Merge pull request #60 from FredHutch/nonstandard-outputs

Adding initial version of nonstandard outputs WDL unit test

nonstandardOutputs/README.md

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+# Unit test for Nonstandard Outputs
+
+## Overview
+The test_nonstandard_outputs workflow is a unit test designed to validate and demonstrate handling of various non-standard output file scenarios in WDL (Workflow Description Language). It tests the workflow engine's ability to handle:
+
+- Files with special characters in names
+- Files without extensions
+- Files in nested directories
+- Symbolic links
+- Pattern-based file globbing
+
+## Purpose
+This workflow serves as a comprehensive test case for:
+- Special character handling in file names
+- Path handling for files without extensions
+- Nested directory structure handling
+- Symbolic link resolution
+- Glob pattern file collection
+- File system operations
+- Output file declaration patterns
+- Docker container file system interaction
+
+## Workflow Components
+
+### Workflow: `test_nonstandard_outputs`
+The main workflow demonstrates various non-standard output file handling capabilities.
+
+**Outputs:**
+- `special_chars`: File - Output file containing special characters in name
+- `no_extension`: File - Output file without a file extension
+- `nested_output`: File - Output file from a nested directory structure
+- `symlink_file`: File - Symbolic link to another file
+- `glob_files`: Array[File] - Collection of files matching a pattern
+
+### Tasks
+
+#### Task: `generate_diverse_outputs`
+Creates various types of output files to test the workflow engine's handling capabilities.
+
+**Operations:**
+- Creates a file with special characters (@, #) in the name
+- Generates a file without an extension
+- Creates a nested directory structure with files
+- Creates and manages symbolic links
+- Generates multiple files matching a pattern
+
+**Runtime Requirements:**
+- Docker: ubuntu:noble-20241118.1
+
+## Usage
+```bash
+# Execute with cromwell
+java -jar cromwell.jar run nonstandardOutputs.wdl
+
+# Execute with miniwdl
+miniwdl run nonstandardOutputs.wdl
+```
+
+No input parameters are required for this workflow.
+
+Expected outputs:
+```
+outputs/
+├── special_chars        # File named "test@file#1.txt"
+├── no_extension        # File named "datafile"
+├── nested_output      # File from nested/dir/test.txt
+├── symlink_file       # Symbolic link "link.txt"
+└── glob_files/        # Directory containing pattern_*.out files
+    ├── pattern_1.out
+    ├── pattern_2.out
+    └── pattern_3.out
+```
+
+## Version
+WDL 1.0
+
+## Additional Notes
+- Tests workflow engine's ability to handle non-standard file names
+- Verifies proper handling of nested directory structures
+- Validates symbolic link resolution
+- Demonstrates glob pattern functionality
+- Tests Docker container file system interactions
+- Useful for validating output handling in different execution environments
+- Helps identify potential file system compatibility issues
+- Verifies proper path resolution and file access patterns

nonstandardOutputs/nonstandardOutputs.wdl

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+version 1.0
+
+workflow test_nonstandard_outputs {
+    call generate_diverse_outputs
+
+    output {
+        File special_chars = generate_diverse_outputs.file_special_chars
+        File no_extension = generate_diverse_outputs.file_no_extension
+        File nested_output = generate_diverse_outputs.nested_file
+        File symlink_file = generate_diverse_outputs.symlink_output
+        Array[File] glob_files = generate_diverse_outputs.pattern_files
+    }
+}
+
+task generate_diverse_outputs {
+    command <<<
+        # File with special characters
+        echo "test content" > "test@file#1.txt"
+
+        # File without extension
+        echo "no extension" > datafile
+
+        # Nested directory output
+        mkdir -p nested/dir
+        echo "nested content" > nested/dir/test.txt
+
+        # Create a symlink
+        echo "original" > original.txt
+        ln -s original.txt link.txt
+
+        # Multiple pattern files
+        for i in {1..3}; do
+            echo "pattern $i" > "pattern_$i.out"
+        done
+    >>>
+
+    output {
+        File file_special_chars = "test@file#1.txt"
+        File file_no_extension = "datafile"
+        File nested_file = "nested/dir/test.txt"
+        File symlink_output = "link.txt"
+        Array[File] pattern_files = glob("pattern_*.out")
+    }
+
+    runtime {
+        docker: "ubuntu:noble-20241118.1"
+    }
+}

nonstandardOutputs/options.json

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+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}