Merge branch 'dev' of https://github.com/nf-core/differentialabundance …

…into dev

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - [[#342](https://github.com/nf-core/differentialabundance/pull/342)] - Fixed incorrectly colored dots in report volcano plots for logFC thresholds <1 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#330](https://github.com/nf-core/differentialabundance/pull/330)] - Fixed broken docs by removing g:profiler colons ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#304](https://github.com/nf-core/differentialabundance/pull/304)] - Removed TXT file options from nextflow_schema where they are equivalent to TSV to make the input files clearer ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#299](https://github.com/nf-core/differentialabundance/pull/299)] - Add exclusions for 3.0.1 template update ([@pinin4fjords](https://github.com/pinin4fjords))
 - [[#289](https://github.com/nf-core/differentialabundance/pull/289)] - Fix missing ch_gene_sets default for gprofiler2 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))

assets/differentialabundance_report.Rmd

@@ -726,7 +726,7 @@ iv_min_group_sizes <- unlist(lapply(informative_variables, function(x) min(table
 
 if (any(iv_min_group_sizes > 2)){
     cat("\n### Outlier detection {.tabset}\n")
-    cat("\nOutlier detection based on [median absolute deviation](https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf) was undertaken, the outlier scoring is plotted below.\n")
+    cat("\nOutlier detection based on [median absolute deviation](https://archive.ph/o3thZ) was undertaken, the outlier scoring is plotted below. For more on MAD, see [this wiki article](https://en.wikipedia.org/wiki/Median_absolute_deviation).\n")
 }
 
 foo <- lapply(informative_variables[iv_min_group_sizes > 2], function(iv){

docs/usage.md

@@ -286,16 +286,16 @@ Currently, two tools can be used to do gene set enrichment analysis.
 --gene_sets_files gene_sets.gmt
 ```
 
-### g:Profiler
+### gProfiler2
 
-The [gprofiler2](https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html) package can be used to test which pathways are enriched in the sets of differential genes produced by the the DESeq2 or limma modules. It is an R interface for the g:Profiler webtool. In the simplest form, this feature can be enabled with the parameters from the following example:
+The [gprofiler2](https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html) package can be used to test which pathways are enriched in the sets of differential genes produced by the the DESeq2 or limma modules. It is an R interface for the gprofiler webtool. In the simplest form, this feature can be enabled with the parameters from the following example:
 
 ```bash
 --gprofiler2_run true \
 --gprofiler2_organism mmusculus
 ```
 
-If gene sets have been specified to the workflow via `--gene_sets_files` these are used by default. Specifying `--gprofiler2_organism` (mmusculus for Mus musculus, hsapiens for Homo sapiens etc.) will override those gene sets with g:profiler's own for the relevant species. `--gprofiler2_token` will override both options and use gene sets from a previous g:profiler run.
+If gene sets have been specified to the workflow via `--gene_sets_files` these are used by default. Specifying `--gprofiler2_organism` (mmusculus for Mus musculus, hsapiens for Homo sapiens etc.) will override those gene sets with gprofiler's own for the relevant species. `--gprofiler2_token` will override both options and use gene sets from a previous gprofiler run.
 
 By default the analysis will be run with a background list of genes that passed the abundance filter (i.e. those genes that actually had some expression); see for example https://doi.org/10.1186/s13059-015-0761-7 for why this is advisable. You can provide your own background list with `--gprofiler2_background_file background.txt`or if you want to not use any background, set `--gprofiler2_background_file false`.
 

nextflow_schema.json

@@ -373,7 +373,7 @@
                 "exploratory_mad_threshold": {
                     "type": "integer",
                     "default": -5,
-                    "help_text": "MAD = median absolute deviation. A threshold on this value is used to define observations (samples) as outliers, or not, in exploratory plots. Based on the definition at https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf. ",
+                    "help_text": "MAD = median absolute deviation. A threshold on this value is used to define observations (samples) as outliers, or not, in exploratory plots. Based on the definition at https://archive.ph/o3thZ. For more on MAD, see https://en.wikipedia.org/wiki/Median_absolute_deviation.",
                     "description": "Threshold on MAD score for outlier identification",
                     "fa_icon": "fas fa-angry"
                 },