Release v1.3.0

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).
 
-## v1.3.0dev - [date]
+## v1.3.0 - 2023-10-20
 
 ### `Added`
 

CITATIONS.md

@@ -16,13 +16,9 @@
 
 ## R packages
 
-- [R](https://www.R-project.org/)
-
-  > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
-
-- [shinyngs](https://github.com/pinin4fjords/shinyngs)
+- [affy](https://pubmed.ncbi.nlm.nih.gov/14960456/)
 
-  > 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.
+  > Gautier L, Cope L, Bolstad BM, Irizarry RA. Affy--analysis of affymetrix genechip data at the probe level. Bioinformatics. 2004;20(3):307-315.
 
 - [DESeq2](https://pubmed.ncbi.nlm.nih.gov/25516281/)
 
@@ -32,26 +28,46 @@
 
   > H. Wickham (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York.
 
-- [plotly](https://plotly.com/r/)
+- [GEOQuery](https://pubmed.ncbi.nlm.nih.gov/17496320/)
 
-  > C. Sievert (2020). Interactive Web-Based Data Visualization with R, plotly, and shiny. Chapman and Hall/CRC Florida.
+  > Davis S, Meltzer PS. Geoquery: a bridge between the gene expression omnibus (Geo) and bioconductor. Bioinformatics. 2007;23(14):1846-1847.
+
+- [Limma](https://pubmed.ncbi.nlm.nih.gov/25605792/)
+
+  > Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expression analyses for rna-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.
 
 - [optparse](https://CRAN.R-project.org/package=optparse)
 
   > Trevor L Davis (2018). optparse: Command Line Option Parser.
 
-- [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)
+- [plotly](https://plotly.com/r/)
 
-  > Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.
+  > C. Sievert (2020). Interactive Web-Based Data Visualization with R, plotly, and shiny. Chapman and Hall/CRC Florida.
 
-- [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html)
+- [Proteus](https://doi.org/10.1101/416511)
 
-  > Morgan M, Obenchain V, Hester J and Pagès H (2020). SummarizedExperiment: SummarizedExperiment container.
+  > Gierlinski M, Gastaldello F, Cole C, Barton GJ. Proteus : An r Package for Downstream Analysis of Maxquant Output. Bioinformatics; 2018.
+
+- [R](https://www.R-project.org/)
+
+  > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
+
+- [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)
+
+  > Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.
 
 - [RMarkdown](https://rmarkdown.rstudio.com)
 
   > JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone (2022). rmarkdown: Dynamic Documents for R.
 
+- [shinyngs](https://github.com/pinin4fjords/shinyngs)
+
+  > 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.
+
+- [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html)
+
+  > Morgan M, Obenchain V, Hester J and Pagès H (2020). SummarizedExperiment: SummarizedExperiment container.
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/differentialabundance/releases/tag/dev" target="_blank">nf-core/differentialabundance</a>
+  This report has been generated by the <a href="https://github.com/nf-core/differentialabundance/releases/tag/1.3.0" target="_blank">nf-core/differentialabundance</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/differentialabundance/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/differentialabundance/1.3.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-differentialabundance-methods-description":
     order: -1000

lib/WorkflowDifferentialabundance.groovy

@@ -47,14 +47,20 @@ class WorkflowDifferentialabundance {
     //
 
     public static String toolCitationText(params) {
-
-        // TODO nf-core: Optionally add in-text citation tools to this list.
-        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
-        // Uncomment function in methodsDescriptionText to render in MultiQC report
         def citation_text = [
                 "Tools used in the workflow included:",
-                "FastQC (Andrews 2010),",
-                "MultiQC (Ewels et al. 2016)",
+                params["study_type"] == 'affy_array' ? "affy (Gautier et al. 2004": "",
+                params["study_type"] == 'rnaseq' ? "DESeq2 (Love et al 2014)," : "",
+                "ggplot2 (Wickham 2016)",
+                "GEOQuery (Davis et al. 2007",
+                params["study_type"] != 'rnaseq' ? "Limma (Ritchie eta al 2015" : "",
+                "optparse (Davis 2018)",
+                "plotly (Sievert 2020)",
+                params["study_type"] != 'maxquant' ? "Proteus (Gierlinski 2018)" : "",
+                "RColorBrewer (Neuwirth 2014)",
+                "RMarkdown (Allaire et al. 2022)",
+                "shinyngs (Manning 2022)",
+                "SummarizedExperiment (Morgan et al. 2020)",
                 "."
             ].join(' ').trim()
 

modules.json

@@ -17,7 +17,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
+                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
                         "installed_by": ["modules"]
                     },
                     "custom/matrixfilter": {
@@ -52,7 +52,7 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
+                        "git_sha": "8663c9d215573d4bd0417c93dbc310aa9e6720a4",
                         "installed_by": ["modules"]
                     },
                     "limma/differential": {

nextflow.config

@@ -384,7 +384,7 @@ manifest {
     description     = 'Differential abundance analysis'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.3.0dev'
+    version         = '1.3.0'
     doi             = '10.5281/zenodo.7568000'
 }