update pipeline name

.github/dependabot.yml

@@ -1,6 +1,7 @@
+---
 version: 2
 updates:
-  - package-ecosystem: "gitsubmodule" # See documentation for possible values
-    directory: "/" # Location of package manifests
+  - package-ecosystem: "gitsubmodule"  # See documentation for possible values
+    directory: "/"  # Location of package manifests
     schedule:
       interval: "weekly"

CHANGELOG.md

@@ -1,5 +1,5 @@
 # Changelog
-All notable changes to the pipeline-name pipeline.
+All notable changes to the calculate-targeted-coverage pipeline.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
@@ -8,6 +8,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+### Changed
+- Update pipeline name to match Boutros Lab standards
 
 ## [v1.0.0-rc.1] - 2023-01-09
 ### Added

README.md

@@ -1,6 +1,6 @@
-# Targeted Coverage
+# Calculate Targeted Coverage
 
-- [Targeted Coverage](#pipeline-name)
+- [Calculate Targeted Coverage](#pipeline-name)
   - [Overview](#overview)
   - [How To Run](#how-to-run)
   - [Flow Diagram](#flow-diagram)
@@ -42,7 +42,7 @@ This pipeline performs coverage calculations from a BAM file at intervals specif
 
 A directed acyclic graph of your pipeline.
 
-![pipeline-targeted-coverage graph](pipeline-targeted-coverage.drawio.svg?raw=true)
+![pipeline-calculate-targeted-coverage graph](pipeline-calculate-targeted-coverage.drawio.svg?raw=true)
 
 ---
 
@@ -174,8 +174,8 @@ Included is a template for validating your input files. For more information on
 ## Discussions
 
 - [Issue tracker](https://github.com/uclahs-cds/pipeline-targeted-coverage/issues) to report errors and enhancement ideas.
-- Discussions can take place in [pipeline-targeted-coverage Discussions](https://github.com/uclahs-cds/pipeline-targeted-coverage/discussions)
-- [pipeline-targeted-coverage pull requests](https://github.com/uclahs-cds/pipeline-targeted-coverage/pulls) are also open for discussion.
+- Discussions can take place in [pipeline-calculate-targeted-coverage Discussions](https://github.com/uclahs-cds/pipeline-targeted-coverage/discussions)
+- [pipeline-calculate-targeted-coverage pull requests](https://github.com/uclahs-cds/pipeline-targeted-coverage/pulls) are also open for discussion.
 
 ---
 
@@ -187,10 +187,10 @@ Please see list of [Contributors](https://github.com/uclahs-cds/pipeline-targete
 
 ## License
 
-pipeline-targeted-coverage is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
+pipeline-calculate-targeted-coverage is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
 
 <one line to give the program's name and a brief idea of what it does.>
-pipeline-targeted-coverage performs read-depth related calculations on BAMs from targeted sequencing experiments.
+pipeline-calculate-targeted-coverage performs read-depth related calculations on BAMs from targeted sequencing experiments.
 
 Copyright (C) 2022 University of California Los Angeles ("Boutros Lab") All rights reserved.
 

main.nf

@@ -29,7 +29,7 @@ include { generate_checksum_PipeVal as generate_sha512sum } from './external/pip
 // Log info here
 log.info """\
         ======================================
-        T A R G E T E D - C O V E R A G E
+        C A L C U L A T E - T A R G E T E D - C O V E R A G E
         ======================================
         Boutros Lab
 

nextflow.config

@@ -1,6 +1,6 @@
 // Metadata
 manifest {
-    name = 'targeted-coverage'
+    name = 'calculate-targeted-coverage'
     author = 'Nicole Zeltser'
     description = 'Nextflow pipeline for calculating read-depth related statistics for targeted sequencing experiments'
     version = '1.0.0-rc.1'