installPhase = ''
@@ -138,7 +165,7 @@
           tested = pkgs.devshell.mkShell {
             name = "TESTed";
 
-            packages = [ python-dev-env pkgs.nodePackages.pyright poetry-package ]
+            packages = [ python-dev-env pkgs.pyright poetry-package ]
               ++ all-other-dependencies;
 
             devshell.startup.link.text = ''
@@ -155,6 +182,19 @@
                 name = "NODE_PATH";
                 prefix = "${ast}/lib/node_modules";
               }
+
+              {
+                name = "ESLINT_USE_FLAT_CONFIG";
+                eval = "false";
+              }
+              {
+                name = "NXF_DISABLE_CHECK_LATEST";
+                eval = "true";
+              }
+              {
+                name = "NXF_OFFLINE";
+                eval = "true";
+              }
             ];
             commands = [
               {
@@ -172,7 +212,7 @@
             ];
           };
           types = pkgs.mkShell {
-            packages = [ python-dev-env pkgs.nodePackages.pyright ];
+            packages = [ python-dev-env pkgs.pyright ];
           };
           format = pkgs.mkShell { packages = [ python-dev-env poetry-package ]; };
         };

tested/internationalization/en.yaml

@@ -107,6 +107,11 @@ en:
         timeout: "HLint exceeded time limit"
         memory: "HLint exceeded memory limit"
         output: "HLint produced bad output."
+    nextflow:
+      linter:
+        timeout: "CodeNarc exceeded time limit"
+        memory: "CodeNarc exceeded memory limit"
+        output: "CodeNarc produced bad output."
     kotlin:
       linter:
         timeout: "KTLint exceeded time limit"

tested/languages/__init__.py

@@ -17,6 +17,7 @@
 from tested.languages.javascript.config import JavaScript
 from tested.languages.kotlin.config import Kotlin
 from tested.languages.language import Language
+from tested.languages.nextflow.config import Nextflow
 from tested.languages.python.config import Python
 from tested.languages.runhaskell.config import RunHaskell
 
@@ -31,6 +32,7 @@
     "java": Java,
     "javascript": JavaScript,
     "kotlin": Kotlin,
+    "nextflow": Nextflow,
     "python": Python,
     "runhaskell": RunHaskell,
     "csharp": CSharp,

tested/languages/haskell/linter.py

@@ -20,7 +20,7 @@ def run_hlint(
     config: DodonaConfig, remaining: float
 ) -> tuple[list[Message], list[AnnotateCode]]:
     """
-    Calls eslint to annotate submitted source code and adds resulting score and
+    Calls hlint to annotate submitted source code and adds resulting score and
     annotations to tab.
     """
     submission = config.source