21 wildcard input handling

WildcardsandConditions/README.md

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+
+# Unit Test for Wildcard Resolution and Conditional Logic (WildcardsandConditions)
+
+## Overview
+
+The `WildcardsandConditions` workflow is a unit test designed to validate the behavior of wildcard resolution and conditional logic in WDL (Workflow Description Language). It includes tests for:
+
+- **Wildcard Resolution**: Ensures that files matching the wildcard pattern (e.g., `*.txt`) are correctly identified and handled in the workflow.
+- **Conditional Logic**: Verifies that conditional logic within the command block works properly, such as the creation of files based on boolean conditions.
+- **Input Parsing**: Confirms that inputs passed to the workflow are correctly parsed and used within the command block.
+
+## Purpose
+
+This workflow serves as a test case for:
+- Wildcard handling in file operations (creating and globbing files).
+- Conditional logic inside the command block (such as `if` statements).
+- Parsing and using workflow inputs in commands.
+- Validation of input parameters (required and default inputs).
+
+## Workflow Components
+
+### Workflow: `WildcardsandConditions`
+
+This workflow demonstrates wildcard handling, conditional file creation, and input parsing in a WDL task.
+
+**Inputs:**
+- `prefix`: String - The prefix used to create files (e.g., `sample`) (required).
+- `create_extra_file`: Boolean - A flag to control the conditional creation of an extra file (optional, defaults to `true`).
+
+**Outputs:**
+- `txt_files`: Array[File] - A list of `.txt` files created in the task, resolved using a wildcard.
+- `conditional_result`: String - The content of the file that shows the parsed `prefix` input.
+
+### Tasks
+
+#### Task: `wildcard_and_conditions_test`
+- **Purpose**: Creates `.txt` files using a wildcard pattern, conditionally creates an extra file, and parses the `prefix` input.
+- **Key Operations**:
+  - Create `.txt` files with a dynamic name using a loop and wildcard.
+  - Conditionally create an additional file based on the `create_extra_file` input.
+  - Output the parsed `prefix` in a file to verify input parsing.
+
+**Runtime Requirements:**
+- **Docker Image**: `ubuntu:20.04`
+- **CPU**: 1 core
+- **Memory**: 1 GB
+
+---
+
+## Usage
+
+### Input JSON
+
+To run the workflow, you need to specify the required `prefix` input in an `inputs.json` file. Here's an example:
+
+```json
+{
+  "WildcardsandConditions.prefix": "testfile",
+  "WildcardsandConditions.create_extra_file": true
+}
+```
+
+You can run the workflow with the following command:
+
+```bash
+# Using Cromwell
+java -jar cromwell.jar run WildcardsandConditions.wdl -i inputs.json
+
+# Using MiniWDL
+miniwdl run WildcardsandConditions.wdl prefix="testfile" create_extra_file=true
+```
+
+### Expected Output Files
+
+1. **txt_files**: This output will contain a list of `.txt` files matching the wildcard pattern (`*.txt`) created during the task execution, including the ones with the prefix provided.
+
+   Example:
+   - `testfile_1.txt`
+   - `testfile_2.txt`
+   - `testfile_3.txt`
+   - If `create_extra_file` is `true`, there will also be `testfile_extra.txt`.
+
+2. **conditional_result**: This output will contain the content of the file created by the task that verifies the parsing of the `prefix` input.
+
+   Example:
+   - Content of `parsed_output.txt`: `"Parsed prefix: testfile"`
+
+---
+
+## Version
+- **WDL Version**: 1.0
+
+---
+
+## Additional Notes
+- This workflow demonstrates the usage of wildcards in WDL, which can be particularly useful when working with large datasets where files follow a consistent naming pattern.
+- The conditional logic in this test checks whether a specific file is created based on the value of the input parameter `create_extra_file`.
+- The workflow also tests how inputs are parsed and used in the command block, allowing for dynamic file creation and manipulation based on workflow parameters.
+- If no value for `prefix` is provided, the workflow will fail with an error message, as the input is required. You can provide a default value in the `input` block if you want to make it optional.
+

WildcardsandConditions/WildcardsandConditions.wdl

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+version 1.0
+
+workflow WildcardsandConditions {
+    input {
+        String prefix  # Required input for the file prefix (no default value)
+    }
+
+    call wildcard_and_conditions_test {
+        input:
+            prefix = prefix  # Explicitly pass the workflow input to the task
+    }
+
+    output {
+        Array[File] txt_files = wildcard_and_conditions_test.txt_files
+        String conditional_result = wildcard_and_conditions_test.conditional_output
+    }
+}
+
+task wildcard_and_conditions_test {
+    input {
+        String prefix  # Required input for file creation
+        Boolean create_extra_file = true  # Default value for conditional logic
+    }
+
+    command <<<
+        # Create multiple .txt files to test wildcard resolution
+        for i in {1..3}; do
+            echo "File content $i" > ~{prefix}_$i.txt
+        done
+
+        # Create an extra file conditionally
+        if [[ ~{create_extra_file} == "true" ]]; then
+            echo "Extra file content" > ~{prefix}_extra.txt
+        fi
+
+        # Parse inputs directly in the command
+        echo "Parsed prefix: ~{prefix}" > parsed_output.txt
+    >>>
+
+    output {
+        Array[File] txt_files = glob("*.txt")  # Test wildcard resolution
+        String conditional_output = read_string("parsed_output.txt")  # Verify input parsing
+    }
+
+    runtime {
+        docker: "ubuntu:20.04"
+    }
+}

WildcardsandConditions/inputs.json

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+{
+  "WildcardsandConditions.prefix": "testfile"
+}