From c2e84c9864c4633348bdc092646c65e1e9a9c7a2 Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Wed, 15 Mar 2023 10:34:38 +0000
Subject: [PATCH] Include clean up script

Former-commit-id: 6002103a38d9ef253953a409715fca80dd37cb79
---
 README.md      | 19 +++++++++++++++----
 clean_pipeline |  8 ++++++++
 2 files changed, 23 insertions(+), 4 deletions(-)
 create mode 100755 clean_pipeline

diff --git a/README.md b/README.md
index 2572b37..8b82a36 100644
--- a/README.md
+++ b/README.md
@@ -101,16 +101,27 @@ The development of this pipeline is part of the GPS Project ([Global Pneumococca
 
 ## Clean Up
 - During the run of the pipeline, Nextflow generates a considerable amount of intermediate files
-- If the run has been completed and you do not intend to use the `-resume` option, you can remove the intermediate files by one of following two ways:
-  - Manual removal - remove the `work` directory within the `gps-unified-pipeline` local repository
+- If the run has been completed and you do not intend to use the `-resume` option, you can remove the intermediate files by one of following three ways:
+  - Run `clean_pipeline` script
+    - It runs the commands in manual removal for you
+    - It removes the `work` directory and log files within the `gps-unified-pipeline` local repository
+    ```
+    ./clean_pipeline
+    ```
+  - Manual removal 
+    - Remove the `work` directory and log files within the `gps-unified-pipeline` local repository
     ```
     rm -rf work
+    rm -rf .nextflow.log*
     ```
-  - `nextflow clean` command - use this built-in command to clean up cache and work directories  (default: the latest run only)
+  - Run `nextflow clean` command
+    - This built-in command clean up cache and work directories
+    - By default, it only clean up the latest run
+    - For details and available options of `nextflow clean`, refer to the [Nextflow documentation](https://www.nextflow.io/docs/latest/cli.html#clean)
     ```
     ./nextflow clean
     ```
-    For options of `nextflow clean`, refer to the [Nextflow documentation](https://www.nextflow.io/docs/latest/cli.html#clean)
+    
     
 &nbsp;
 # Pipeline Options
diff --git a/clean_pipeline b/clean_pipeline
new file mode 100755
index 0000000..31c70e3
--- /dev/null
+++ b/clean_pipeline
@@ -0,0 +1,8 @@
+#! /bin/sh
+
+# Basic wrapper script, clean-up tasks temporary files and log files
+
+pipelineDir=$(dirname -- "$(readlink -f -- "$0")")
+
+rm -rf $pipelineDir/work
+rm -rf $pipelineDir/.nextflow.log*
\ No newline at end of file