From 8f212f8ea46cd33856125037485c6446d6946100 Mon Sep 17 00:00:00 2001 From: Nicole Zeltser Date: Wed, 14 Feb 2024 12:41:03 -0800 Subject: [PATCH 1/7] update README --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 2d4f0b0..ed14de7 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -# Targeted Coverage +# Compute Targeted Coverage -- [Targeted Coverage](#pipeline-name) +- [Compute 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-compute-targeted-coverage graph](pipeline-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-compute-targeted-coverage Discussions](https://github.com/uclahs-cds/pipeline-targeted-coverage/discussions) +- [pipeline-compute-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-compute-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-targeted-coverage performs read-depth related calculations on BAMs from targeted sequencing experiments. +pipeline-compute-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. From 4bdd9c6bb82d380136feec1da2a804624ae2d1b9 Mon Sep 17 00:00:00 2001 From: Nicole Zeltser Date: Wed, 14 Feb 2024 12:42:20 -0800 Subject: [PATCH 2/7] rename graph --- README.md | 2 +- ....drawio.svg => pipeline-compute-targeted-coverage.drawio.svg | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename pipeline-targeted-coverage.drawio.svg => pipeline-compute-targeted-coverage.drawio.svg (100%) diff --git a/README.md b/README.md index ed14de7..150c7f4 100644 --- a/README.md +++ b/README.md @@ -42,7 +42,7 @@ This pipeline performs coverage calculations from a BAM file at intervals specif A directed acyclic graph of your pipeline. -![pipeline-compute-targeted-coverage graph](pipeline-targeted-coverage.drawio.svg?raw=true) +![pipeline-compute-targeted-coverage graph](pipeline-compute-targeted-coverage.drawio.svg?raw=true) --- diff --git a/pipeline-targeted-coverage.drawio.svg b/pipeline-compute-targeted-coverage.drawio.svg similarity index 100% rename from pipeline-targeted-coverage.drawio.svg rename to pipeline-compute-targeted-coverage.drawio.svg From 27cb35b9cbbe6481de312015f3ac9aac87aac39f Mon Sep 17 00:00:00 2001 From: Nicole Zeltser Date: Wed, 14 Feb 2024 12:44:48 -0800 Subject: [PATCH 3/7] update changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9aaef53..146e1af 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,5 @@ # Changelog -All notable changes to the pipeline-name pipeline. +All notable changes to the compute-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 From 1ebfcb79a413a7584297b916f700673646417367 Mon Sep 17 00:00:00 2001 From: Nicole Zeltser Date: Wed, 14 Feb 2024 12:50:01 -0800 Subject: [PATCH 4/7] update manifest --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index fa4c470..deee2e9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ // Metadata manifest { - name = 'targeted-coverage' + name = 'compute-targeted-coverage' author = 'Nicole Zeltser' description = 'Nextflow pipeline for calculating read-depth related statistics for targeted sequencing experiments' version = '1.0.0-rc.1' From 14304355d665f60da0df6ded173cc35ed853c84f Mon Sep 17 00:00:00 2001 From: Nicole Zeltser Date: Wed, 14 Feb 2024 14:33:21 -0800 Subject: [PATCH 5/7] change from compute to calculate --- CHANGELOG.md | 2 +- README.md | 14 +++++++------- nextflow.config | 2 +- ...pipeline-calculate-targeted-coverage.drawio.svg | 0 4 files changed, 9 insertions(+), 9 deletions(-) rename pipeline-compute-targeted-coverage.drawio.svg => pipeline-calculate-targeted-coverage.drawio.svg (100%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 146e1af..cfe8f85 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,5 @@ # Changelog -All notable changes to the compute-targeted-coverage 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/). diff --git a/README.md b/README.md index 150c7f4..37d697d 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -# Compute Targeted Coverage +# Calculate Targeted Coverage -- [Compute 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-compute-targeted-coverage graph](pipeline-compute-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-compute-targeted-coverage Discussions](https://github.com/uclahs-cds/pipeline-targeted-coverage/discussions) -- [pipeline-compute-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-compute-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. -pipeline-compute-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. diff --git a/nextflow.config b/nextflow.config index deee2e9..1170297 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ // Metadata manifest { - name = 'compute-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' diff --git a/pipeline-compute-targeted-coverage.drawio.svg b/pipeline-calculate-targeted-coverage.drawio.svg similarity index 100% rename from pipeline-compute-targeted-coverage.drawio.svg rename to pipeline-calculate-targeted-coverage.drawio.svg From 7c5cc671f14714f1c0fb6a2cd5718811133807e5 Mon Sep 17 00:00:00 2001 From: Nicole Zeltser Date: Wed, 14 Feb 2024 15:38:39 -0800 Subject: [PATCH 6/7] update main.nf --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index b95218d..052c9a7 100644 --- a/main.nf +++ b/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 From 59b0824907e155ca16eb54cae80c56a42c6a1a59 Mon Sep 17 00:00:00 2001 From: Nicole Zeltser Date: Wed, 14 Feb 2024 15:46:11 -0800 Subject: [PATCH 7/7] fix yaml formatting --- .github/dependabot.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index b65abd5..e2dd116 100644 --- a/.github/dependabot.yml +++ b/.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"