Merge pull request #50 from nf-core/dev

Dev -> master for v1.0.1

CHANGELOG.md

@@ -3,14 +3,18 @@
 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 - 2022-01-25
+
+- [[#49](https://github.com/nf-core/differentialabundance/pull/49) - Add citation fixes, missing logos, output detail, and trigger Zenodo ([@pinin4fjords](https://github.com/pinin4fjords), review by [@apeltzer](https://github.com/apeltzer), [@jfy133](https://github.com/jfy133))
+
 ## v1.0.0 - 2022-01-23
 
 Initial release of nf-core/differentialabundance, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 
 - [[#1](https://github.com/nf-core/differentialabundance/issues/3)] - Set up initial modules, define and validate workflow inputs ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
-- [[#4](https://github.com/nf-core/differentialabundance/issues/4)] - Add input checking ([@pinin4fjords](https://github.com/pinin4fjords), , review by [@WackerO](https://github.com/WackerO))
+- [[#4](https://github.com/nf-core/differentialabundance/issues/4)] - Add input checking ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#5](https://github.com/nf-core/differentialabundance/issues/5)] - Add differential analysis ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#6](https://github.com/nf-core/differentialabundance/issues/6)] - Add exploratory plotting ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#7](https://github.com/nf-core/differentialabundance/issues/7)] - Add differential plotting ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))

CITATIONS.md

@@ -22,19 +22,19 @@
 
 - [shinyngs](https://github.com/pinin4fjords/shinyngs)
 
-  > Jonathan R Manning. Shiny apps for NGS etc based on reusable components created using Shiny modules. Computer software. Vers. 1.5.3. Jonathan Manning, Dec. 2022. Web.
+  > Jonathan R Manning (2022). Shiny apps for NGS etc based on reusable components created using Shiny modules. Computer software. Vers. 1.5.3. Jonathan Manning, Dec. 2022. Web.
 
 - [DESeq2](https://pubmed.ncbi.nlm.nih.gov/25516281/)
 
-  > Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMC4302049.
+  > Love MI, Huber W, Anders S (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMC4302049.
 
 - [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)
 
-  > H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
+  > H. Wickham (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York.
 
 - [plotly](https://plotly.com/r/)
 
-  > C. Sievert. Interactive Web-Based Data Visualization with R, plotly, and shiny. Chapman and Hall/CRC Florida, 2020.
+  > C. Sievert (2020). Interactive Web-Based Data Visualization with R, plotly, and shiny. Chapman and Hall/CRC Florida.
 
 - [optparse](https://CRAN.R-project.org/package=optparse)
 

README.md

@@ -64,7 +64,7 @@ The nf-core/differentialabundance pipeline comes with documentation about the pi
 
 ## Credits
 
-nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)).
+nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning is an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. We are grateful for their support of open science in this project.
 
 We thank the many members of the nf-core community who assisted with this pipeline, often by reviewing module pull requests including but not limited to:
 

docs/output.md

@@ -40,6 +40,8 @@ Stand-alone graphical outputs are placed in this directory. They may be useful i
 
 </details>
 
+Most plots are included in the HTML report (see above), but are also included in static files in this folder to facilitate use in external reporting.
+
 ## Tables
 
 <details markdown="1">
@@ -56,6 +58,8 @@ Stand-alone graphical outputs are placed in this directory. They may be useful i
 
 </details>
 
+The `differential` folder is likely to be the core result set for most users, containing the main tables of differential statistics.
+
 ### Pipeline information
 
 <details markdown="1">

nextflow.config

@@ -273,7 +273,7 @@ manifest {
     description     = 'Differential abundance analysis'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version = '1.0.0'
+    version = '1.0.1'
     doi             = ''
 }