Release 1.0.0

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/ensemblrepeatdownload v1.0.0 - Gwaihir the Windlord
+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.7183380
+repository-code: "https://github.com/sanger-tol/ensemblrepeatdownload"
+license: MIT
+commit: TODO
+version: 1.0.0
+date-released: "2022-10-19"

README.md

@@ -1,8 +1,10 @@
+# ![sanger-tol/ensemblrepeatdownload](docs/images/sanger-tol-ensemblrepeatdownload_logo.png)
+
 [![GitHub Actions CI Status](https://github.com/sanger-tol/ensemblrepeatdownload/workflows/nf-core%20CI/badge.svg)](https://github.com/sanger-tol/ensemblrepeatdownload/actions?query=workflow%3A%22nf-core+CI%22)
 
 <!-- [![GitHub Actions Linting Status](https://github.com/sanger-tol/ensemblrepeatdownload/workflows/nf-core%20linting/badge.svg)](https://github.com/sanger-tol/ensemblrepeatdownload/actions?query=workflow%3A%22nf-core+linting%22) -->
 
-[![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.7183380-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7183380)
 
 [![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/)
@@ -77,7 +79,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use sanger-tol/ensemblrepeatdownload 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/ensemblrepeatdownload for your analysis, please cite it using the following doi: [10.5281/zenodo.7183380](https://doi.org/10.5281/zenodo.7183380)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

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.7183380\n\n" +
             "* The nf-core framework\n" +
             "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
             "* Software dependencies\n" +

nextflow.config

@@ -173,7 +173,7 @@ manifest {
     description     = 'Pipeline that downloads repeats annotations from Ensembl into the Tree of Life directory structure'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.04.0'
-    version         = '1.0dev'
+    version         = '1.0.0'
 }
 
 // Load modules.config for DSL2 module specific options