Merge pull request #164 from nf-core/rlog_fixes

Rlog + other small fixes

CHANGELOG.md

@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#138](https://github.com/nf-core/differentialabundance/issues/138)]- Fix bugs with --control_features and --sizefactors_from_controls ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#133](https://github.com/nf-core/differentialabundance/issues/133)] - Sample exclusion options fail due to contrast-wise normalisation ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#160](https://github.com/nf-core/differentialabundance/issues/160)]- Fix merge conflicts for Template update 2.10 by nf-core-bot ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#164](https://github.com/nf-core/differentialabundance/pull/164)] - Rlog + other small fixes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@drpatelh](https://github.com/drpatelh))
 
 ### `Changed`
 

assets/differentialabundance_report.Rmd

@@ -618,16 +618,17 @@ for (assay_type in rev(names(assay_data))){
 }
 ```
 
-### Outlier detection {.tabset}
-
-Outlier detection based on [median absolute deviation](https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf) was undertaken, the outlier scoring is plotted below.
-
 ```{r, echo=FALSE, results='asis', warning=FALSE}
 
 # We can't look for ouliers in sets of less than 3 samples, so exclude variables
 # unless the minimum group size is larger than that
 iv_min_group_sizes <- unlist(lapply(informative_variables, function(x) min(table(observations[[x]]))))
 
+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")
+}
+
 foo <- lapply(informative_variables[iv_min_group_sizes > 2], function(iv){
   
   cat(paste("\n####", iv, "\n"))

workflows/differentialabundance.nf

@@ -327,14 +327,19 @@ workflow DIFFERENTIALABUNDANCE {
         // variance-stabilised matrices are not (IIUC) impacted by the model.
 
         ch_norm = DESEQ2_NORM.out.normalised_counts
-        ch_vst = DESEQ2_NORM.out.vst_counts
         ch_differential = DESEQ2_DIFFERENTIAL.out.results
 
         ch_versions = ch_versions
             .mix(DESEQ2_DIFFERENTIAL.out.versions)
 
         ch_processed_matrices = ch_norm
-            .join(ch_vst)
+        if ('rlog' in params.deseq2_vs_method){
+            ch_processed_matrices = ch_processed_matrices.join(DESEQ2_NORM.out.rlog_counts)
+        }
+        if ('vst' in params.deseq2_vs_method){
+            ch_processed_matrices = ch_processed_matrices.join(DESEQ2_NORM.out.vst_counts)
+        }
+        ch_processed_matrices = ch_processed_matrices
             .map{ it.tail() }
     }
 
@@ -507,7 +512,7 @@ workflow DIFFERENTIALABUNDANCE {
     // Condition params reported on study type
 
     def params_pattern = ~/^(report|study|observations|features|filtering|exploratory|differential|deseq2|gsea).*/
-    if (params.study_type == 'affy_array' || 'geo_soft_file'){
+    if (params.study_type == 'affy_array' || params.study_type == 'geo_soft_file'){
         params_pattern = ~/^(report|study|observations|features|filtering|exploratory|differential|affy|limma|gsea).*/
     }