Inlcude decoupler config

Author: antoniasaracco

conf/modules.config

@@ -375,6 +375,7 @@ process {
 
     withName: GSEA_GSEA {
         ext.prefix = { "${meta.id}.${gene_sets.baseName}." }
+
         publishDir = [
             [
                 path: { "${params.outdir}/report/gsea/${meta.id}/${gene_sets.baseName}" },
@@ -463,6 +464,34 @@ process {
         ].join(' ').trim() }
     }
 
+    withName: DECOUPLER_DECOUPLER {
+        ext.prefix = {
+            def method = meta.params.differential_method ?: meta.differential_method ?: "unknown"
+            def prefix = "${method}_${meta.id}"
+            return prefix
+        }
+        ext.args = {
+            def features_id = meta.params?.features_id_col ?: 'gene_id'
+            def features_symbol = meta.params?.features_name_col ?: 'gene_name'
+            def min_n = meta.params?.decoupler_min_n ?: 5
+            def methods = meta.params?.decoupler_methods ?: 'mlm'
+
+            "--min_n ${min_n} --transpose TRUE --ensembl_ids TRUE --methods ${methods} --features_id_col ${features_id} --features_symbol_col ${features_symbol} --column ${params.differential_fc_column}"
+        }
+        publishDir = [
+            [
+                path: { "${params.outdir}/tables/decoupler" },
+                mode: params.publish_dir_mode,
+                pattern: '*.tsv'
+            ],
+            [
+                path: { "${params.outdir}/plots/decoupler" },
+                mode: params.publish_dir_mode,
+                pattern: '*_estimate_decoupler_plot.png'
+            ]
+        ]
+    }
+
     // ==================================================================================
     // plotting and reports
     // ==================================================================================

conf/test.config

@@ -55,4 +55,8 @@ params {
 
     // Other
     round_digits = 3
+
+    // DECOUPLER
+    decoupler_network     = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/progeny/mouse_network.tsv'
+
 }

conf/test_rnaseq_dream.config

@@ -55,4 +55,7 @@ params {
 
     // Other
     round_digits = 3
+
+    // DECOUPLER
+    decoupler_network     = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/progeny/mouse_network.tsv'
 }

conf/test_rnaseq_limma.config

@@ -61,4 +61,7 @@ params {
 
     // Other
     round_digits = 3
+
+    // DECOUPLER
+    decoupler_network     = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/progeny/mouse_network.tsv'
 }

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
@@ -49,8 +49,8 @@ Stand-alone graphical outputs are placed in this directory. They may be useful i
     - `[contrast]/[norm_function].normalized_mean_variance_relationship.png`: Plots of log intensity vs mean log intensity after normalization of each contrast level.
     - `[contrast]/[norm_function].normalized_distributions.png`: A plot of sample distributions after normalization.
     - `[contrast]/raw_distributions.png`: A plot of sample distributions without normalization.
-
-</details>
+  - `decoupler/`: Directory containing plots of decoupler results - `[differential_method]_[contrast_name]_[decoupler_method]_estimate_decoupler_plot.png`: contains the plot for the estimated activity scores for each regulator (rows) across all samples (columns).
+  </details>
 
 Most plots are included in the HTML report (see above), but are also included in static files in this folder to facilitate use in external reporting.
 
@@ -78,6 +78,9 @@ Most plots are included in the HTML report (see above), but are also included in
   - `gprofiler2/`: Directory containing tables of differential gene set analyis from gprofiler2 (where enabled)
     - `[contrast]/[contrast].gprofiler2.all_enriched_pathways.tsv`: A gprofiler2 report table for all enrichment results
     - `[contrast]/[contrast].gprofiler2.[source].sub_enriched_pathways.tsv`: A gprofiler2 report table of enriched pathways from one specific source/database, e.g. REAC
+  - `decoupler/`: Directory containing tables of decoupler results
+    - `[differential_method]_[contrast_name]_[decoupler_method]_estimate_decoupler.tsv`: contains the estimated activity scores for each regulator (rows) across all samples (columns).
+    - `[differential_method]_[contrast_name]_[decoupler_method]_pvals_decoupler.{tsv}.tsv`: contains the associated p-values for those activity scores, when the method supports statistical significance estimation.
   - `proteus/`: If `--study_type maxquant`: Directory containing abundance values produced by the proteus module which is used for processing MaxQuant input. Files are prefixed with the associated contrast and chosen normalization function (if any).
     - `[contrast]/[norm_function].normalized_proteingroups_tab.tsv`: Abundance table after normalization.
     - `[contrast]/raw_proteingroups_tab.tsv`: Abundance table without normalization.
@@ -92,7 +95,7 @@ The `differential` folder is likely to be the core result set for most users, co
 <summary>Output files</summary>
 
 - `shinyngs_app/`
-  - `[study name]`:
+  - `[study_name]`:
     - `data.rds`: serialized R object which can be used to generate a Shiny application
     - `app.R`: minimal R script that will source the data object and generate the app