Add documentation about the Nextflow judge

en/references/judges/index.md

@@ -45,6 +45,12 @@ It does render the Markdown code of a student and can be useful to manually eval
 **Get started** [Documentation](https://github.com/dodona-edu/judge-markdown) \
 **Created by:** [Team Dodona](mailto:[email protected])
 
+## Nextflow
+The Nextflow judge uses CodeNarc to lint workflows and also checks the existence of produced files.\
+**Programming languages:** Nextflow\
+**Get started** [Git repo](https://github.com/dodona-edu/judge-nextflow), [examples](https://github.com/Bond-009/dodona-nextflow-exercises) \
+**Created by:** [Lode Willems](mailto:[email protected])
+
 ## Prolog
 Prolog is a judge that can be used for exercises on the Prolog programming language.
 It supports PLUnit, QuickCheck and simple input output tests.\

en/references/judges/nextflow-judge/index.md

@@ -0,0 +1,47 @@
+---
+title: "Nextflow judge"
+description: "Nextflow judge"
+order: 7
+---
+# Nextflow judge
+
+The Nextflow judge annotates the submitted code using CodeNarc, executes the submitted script and optionally checks the existence of directories and files.
+The following bioinformatics tools are available by default:
+* FastQC
+* MultiQC
+* Trimmomatic.
+
+Also available are Perl and Python3.
+
+## Configuration
+
+The judge configuration is split between multiple files.
+
+Passing extra argument to Nextflow can be accomplished by modifying the exercises `config.json`:
+```json
+{
+  "evaluation": {
+    "nextflow_arguments": "--reads /dev/null"
+  }
+}
+```
+
+A `judge.json` configuration file inside of the `evaluation` directory that contains a JSON array of JSON objects.
+Each object represents either a file or a directory, this is specified by the `type` property.
+The object contains a `path` property which contains the expected location of the file/directory.
+
+An example `judge.json`:
+```json
+[
+    { "type": "directory", "path": "work" },
+    { "type": "file", "path": "ggal_gut_1_fastqc.html" },
+    { "type": "file", "path": "ggal_gut_1_fastqc.zip" },
+    { "type": "file", "path": "ggal_gut_2_fastqc.html" },
+    { "type": "file", "path": "ggal_gut_2_fastqc.zip" },
+    { "type": "directory", "path": "multiqc" },
+    { "type": "file", "path": "multiqc/multiqc_report.html" }
+]
+```
+
+### Scripts
+Due to limited resources available to the judge, it isn't always possible to run the tools required for an exercise. To work around this limitation, I suggest you create a dummy script that emulates the behaviour of the required tool, this script should be placed inside of the `resources/bin` directory of the exercise.