From bd2cf279e2391a8f259d159576ef0f47a416f983 Mon Sep 17 00:00:00 2001 From: Ksenia Date: Fri, 15 Dec 2023 16:21:43 +0000 Subject: [PATCH 1/6] Update README.md Add info for zenodo --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 02cb893..b1a0e92 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10391851-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10391851) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) @@ -81,6 +81,8 @@ If you would like to contribute to this pipeline, please see the [contributing g ## Citations +If you use sanger-tol/genomeassembly for your analysis, please cite it using the following doi: [10.5281/zenodo.10391851](https://zenodo.org/records/10391852). + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE). From b387b416e8a10c05b47386fd172150a5ecca14f1 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 15 Dec 2023 16:29:15 +0000 Subject: [PATCH 2/6] Added CITATION.cff --- .github/workflows/linting.yml | 2 +- CITATION.cff | 31 +++++++++++++++++++++++++++++++ 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 CITATION.cff diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index eefd788..16bdf6d 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -22,7 +22,7 @@ jobs: run: npm install -g editorconfig-checker - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile\|drawio') + run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|cff\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile\|drawio') Prettier: runs-on: ubuntu-latest diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..5e8b2af --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,31 @@ +cff-version: 1.2.0 +title: "sanger-tol/genomeassembly: v0.9.0 - Black Fury" +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - affiliation: Wellcome Sanger Institute + family-names: Krasheninnikova + given-names: Ksenia + orcid: 0000-0002-0604-2047 + - affiliation: Wellcome Trust Sanger Institute + family-names: Qi + given-names: Guoying + orcid: 0000-0003-1262-8973 + - affiliation: Wellcome Sanger Institute + family-names: Muffato + given-names: Matthieu + orcid: 0000-0002-7860-3560 + - affiliation: Wellcome Sanger Institute + family-names: Surana + given-names: Priyanka + orcid: 0000-0002-7167-0875 +identifiers: + - type: doi + value: 10.5281/zenodo.10391852 +repository-code: "https://github.com/sanger-tol/genomeassembly" +license: MIT +commit: TODO +version: 0.9.0 +date-released: "2023-12-15" From 3cb2594af06dada9eeb3326010ee951da0eddb46 Mon Sep 17 00:00:00 2001 From: Ksenia Date: Fri, 15 Dec 2023 16:32:24 +0000 Subject: [PATCH 3/6] Add doi to WorkflowMain.groovy --- lib/WorkflowMain.groovy | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index c3e4f72..891d4b4 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -11,9 +11,8 @@ class WorkflowMain { // public static String citation(workflow) { return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - // TODO nf-core: Add Zenodo DOI for pipeline after first release - //"* The pipeline\n" + - //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + + "* The pipeline\n" + + " https://doi.org/10.5281/zenodo.10391851\n\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + From 300735f5fa60edc69d75b6d5c9d5b30934ce3d49 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 15 Dec 2023 17:01:52 +0000 Subject: [PATCH 4/6] Forgot one DOI update --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 936d7a4..3b1cfda 100644 --- a/nextflow.config +++ b/nextflow.config @@ -220,7 +220,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' version = '0.9.0' - doi = '' + doi = '10.5281/zenodo.10391851' } // Load modules.config for DSL2 module specific options From 68ede324ac9219c9502f77bee7a0d4c963924e3e Mon Sep 17 00:00:00 2001 From: Ksenia Krasheninnikova Date: Fri, 15 Dec 2023 16:19:04 +0000 Subject: [PATCH 5/6] New dev branch --- CHANGELOG.md | 2 ++ nextflow.config | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d64fb58..84fc662 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v0.9.1dev - [date] + ## [[0.9.0](https://github.com/sanger-tol/genomeassembly/releases/tag/0.9.0)] - Night Fury - [2023-12-15] Initial release of sanger-tol/genomeassembly, created with the [nf-core](https://nf-co.re/) template. diff --git a/nextflow.config b/nextflow.config index 3b1cfda..06f099e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -219,7 +219,7 @@ manifest { description = """A bioinformatics best-practice analysis pipeline for genome assembly from PacBio CCS and HiC reads""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '0.9.0' + version = '0.9.1dev' doi = '10.5281/zenodo.10391851' } From 2f4b37f8db148829bdc1cbd33485e4a3e3638239 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 15 Dec 2023 17:08:06 +0000 Subject: [PATCH 6/6] Added the template CHANGELOG entry --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 84fc662..3db051c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v0.9.1dev - [date] +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## [[0.9.0](https://github.com/sanger-tol/genomeassembly/releases/tag/0.9.0)] - Night Fury - [2023-12-15] Initial release of sanger-tol/genomeassembly, created with the [nf-core](https://nf-co.re/) template.