diff --git a/CHANGELOG.md b/CHANGELOG.md index 50db2a3..b22ea08 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v1.0.0 - [date] +## v1.0.0 - [2022-10-07] Initial release of sanger-tol/ensemblgenedownload, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATION.cff b/CITATION.cff index 4533e2f..93f29a0 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,56 +1,26 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + cff-version: 1.2.0 -message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication" +title: sanger-tol/insdcdownload v1.0.0 - Hefty oliphaunt +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software authors: - - family-names: Ewels - given-names: Philip - - family-names: Peltzer - given-names: Alexander - - family-names: Fillinger - given-names: Sven - - family-names: Patel - given-names: Harshil - - family-names: Alneberg - given-names: Johannes - - family-names: Wilm - given-names: Andreas - - family-names: Ulysse Garcia - given-names: Maxime - - family-names: Di Tommaso - given-names: Paolo - - family-names: Nahnsen - given-names: Sven -title: "The nf-core framework for community-curated bioinformatics pipelines." -version: 2.4.1 -doi: 10.1038/s41587-020-0439-x -date-released: 2022-05-16 -url: https://github.com/nf-core/tools -prefered-citation: - type: article - authors: - - family-names: Ewels - given-names: Philip - - family-names: Peltzer - given-names: Alexander - - family-names: Fillinger - given-names: Sven - - family-names: Patel - given-names: Harshil - - family-names: Alneberg - given-names: Johannes - - family-names: Wilm - given-names: Andreas - - family-names: Ulysse Garcia - given-names: Maxime - - family-names: Di Tommaso - given-names: Paolo - - family-names: Nahnsen - given-names: Sven - doi: 10.1038/s41587-020-0439-x - journal: nature biotechnology - start: 276 - end: 278 - title: "The nf-core framework for community-curated bioinformatics pipelines." - issue: 3 - volume: 38 - year: 2020 - url: https://dx.doi.org/10.1038/s41587-020-0439-x + - given-names: Matthieu + family-names: Muffato + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0002-7860-3560" + - given-names: Priyanka + family-names: Surana + orcid: "https://orcid.org/0000-0002-7167-0875" + affiliation: Wellcome Sanger Institute +identifiers: + - type: doi + value: 10.5281/zenodo.7155207 +repository-code: "https://github.com/sanger-tol/ensemblgenedownload" +license: MIT +commit: TODO +version: 1.0.0 +date-released: "2022-10-07" diff --git a/README.md b/README.md index 3e3fac4..d6d3182 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ -[![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.7155207-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7155207) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.04.0-23aa62.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/) @@ -79,7 +79,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If you use sanger-tol/ensemblgenedownload for your analysis, please cite it using the following doi: [10.5281/zenodo.6983933](https://doi.org/10.5281/zenodo.xxxxxxxx6983933) +If you use sanger-tol/ensemblgenedownload for your analysis, please cite it using the following doi: [10.5281/zenodo.7155207](https://doi.org/10.5281/zenodo.7155207) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 0ec4d79..5aa625b 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -9,9 +9,8 @@ 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.7155207\n\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" +