3 file handling create move rename

testFileoperations/README.md

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+# Unit Test for File Operations (testFileoperations)
+
+## Overview
+The `testFileoperations` workflow is a unit test designed to validate and demonstrate essential file manipulation capabilities in WDL (Workflow Description Language). It includes tests for:
+
+- Creating multiple files within a task environment.
+- Moving a file to a specific directory.
+- Renaming a file to a new name.
+- Ensuring all intermediate and final file states are properly handled and outputted.
+
+## Purpose
+This workflow is intended to:
+- Verify file creation and content generation during task execution.
+- Test file relocation to specified directories.
+- Validate file renaming to new names.
+- Ensure proper handling and cleanup of intermediate file states.
+- Confirm that all required files are accessible as task outputs after execution.
+
+## Workflow Components
+
+### Workflow: `testFileoperations`
+This workflow demonstrates creating three files, moving one of them to a new directory, and renaming another.
+
+**Inputs:**
+- No inputs are required. All operations are self-contained within the task.
+
+**Outputs:**
+- `created_file1`: File - The first file created during task execution.
+- `moved_file`: File - The second file after being moved to a new directory.
+- `renamed_file`: File - The third file after being renamed.
+
+### Tasks
+
+#### Task: `file_operations`
+Performs the following operations:
+1. Creates three files: `file1.txt`, `file2.txt`, and `file3.txt`.
+2. Moves `file2.txt` to the `output_dir` directory.
+3. Renames `file3.txt` to `file3_renamed.txt`.
+
+**Task Outputs:**
+- `created_file1`: The file `file1.txt`, which remains in the root directory.
+- `moved_file`: The file `file2.txt` after being moved to `output_dir`.
+- `renamed_file`: The file `file3.txt` after being renamed to `file3_renamed.txt`.
+
+**Runtime Requirements:**
+- CPU: 1 core
+- Memory: 1 GB
+- Docker: `ubuntu:20.04`
+
+## Usage
+```bash
+# Execute with Cromwell
+java -jar cromwell.jar run testFileoperations.wdl
+
+# Execute with MiniWDL
+miniwdl run testFileoperations.wdl
+```
+
+This workflow does not require any input JSON as it is fully self-contained.
+
+## Outputs Directory
+Upon successful execution, the output directory will contain:
+- `file1.txt`: The first created file.
+- `output_dir/file2.txt`: The file after being moved to the `output_dir` directory.
+- `file3_renamed.txt`: The file after being renamed.
+- Execution logs (`stdout` and `stderr`) for debugging purposes.
+
+## Example Outputs
+- `file1.txt`:
+  ```
+  This is the first created file.
+  ```
+- `output_dir/file2.txt`:
+  ```
+  This is the second file that will be moved.
+  ```
+- `file3_renamed.txt`:
+  ```
+  This is the third file that will be renamed.
+  ```
+
+## Version
+WDL 1.0

testFileoperations/testFileoperations.wdl

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+version 1.0
+
+workflow testFileoperations {
+    call file_operations
+
+    output {
+        File created_file1 = file_operations.created_file1
+        File moved_file = file_operations.moved_file
+        File renamed_file = file_operations.renamed_file
+    }
+}
+
+task file_operations {
+    command <<<
+        # Create three different files
+        echo "This is the first created file." > file1.txt
+        echo "This is the second file that will be moved." > file2.txt
+        echo "This is the third file that will be renamed." > file3.txt
+
+        # Move the second file to a new directory
+        mkdir -p output_dir
+        mv file2.txt output_dir/
+
+        # Rename the third file
+        mv file3.txt file3_renamed.txt
+    >>>
+
+    output {
+        # Output the actual existing files
+        File created_file1 = "file1.txt"                  # The first file remains unchanged
+        File moved_file = "output_dir/file2.txt"          # The second file after being moved
+        File renamed_file = "file3_renamed.txt"           # The third file after being renamed
+    }
+
+    runtime {
+        docker: "ubuntu:20.04"
+    }
+}