minor code restructuring

nf-core · Sep 20, 2024 · 4a41e66 · 4a41e66
1 parent b71b83e
commit 4a41e66
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Showing 2 changed files with 25 additions and 16 deletions.
diff --git a/subworkflows/local/differential/main.nf b/subworkflows/local/differential/main.nf
@@ -13,39 +13,48 @@ workflow DIFFERENTIAL {
     ch_tools
 
     main:
+    ch_tools
+        .branch {
+            propd:  it[0]["diff_method"] == "propd"
+            deseq2: it[0]["diff_method"] == "deseq2"
+        }
+        .set { ch_tools_single }
+
+
+    // Perform differential analysis with PROPD
     ch_counts
-        .join(ch_samplesheet)
-        .first()
-        .combine(ch_tools)
+        .combine(ch_tools_single.propd)
         .combine(ch_contrasts)
         .map {
-            meta_counts, counts, samplesheet, tools, meta_contrast, contrast_variable, reference, target ->
+            meta_counts, counts, tools, meta_contrast, contrast_variable, reference, target ->
                 def meta = meta_counts.clone() + tools.clone()
                 meta.args_diff = (meta.args_diff ?: "") + " --group_col $contrast_variable"
-                [ meta, samplesheet, counts ]
+                [ meta, counts ]
         }
         .unique()
-        .branch {
-            propd:  it[0]["diff_method"] == "propd"
-                return [it[0], it[2]]
-            deseq2: it[0]["diff_method"] == "deseq2"
-        }
-        .set { ch_counts_tools }
+        .set { ch_counts_propd }
 
     PROPD(
-        ch_counts_tools.propd,
+        ch_counts_propd,
         ch_samplesheet.first()
     )
     ch_results   = PROPD.out.results
     ch_adjacency = PROPD.out.adj
 
+    // Perform differential analysis with DESeq2
     // ToDo: In order to use deseq2 the downstream processes need to be updated to process the output correctly
     // if (params.transcript_length_matrix) { ch_transcript_lengths = Channel.of([ exp_meta, file(params.transcript_length_matrix, checkIfExists: true)]).first() } else { ch_transcript_lengths = [[],[]] }
     // if (params.control_features) { ch_control_features = Channel.of([ exp_meta, file(params.control_features, checkIfExists: true)]).first() } else { ch_control_features = [[],[]] }
 
+    // ch_samplesheet
+    //     .join(ch_counts)
+    //     .first()
+    //     .combine(ch_tools_single.deseq2)
+    //     .set { ch_counts_deseq2 }
+
     // DESEQ2_DIFFERENTIAL (
     //     ch_contrasts,
-    //     ch_counts_tools.deseq2,
+    //     ch_counts_deseq2,
     //     ch_control_features,
     //     ch_transcript_lengths
     // )

diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf
@@ -365,20 +365,20 @@ workflow DIFFERENTIALABUNDANCE {
 
         if (params.pathway == "all") {
             ch_tools
-                .set{ ch_tools_single }
+                .set{ ch_tools_filtered }
         } else {
             ch_tools
                 .filter{
                     it[0]["pathway_name"] in params.pathway.tokenize(',')
                 }
-                .set{ ch_tools_single }
+                .set{ ch_tools_filtered }
         }
 
         EXPERIMENTAL(
             ch_contrasts,
             VALIDATOR.out.sample_meta,
             CUSTOM_MATRIXFILTER.out.filtered,
-            ch_tools_single
+            ch_tools_filtered
         )
 
         ch_norm = Channel.empty()