add indexFile

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

README.md

@@ -188,6 +188,22 @@ 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
+
+##### 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 ([email protected])

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.")
+        }
+    }