From a82d61df65df2ddfdfb9c47e86403cb5f8e648b6 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 19 Oct 2023 14:10:29 +0100 Subject: [PATCH 1/2] Bump versions, tidy up citations, update modules --- CHANGELOG.md | 2 +- CITATIONS.md | 40 +++++++++++++++++------- assets/multiqc_config.yml | 4 +-- lib/WorkflowDifferentialabundance.groovy | 18 +++++++---- modules.json | 4 +-- nextflow.config | 2 +- 6 files changed, 46 insertions(+), 24 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bc0b398f..f5a5b961 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/CITATIONS.md b/CITATIONS.md index e86f4eff..200368b1 100644 --- a/CITATIONS.md +++ b/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) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 211358cb..15a57fd3 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/differentialabundance + This report has been generated by the nf-core/differentialabundance analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-differentialabundance-methods-description": order: -1000 diff --git a/lib/WorkflowDifferentialabundance.groovy b/lib/WorkflowDifferentialabundance.groovy index f9570cd6..4acad311 100755 --- a/lib/WorkflowDifferentialabundance.groovy +++ b/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() diff --git a/modules.json b/modules.json index 102495bb..ff601367 100644 --- a/modules.json +++ b/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": { diff --git a/nextflow.config b/nextflow.config index 0e07ee51..e771183e 100644 --- a/nextflow.config +++ b/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' } From f1643cec062f9bfbbb6bf77f0992afd9f002565c Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 19 Oct 2023 15:44:22 +0100 Subject: [PATCH 2/2] Clean up after 'nf-core bump-version' --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index e771183e..3912922d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -384,7 +384,7 @@ manifest { description = 'Differential abundance analysis' mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.3.0' + version = '1.3.0' doi = '10.5281/zenodo.7568000' }