apply suggestions

Author: SusiJo

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [[#476](https://github.com/nf-core/differentialabundance/pull/476)] - Fixed null.csv and warning at top of report ([@SusiJo](https://github.com/SusiJo), reviewed by [@pinin4fjords](https://github.com/pinin4fjords), [@atrigila](https://github.com/atrigila), [@maxulysse](https://github.com/maxulysse))
 - [[#358](https://github.com/nf-core/differentialabundance/pull/358)] - Fixed nf-tests not running due to `--changed-since HEAD^`([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#344](https://github.com/nf-core/differentialabundance/pull/344)] - Fixed replacement of NA sub-strings
   ([@atrigila](https://github.com/atrigila), suggested by [@BEFH](https://github.com/BEFH), review by [@apeltzer](https://github.com/apeltzer) and [@nschcolnicov](https://github.com/nschcolnicov))
@@ -40,7 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
-- [[#476](https://github.com/nf-core/differentialabundance/pull/476)] - Update documentation ([@SusiJo](https://github.com/SusiJo), reviewed by [](), []())
+- [[#476](https://github.com/nf-core/differentialabundance/pull/476)] - Update documentation & report fixes ([@SusiJo](https://github.com/SusiJo), reviewed by [@pinin4fjords](https://github.com/pinin4fjords), [@atrigila](https://github.com/atrigila), [@maxulysse](https://github.com/maxulysse))
 - [[#468](https://github.com/nf-core/differentialabundance/pull/468)] - Template update for nf-core/tools v3.3.1 ([@SusiJo](https://github.com/SusiJo), reviewed by [@famosab](https://github.com/famosab), [@mashehu](https://github.com/mashehu))
 - [[#448](https://github.com/nf-core/differentialabundance/pull/448)] - Simplify toolsheet handling and restructure workflow to use paramset in meta. ([@pinin4fjords](https://github.com/pinin4fjords), review by [@suzannejin](https://github.com/suzannejin) and [@grst](https://github.com/grst))
 - [[#431](https://github.com/nf-core/differentialabundance/pull/431)] - Replace the calls to differential and functional analysis modules by subworkflows. ([@suzannejin](https://github.com/suzannejin), review by [@pinin4fjords](https://github.com/pinin4fjords))

conf/modules.config

@@ -381,7 +381,7 @@ process {
                 path: { "${params.outdir}/report/gsea/${meta.id}/${gene_sets.baseName}" },
                 mode: params.publish_dir_mode,
                 pattern: '*.{html,zip,png,tsv,rpt}'
-            ],
+            ]
         ]
         ext.args = { [
             "-nperm $meta.params.gsea_nperm",

docs/output.md

@@ -14,6 +14,8 @@ This directory contains the main reporting output of the workflow.
 - `report/`
   - `*.html`: an HTML report file named according to the value of `params.study_name`, containing graphical and tabular summary results for the workflow run.
   - `*.zip`: a zip file containing an R markdown file with parameters set and all necessary input files to open and customise the reporting.
+  - `gsea/`: Directory containing graphical outputs from GSEA (where enabled). Plots are stored in directories named for the associated contrast.
+    - `[contrast]/png/[gsea_plot_type].png`
 
 </details>
 
@@ -38,8 +40,6 @@ Stand-alone graphical outputs are placed in this directory. They may be useful i
     - `[contrast]/png/volcano.png`: Volcano plots of -log(10) p value agains log(2) fold changes
   - `immunedeconv/`: Directory containing graphical outputs of immunedeconv results
     - `${prefix}.plot1_stacked_bar_chart.png`
-  - `gsea/`: Directory containing graphical outputs from GSEA (where enabled). Plots are stored in directories named for the associated contrast.
-    - `[contrast]/png/[gsea_plot_type].png`
   - `gprofiler2/`: Directory containing graphical outputs from gprofiler2 (where enabled). Plots are stored in directories named for the associated contrast.
     - `[contrast]/[contrast].gprofiler2.[source].gostplot.html`: An interactive gprofiler2 Manhattan plot of enriched pathways from one specific source/database, e.g. REAC
     - `[contrast]/[contrast].gprofiler2.[source].gostplot.png`: A static gprofiler2 Manhattan plot of enriched pathways from one specific source/database, e.g. REAC