Merge pull request #56 from nf-core/dev

Dev -> master for v1.0.1

Author: pinin4fjords

CHANGELOG.md

@@ -3,6 +3,17 @@
 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).
 
+## v1.0.1 - 2024-04-17
+
+### `Added`
+
+- [#53](https://github.com/nf-core/riboseq/pull/53) - Bump to v1.0.1 and set Zenodo ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
+- [#54](https://github.com/nf-core/riboseq/pull/54) - Add legal logos and first metro map ([@FelixKrueger](https://github.com/FelixKrueger), review by [@maxulysse](https://github.com/maxulysse))
+
+### `Fixed`
+
+- [#57](https://github.com/nf-core/riboseq/pull/57) - Minor spacing changes to logo svg ([@JackCurragh](https://github.com/JackCurragh), reviewed by [@FelixKrueger](https://github.com/FelixKrueger))
+
 ## v1.0.0 - 2024-04-12
 
 Initial release of nf-core/riboseq, created with the [nf-core](https://nf-co.re/) template.
@@ -17,7 +28,7 @@ Initial release of nf-core/riboseq, created with the [nf-core](https://nf-co.re/
 - [#35](https://github.com/nf-core/riboseq/pull/35) - Sortmerna: index once ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
 - [#40](https://github.com/nf-core/riboseq/pull/40) - Ribotricer orf prediction ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
 - [#42](https://github.com/nf-core/riboseq/pull/42) - Add alignment based quantification with Salmon ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
-- [#43](https://github.com/nf-core/riboseq/pull/43) - Add translational efficiency analysis with anota2seq ([@pinin4fjords](https://github.com/pinin4fjords), review by )
+- [#43](https://github.com/nf-core/riboseq/pull/43) - Add translational efficiency analysis with anota2seq ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
 
 ### `Changed`
 

README.md

@@ -6,7 +6,7 @@
 </h1>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/riboseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/riboseq/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/riboseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/riboseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/riboseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions Linting Status](https://github.com/nf-core/riboseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/riboseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/riboseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10966364-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10966364)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
@@ -21,6 +21,8 @@
 
 **nf-core/riboseq** is a bioinformatics pipeline for analysis of Ribo-seq data. It borrows heavily from nf-core/rnaseq in the preprocessing stages:
 
+![nf-core/riboseq metro map](docs/images/nf-core-riboseq_metro_map.png)
+
 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))
 2. Sub-sample FastQ files and auto-infer strandedness ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/))
 3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
@@ -115,8 +117,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/riboseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use nf-core/riboseq for your analysis, please cite it using the following doi: [10.5281/zenodo.10966364](https://doi.org/10.5281/zenodo.10966364)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/nf-core/riboseq/releases/tag/1.0.0" target="_blank">nf-core/riboseq</a> analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/riboseq/1.0.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/riboseq/releases/tag/1.0.1" target="_blank">nf-core/riboseq</a> analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/riboseq/1.0.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-riboseq-methods-description":
     order: -1000