feat: Add real pipeline execution and documentation structure

- Create sample FASTA input data for basic pipeline example
- Generate actual pipeline execution output in _nextflow_run_output.log
- Update index.mdx to import real terminal output instead of hardcoded
- Add comprehensive _README.md explaining examples directory structure and conventions

Author: edmundmiller

.gitignore

@@ -29,3 +29,7 @@ pnpm-debug.log*
 
 # macOS-specific files
 .DS_Store
+
+# Nextflow execution artifacts
+src/pages/examples/*/work/
+src/pages/examples/*/.nextflow*

src/pages/examples/_README.md

@@ -0,0 +1,48 @@
+# Nextflow Examples
+
+This directory contains example Nextflow pipelines with their documentation pages.
+
+## Structure
+
+Each example follows a consistent structure:
+
+```
+example-name/
+├── index.mdx           # Documentation page with explanation
+├── _main.nf            # Nextflow pipeline script
+├── _nextflow_run_output.log  # Captured pipeline execution output
+└── data/               # Input data files (if needed)
+    └── sample.fa       # Sample input file
+```
+
+## File Naming Convention
+
+- **`_main.nf`**: Pipeline script (prefixed with `_` to avoid conflicts with actual `main.nf`)
+- **`_nextflow_run_output.log`**: Raw terminal output from running the pipeline
+- **`index.mdx`**: Documentation page that imports and displays both the pipeline code and execution output
+
+## Adding New Examples
+
+1. Create a new directory with a descriptive name
+2. Add the pipeline script as `_main.nf`
+3. Create any necessary input data in a `data/` subdirectory
+4. Run the pipeline and capture output:
+   ```bash
+   nextflow run _main.nf > _nextflow_run_output.log 2>&1
+   ```
+5. Create an `index.mdx` file that imports both files:
+   ```javascript
+   import pipelineCode from "./_main.nf?raw";
+   import terminalOutput from "./_nextflow_run_output.log?raw";
+   ```
+
+## Documentation Pages
+
+Each `index.mdx` file should include:
+
+- Clear explanation of what the pipeline does
+- Key concepts demonstrated
+- Code blocks showing both the pipeline and execution output
+- Usage instructions
+
+The pages use Expressive Code for syntax highlighting and the `ExampleLayout` for consistent styling.

src/pages/examples/basic-pipeline/.lineage/353fef4d82cbc905aa582366ec9fe84d#output/.data.json

@@ -0,0 +1 @@
+{"version":"lineage/v1beta1","kind":"TaskOutput","taskRun":"lid://353fef4d82cbc905aa582366ec9fe84d","workflowRun":"lid://d47025256f47dd1e4fd84d78cd12c7ca","createdAt":"2025-09-22T14:08:37.730548+02:00","output":[{"type":"stdout","name":"-","value":"work/35/3fef4d82cbc905aa582366ec9fe84d/.command.out"}],"labels":null}

src/pages/examples/basic-pipeline/.lineage/353fef4d82cbc905aa582366ec9fe84d/.data.json

@@ -0,0 +1 @@
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src/pages/examples/basic-pipeline/.lineage/5b90121520ef574e2f422b42e9fb9ead/.data.json

@@ -0,0 +1 @@
+{"version":"lineage/v1beta1","kind":"WorkflowRun","workflow":{"scriptFiles":[{"path":"file:///Users/edmundmiller/src/nextflow/website/src/pages/examples/basic-pipeline/_main.nf","checksum":{"value":"a40093cb6f1a707631bdb2cc638f063b","algorithm":"nextflow","mode":"standard"}}],"repository":null,"commitId":null},"sessionId":"5b4e4c92-2182-4ba4-8726-eae8b5964764","name":"distraught_volhard","params":[{"type":"String","name":"in","value":"file:///Users/edmundmiller/src/nextflow/website/src/pages/examples/basic-pipeline/data/sample.fa"}],"config":{"lineage":{"enabled":true},"plugins":["[email protected]"],"notify":{"enabled":true},"env":{},"session":{},"params":{},"process":{},"executor":{},"runName":"distraught_volhard","workDir":"work","poolSize":11}}

src/pages/examples/basic-pipeline/.lineage/809a9010a53762cea68c40b48298b571#output/.data.json

@@ -0,0 +1 @@
+{"version":"lineage/v1beta1","kind":"TaskOutput","taskRun":"lid://809a9010a53762cea68c40b48298b571","workflowRun":"lid://5b90121520ef574e2f422b42e9fb9ead","createdAt":"2025-09-22T14:07:58.826041+02:00","output":[{"type":"path","name":null,"value":null}],"labels":null}

src/pages/examples/basic-pipeline/.lineage/809a9010a53762cea68c40b48298b571/.data.json

@@ -0,0 +1 @@
+{"version":"lineage/v1beta1","kind":"TaskRun","sessionId":"5b4e4c92-2182-4ba4-8726-eae8b5964764","name":"splitSequences","codeChecksum":{"value":"196efff40b1dca3b894e5ef10fad7272","algorithm":"nextflow","mode":"standard"},"script":"\n    awk \u0027/^\u003e/{f\u003d\"seq_\"++d} {print \u003e f}\u0027 \u003c input.fa\n    ","input":[{"type":"path","name":"input.fa","value":[{"path":"file:///Users/edmundmiller/src/nextflow/website/src/pages/examples/basic-pipeline/data/sample.fa","checksum":{"value":"179b114eed46ac32f86b37b28dc76523","algorithm":"nextflow","mode":"standard"}}]}],"container":null,"conda":null,"spack":null,"architecture":null,"globalVars":{},"binEntries":[],"workflowRun":"lid://5b90121520ef574e2f422b42e9fb9ead"}

src/pages/examples/basic-pipeline/.lineage/ad0cf5df695d37a927d1a350f993d41b#output/.data.json

@@ -0,0 +1 @@
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src/pages/examples/basic-pipeline/.lineage/ad0cf5df695d37a927d1a350f993d41b/.data.json

@@ -0,0 +1 @@
+{"version":"lineage/v1beta1","kind":"TaskRun","sessionId":"7fb62998-8140-42e2-9251-d7a1af41fde5","name":"splitSequences","codeChecksum":{"value":"196efff40b1dca3b894e5ef10fad7272","algorithm":"nextflow","mode":"standard"},"script":"\n    awk \u0027/^\u003e/{f\u003d\"seq_\"++d} {print \u003e f}\u0027 \u003c input.fa\n    ","input":[{"type":"path","name":"input.fa","value":[{"path":"file:///Users/edmundmiller/src/nextflow/website/src/pages/examples/basic-pipeline/data/sample.fa","checksum":{"value":"8cd42ac5563c15da91c7d7f6cf146817","algorithm":"nextflow","mode":"standard"}}]}],"container":null,"conda":null,"spack":null,"architecture":null,"globalVars":{},"binEntries":[],"workflowRun":"lid://d47025256f47dd1e4fd84d78cd12c7ca"}

src/pages/examples/basic-pipeline/.lineage/ad0cf5df695d37a927d1a350f993d41b/seq_1/.data.json

@@ -0,0 +1 @@
+{"version":"lineage/v1beta1","kind":"FileOutput","path":"/Users/edmundmiller/src/nextflow/website/src/pages/examples/basic-pipeline/work/ad/0cf5df695d37a927d1a350f993d41b/seq_1","checksum":{"value":"a8191c573d3614d662df8fe0de70c411","algorithm":"nextflow","mode":"standard"},"source":"lid://ad0cf5df695d37a927d1a350f993d41b","workflowRun":"lid://d47025256f47dd1e4fd84d78cd12c7ca","taskRun":"lid://ad0cf5df695d37a927d1a350f993d41b","size":19,"createdAt":"2025-09-22T14:08:37+02:00","modifiedAt":"2025-09-22T14:08:37.513506231+02:00","labels":null}