Added filtered DE tables to output; add rounding after gprofiler2 PR …

…is merged

assets/differentialabundance_report.Rmd

@@ -302,6 +302,8 @@ treatment-mCherry-hND6-batcheffect.deseq2.results.tsv
 
 ... where variable, reference, target and blocking come from the contrasts file
 (with blocking being optional) and the suffix is defined in parameters.
+
+Also save the tables again after filtering for DE entries
 -->
 
 ```{r, echo=FALSE}
@@ -333,6 +335,13 @@ differential_results <- lapply(differential_files, function(diff_file){
   if (! is.null(params$features)){
     diff <- merge(features, diff, by.x = params$features_id_col, by.y = params$differential_feature_id_column)
   }
+
+  # Filter tables by logFC threshold and padj threshold and save to TSV
+
+  filtered_diff <- na.omit(diff[log2(params$differential_min_fold_change) <= abs(diff[[params$differential_fc_column]]) & diff[[params$differential_qval_column]] <= params$differential_max_qval,])
+  filtered_diff <- round_dataframe_columns()
+  write.table(filtered_diff, file=file.path(params$artifact_dir, paste0(basename(tools::file_path_sans_ext(diff_file)), "_filtered.tsv")), sep="\t", quote=F, row.names=F)
+
   diff
 })
 names(differential_results) <- contrasts$id

conf/modules.config

@@ -393,9 +393,17 @@ process {
         conda = "bioconda::r-shinyngs=1.8.4"
         container = { "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" }
         publishDir = [
-            path: { "${params.outdir}/report" },
-            mode: params.publish_dir_mode,
-            pattern: '*.html'
+            [
+                path: { "${params.outdir}/report" },
+                mode: params.publish_dir_mode,
+                pattern: '*.html'
+            ],
+            [
+                path: { "${params.outdir}/" },
+                mode: params.publish_dir_mode,
+                pattern: 'artifacts/*_filtered.tsv',
+                saveAs: { filename -> "tables/de_tables2/${filename.split("\\.", 2)[1]}" }
+            ]
         ]
     }