update subworkflows for differential and functional enrichment analysis

subworkflows/nf-core/abundance_differential_filter/main.nf

@@ -195,6 +195,18 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
         .mix(DESEQ2_NORM.out.vst_counts)
         .groupTuple()
 
+    ch_dispersion_plot = DESEQ2_DIFFERENTIAL.out.dispersion_plot_png
+
+    ch_md_plot = LIMMA_DIFFERENTIAL.out.md_plot
+
+    ch_rdata = DESEQ2_DIFFERENTIAL.out.rdata
+        .mix(LIMMA_DIFFERENTIAL.out.rdata)
+
+    ch_size_factors = DESEQ2_DIFFERENTIAL.out.size_factors
+
+    ch_session_info = DESEQ2_DIFFERENTIAL.out.session_info
+        .mix(LIMMA_DIFFERENTIAL.out.session_info)
+
     // ----------------------------------------------------
     // Filter DE results
     // ----------------------------------------------------
@@ -242,16 +254,32 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     ch_versions = ch_versions.mix(CUSTOM_FILTERDIFFERENTIALTABLE.out.versions.first())
 
     emit:
+
     // main results
     results_genewise           = ch_results
     results_genewise_filtered  = CUSTOM_FILTERDIFFERENTIALTABLE.out.filtered
 
     // pairwise results
     adjacency                  = PROPR_PROPD.out.adjacency
 
-    // other
+    // other matrices
     normalised_matrix          = ch_normalised_matrix
     variance_stabilised_matrix = ch_variance_stabilised_matrix
+
+    // differential model
     model                      = ch_model
+
+    // size factors
+    size_factors               = ch_size_factors
+
+    // plots
+    dispersion_plot            = ch_dispersion_plot
+    md_plot                    = ch_md_plot
+
+    // rdata and session info
+    rdata                      = ch_rdata
+    session_info               = ch_session_info
+
+    // versions
     versions                   = ch_versions
 }

subworkflows/nf-core/abundance_differential_filter/meta.yml

@@ -157,6 +157,26 @@ output:
             type: file
             description: Statistical model object file
             pattern: "*.rds"
+  - plots:
+      description: Channel containing plots from differential analysis
+      structure:
+        - meta:
+            type: map
+            description: Metadata map
+        - plots:
+            type: file
+            description: Plot file
+            pattern: "*.{png,pdf}"
+  - other:
+      description: Channel containing other outputs from differential analysis
+      structure:
+        - meta:
+            type: map
+            description: Metadata map
+        - other_files:
+            type: file
+            description: Other output file from differential analysis
+            pattern: "*.{rds,tsv,log}"
 authors:
   - "@pinin4fjords"
   - "@bjlang"

subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test

@@ -234,6 +234,10 @@ nextflow_workflow {
                     workflow.out.normalised_matrix,
                     workflow.out.variance_stabilised_matrix,
                     workflow.out.model,
+                    workflow.out.size_factors.collect { file(it[1]).name }.sort(),
+                    workflow.out.dispersion_plot.collect { file(it[1]).name }.sort(),
+                    workflow.out.rdata.collect { file(it[1]).name }.sort(),
+                    workflow.out.session_info.collect { file(it[1]).name }.sort(),
                     workflow.out.versions
                 ).match() }
             )
@@ -318,6 +322,9 @@ nextflow_workflow {
                     workflow.out.results_genewise_filtered,
                     workflow.out.normalised_matrix,
                     workflow.out.model,
+                    workflow.out.md_plot.collect { file(it[1]).name }.sort(),
+                    workflow.out.rdata.collect { file(it[1]).name }.sort(),
+                    workflow.out.session_info.collect { file(it[1]).name }.sort(),
                     workflow.out.versions
                 ).match() }
             )
@@ -376,6 +383,9 @@ nextflow_workflow {
                     workflow.out.results_genewise_filtered,
                     workflow.out.normalised_matrix,
                     workflow.out.model,
+                    workflow.out.md_plot.collect { file(it[1]).name }.sort(),
+                    workflow.out.rdata.collect { file(it[1]).name }.sort(),
+                    workflow.out.session_info.collect { file(it[1]).name }.sort(),
                     workflow.out.versions
                 ).match() }
             )
@@ -439,6 +449,10 @@ nextflow_workflow {
                     workflow.out.normalised_matrix,
                     workflow.out.variance_stabilised_matrix,
                     workflow.out.model,
+                    workflow.out.size_factors.collect { file(it[1]).name }.sort(),
+                    workflow.out.dispersion_plot.collect { file(it[1]).name }.sort(),
+                    workflow.out.rdata.collect { file(it[1]).name }.sort(),
+                    workflow.out.session_info.collect { file(it[1]).name }.sort(),
                     workflow.out.versions
                 ).match() }
             )
@@ -564,6 +578,11 @@ nextflow_workflow {
                     workflow.out.normalised_matrix,
                     workflow.out.variance_stabilised_matrix,
                     workflow.out.model,
+                    workflow.out.size_factors.collect { file(it[1]).name }.sort(),
+                    workflow.out.dispersion_plot.collect { file(it[1]).name }.sort(),
+                    workflow.out.md_plot.collect { file(it[1]).name }.sort(),
+                    workflow.out.rdata.collect { file(it[1]).name }.sort(),
+                    workflow.out.session_info.collect { file(it[1]).name }.sort(),
                     workflow.out.versions
                 ).match() }
             )
@@ -640,6 +659,11 @@ nextflow_workflow {
                     workflow.out.normalised_matrix,
                     workflow.out.variance_stabilised_matrix,
                     workflow.out.model,
+                    workflow.out.size_factors.collect { file(it[1]).name }.sort(),
+                    workflow.out.dispersion_plot.collect { file(it[1]).name }.sort(),
+                    workflow.out.md_plot.collect { file(it[1]).name }.sort(),
+                    workflow.out.rdata.collect { file(it[1]).name }.sort(),
+                    workflow.out.session_info.collect { file(it[1]).name }.sort(),
                     workflow.out.versions
                 ).match() }
             )