From 9a3b6dc3824b7089390427d22c5ef5cfc38ab53e Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 11 Jul 2024 14:36:06 -0400 Subject: [PATCH 1/3] docs: add Zenodo doi resolves #74 --- CHANGELOG.md | 4 ++++ CITATION.cff | 4 ++++ README.md | 9 ++++++++- docs/index.md | 9 ++++++++- 4 files changed, 24 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e557bba..9d6c0be 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## development version + +- You can now cite XAVIER with the DOI [10.5281/zenodo.12727316](https://doi.org/10.5281/zenodo.12727316). + ## XAVIER 3.0.3 - Bug fixes: diff --git a/CITATION.cff b/CITATION.cff index e8fb07c..3df235b 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -32,5 +32,9 @@ url: https://ccbr.github.io/XAVIER/ repository-code: https://github.com/CCBR/XAVIER license: MIT type: software +identifiers: + - description: Archived snapshots of all versions + type: doi + value: 10.5281/zenodo.12727315 version: 3.0.3 date-released: 2024-07-11 diff --git a/README.md b/README.md index b70253f..fe8ad24 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,11 @@ -# XAVIER - e**X**ome **A**nalysis and **V**ariant explor**ER** 🔬 [![tests](https://github.com/CCBR/XAVIER/workflows/tests/badge.svg)](https://github.com/CCBR/XAVIER/actions/workflows/main.yaml) [![docs](https://github.com/CCBR/XAVIER/workflows/docs/badge.svg)](https://github.com/CCBR/XAVIER/actions/workflows/docs.yml) [![Docker Pulls](https://img.shields.io/docker/pulls/nciccbr/ccbr_wes_base)](https://hub.docker.com/r/nciccbr/ccbr_wes_base) [![GitHub issues](https://img.shields.io/github/issues/CCBR/XAVIER?color=brightgreen)](https://github.com/CCBR/XAVIER/issues) [![GitHub license](https://img.shields.io/github/license/CCBR/XAVIER)](https://github.com/CCBR/XAVIER/blob/main/LICENSE) +# XAVIER - e**X**ome **A**nalysis and **V**ariant explor**ER** 🔬 + +[![tests](https://github.com/CCBR/XAVIER/workflows/tests/badge.svg)](https://github.com/CCBR/XAVIER/actions/workflows/main.yaml) +[![docs](https://github.com/CCBR/XAVIER/workflows/docs/badge.svg)](https://github.com/CCBR/XAVIER/actions/workflows/docs.yml) +[![Docker Pulls](https://img.shields.io/docker/pulls/nciccbr/ccbr_wes_base)](https://hub.docker.com/r/nciccbr/ccbr_wes_base) +[![GitHub Issues](https://img.shields.io/github/issues/CCBR/XAVIER?color=brightgreen)](https://github.com/CCBR/XAVIER/issues) +[![MIT license](https://img.shields.io/github/license/CCBR/XAVIER)](https://github.com/CCBR/XAVIER/blob/main/LICENSE) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12727316.svg)](https://doi.org/10.5281/zenodo.12727316) > **_*XAVIER - eXome Analysis and Variant explorER*_**. This is the home of the pipeline, XAVIER. Its long-term goals: to accurately call germline and somatic variants, to infer CNVs, and to boldly annotate variants like no pipeline before! diff --git a/docs/index.md b/docs/index.md index d7afdb6..344926a 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,4 +1,11 @@ -# XAVIER 🔬 [![tests](https://github.com/CCBR/XAVIER/workflows/tests/badge.svg)](https://github.com/CCBR/XAVIER/actions/workflows/main.yaml) [![docs](https://github.com/CCBR/XAVIER/workflows/docs/badge.svg)](https://github.com/CCBR/XAVIER/actions/workflows/docs.yml) [![Docker Pulls](https://img.shields.io/docker/pulls/nciccbr/ccbr_wes_base)](https://hub.docker.com/r/nciccbr/ccbr_wes_base) [![GitHub issues](https://img.shields.io/github/issues/CCBR/XAVIER?color=brightgreen)](https://github.com/CCBR/XAVIER/issues) [![GitHub license](https://img.shields.io/github/license/CCBR/XAVIER)](https://github.com/CCBR/XAVIER/blob/main/LICENSE) +# XAVIER - e**X**ome **A**nalysis and **V**ariant explor**ER** 🔬 + +[![tests](https://github.com/CCBR/XAVIER/workflows/tests/badge.svg)](https://github.com/CCBR/XAVIER/actions/workflows/main.yaml) +[![docs](https://github.com/CCBR/XAVIER/workflows/docs/badge.svg)](https://github.com/CCBR/XAVIER/actions/workflows/docs.yml) +[![Docker Pulls](https://img.shields.io/docker/pulls/nciccbr/ccbr_wes_base)](https://hub.docker.com/r/nciccbr/ccbr_wes_base) +[![GitHub Issues](https://img.shields.io/github/issues/CCBR/XAVIER?color=brightgreen)](https://github.com/CCBR/XAVIER/issues) +[![MIT license](https://img.shields.io/github/license/CCBR/XAVIER)](https://github.com/CCBR/XAVIER/blob/main/LICENSE) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12727316.svg)](https://doi.org/10.5281/zenodo.12727316) > **_XAVIER - eXome Analysis and Variant explorER_**. **XAVIER** is an open-source, reproducible, and scalable solution for analyzing Whole Exome sequencing data. Its long-term goals: to accurately call germline and somatic variants, to infer CNVs, and to boldly annotate variants like no pipeline before! From e356740a1d2b1b25f25206f1731d0a43db3dd612 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 11 Jul 2024 14:37:39 -0400 Subject: [PATCH 2/3] chore: link PR in changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9d6c0be..3649ace 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ ## development version -- You can now cite XAVIER with the DOI [10.5281/zenodo.12727316](https://doi.org/10.5281/zenodo.12727316). +- You can now cite XAVIER with the DOI [10.5281/zenodo.12727316](https://doi.org/10.5281/zenodo.12727316). (#88, @kelly-sovacool) ## XAVIER 3.0.3 From b7fb7ab4b018d23946958c3f549bbbee3fbcddfe Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 11 Jul 2024 14:39:34 -0400 Subject: [PATCH 3/3] fix: use the all-versions DOI so we don't have to update it --- CHANGELOG.md | 2 +- README.md | 2 +- docs/index.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3649ace..94b14c8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ ## development version -- You can now cite XAVIER with the DOI [10.5281/zenodo.12727316](https://doi.org/10.5281/zenodo.12727316). (#88, @kelly-sovacool) +- You can now cite XAVIER with the DOI [10.5281/zenodo.12727315](https://doi.org/10.5281/zenodo.12727315). (#88, @kelly-sovacool) ## XAVIER 3.0.3 diff --git a/README.md b/README.md index fe8ad24..ae33a14 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![Docker Pulls](https://img.shields.io/docker/pulls/nciccbr/ccbr_wes_base)](https://hub.docker.com/r/nciccbr/ccbr_wes_base) [![GitHub Issues](https://img.shields.io/github/issues/CCBR/XAVIER?color=brightgreen)](https://github.com/CCBR/XAVIER/issues) [![MIT license](https://img.shields.io/github/license/CCBR/XAVIER)](https://github.com/CCBR/XAVIER/blob/main/LICENSE) -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12727316.svg)](https://doi.org/10.5281/zenodo.12727316) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12727315.svg)](https://doi.org/10.5281/zenodo.12727315) > **_*XAVIER - eXome Analysis and Variant explorER*_**. This is the home of the pipeline, XAVIER. Its long-term goals: to accurately call germline and somatic variants, to infer CNVs, and to boldly annotate variants like no pipeline before! diff --git a/docs/index.md b/docs/index.md index 344926a..309c2b1 100644 --- a/docs/index.md +++ b/docs/index.md @@ -5,7 +5,7 @@ [![Docker Pulls](https://img.shields.io/docker/pulls/nciccbr/ccbr_wes_base)](https://hub.docker.com/r/nciccbr/ccbr_wes_base) [![GitHub Issues](https://img.shields.io/github/issues/CCBR/XAVIER?color=brightgreen)](https://github.com/CCBR/XAVIER/issues) [![MIT license](https://img.shields.io/github/license/CCBR/XAVIER)](https://github.com/CCBR/XAVIER/blob/main/LICENSE) -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12727316.svg)](https://doi.org/10.5281/zenodo.12727316) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12727315.svg)](https://doi.org/10.5281/zenodo.12727315) > **_XAVIER - eXome Analysis and Variant explorER_**. **XAVIER** is an open-source, reproducible, and scalable solution for analyzing Whole Exome sequencing data. Its long-term goals: to accurately call germline and somatic variants, to infer CNVs, and to boldly annotate variants like no pipeline before!