Merge pull request #33 from sanger-tol/0.9.1dev

Post-release merge into dev

.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

CHANGELOG.md

@@ -3,6 +3,16 @@
 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]
+
+### `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.

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"

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).

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" +

nextflow.config

@@ -219,8 +219,8 @@ 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'
-    doi             = ''
+    version         = '0.9.1dev'
+    doi             = '10.5281/zenodo.10391851'
 }
 
 // Load modules.config for DSL2 module specific options