From badabb29c54af63519bb1adf69712e82aafd2d0c Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Fri, 22 Dec 2023 14:15:30 -0800
Subject: [PATCH 1/3] add indexFile

---
 CHANGELOG.md                     |  1 +
 README.md                        | 11 +++++++++++
 modules/common/indexFile/main.nf | 16 ++++++++++++++++
 3 files changed, 28 insertions(+)
 create mode 100644 modules/common/indexFile/main.nf

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3135094..3cdcbde 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 ### Added
+- Add `indexFile` module to return index file path
 - Add intermediate file/directory removal module
 - Add genome interval extraction module
 - Add PipeVal validation module
diff --git a/README.md b/README.md
index 9438269..69d818a 100644
--- a/README.md
+++ b/README.md
@@ -188,6 +188,17 @@ Parameters:
 3. Use the `addParams` directive when importing to specify any params.
 4. Call the process with the input channel, a tuple with `id` and `file_path`.
 
+### Return Expected Index File
+##### Description
+Module returns the expected path to the index file for a given input file.
+NOTE! This does not check for the existence of the index file.
+
+Inputs:
+ - input_file: currently supports BAM or VCF
+
+Output:
+ - The input file path with the expected index extension appended: currently `.bai` for BAM files and `.tbi` for VCF files
+
 ## License
 
 Author: Yash Patel (YashPatel@mednet.ucla.edu)
diff --git a/modules/common/indexFile/main.nf b/modules/common/indexFile/main.nf
new file mode 100644
index 0000000..75d9456
--- /dev/null
+++ b/modules/common/indexFile/main.nf
@@ -0,0 +1,16 @@
+/**
+*   Module returns the expected path to a file's index file.
+*   Note that this is not a check for the existence of the index file.
+*/
+
+def indexFile(Object bam_or_vcf) {
+    if(bam_or_vcf.endsWith('.bam')) {
+        return "${bam_or_vcf}.bai"
+        }
+    else if(bam_or_vcf.endsWith('vcf.gz')) {
+        return "${bam_or_vcf}.tbi"
+        }
+    else {
+        throw new Exception("Index file for ${bam_or_vcf} file type not supported. Use .bam or .vcf.gz files.")
+        }
+    }

From de5323bcc24d1140047e74ff4876c144caa43969 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Mon, 8 Jan 2024 12:49:19 -0800
Subject: [PATCH 2/3] update readme

---
 README.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/README.md b/README.md
index 69d818a..05ea58f 100644
--- a/README.md
+++ b/README.md
@@ -199,6 +199,11 @@ Inputs:
 Output:
  - The input file path with the expected index extension appended: currently `.bai` for BAM files and `.tbi` for VCF files
 
+##### How to use
+1. Add this repository as a submodule in the pipeline of interest.
+2. Include the `indexFile` process from the module `main.nf` with a relative path.
+3. Call the function as needed with the approriate input and use returned value as index file name
+
 ## License
 
 Author: Yash Patel (YashPatel@mednet.ucla.edu)

From fcd7ad63e5545f593fe9cf69d9171c16b861673b Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <3223552+sorelfitzgibbon@users.noreply.github.com>
Date: Mon, 8 Jan 2024 13:10:52 -0800
Subject: [PATCH 3/3] Update README.md

Co-authored-by: Yash Patel <86321070+yashpatel6@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 05ea58f..47cfffc 100644
--- a/README.md
+++ b/README.md
@@ -201,7 +201,7 @@ Output:
 
 ##### How to use
 1. Add this repository as a submodule in the pipeline of interest.
-2. Include the `indexFile` process from the module `main.nf` with a relative path.
+2. Include the `indexFile` function from the module `main.nf` with a relative path.
 3. Call the function as needed with the approriate input and use returned value as index file name
 
 ## License