[dev-ratio] simplified toolsheet structure, and modified the subworkflows accordingly

assets/tools_samplesheet.csv

@@ -1,6 +1,6 @@
-pathway_name,diff_method,args_diff,enr_diff_method,args_enr_diff,cor_method,args_cor,enr_cor_method,args_enr_cor,sel_method,args_sel
-diff_prop,propd,--adjacency true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 100 --fixseed true,,,,,,,,
-diff_prop_noperm,propd,--cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 0 --fixseed true,,,,,,,,
-filtered_pcor,propd,--adjacency true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 100 --fixseed true,,,propr,--permutation 10 --adjacency true --cutoff_min 0.005 --cutoff_max 0.5 --cutoff_interval 0.01 --metric pcor.bshrink,,,filtervar,
-prop,,,,,propr,--cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --fixseed true --metric rho --permutation 100 --adjacency true,,,,
-diff_grea,propd,--adjacency true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 10 --fixseed true,grea,--permutation 10,,,,,,
+pathway_name,diff_method,args_diff,cor_method,args_cor,enr_method,args_enr
+propd,propd,--adjacency true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 10,,,,
+propd_noperm,propd,--cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 0,,,,
+pcorbshrink,,,propr,--permutation 10 --adjacency true --cutoff_min 0.005 --cutoff_max 0.5 --cutoff_interval 0.01 --metric pcor.bshrink,,
+propr,,,propr,--cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --metric rho --permutation 10 --adjacency true,,
+propd_grea,propd,--adjacency true --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --permutation 10,,,grea,--permutation 10

subworkflows/local/correlation/main.nf

@@ -7,9 +7,14 @@ workflow CORRELATION {
     take:
     ch_counts
     ch_tools
-    ch_counts_filtered
 
     main:
+
+    // initialize empty results channels
+    ch_results   = Channel.empty()
+    ch_adjacency = Channel.empty()
+
+    // branch tools to select the correct correlation analysis method
     ch_counts
         .combine(ch_tools)
         .map {
@@ -21,22 +26,15 @@ workflow CORRELATION {
         }
         .set { ch_counts_cor }
 
-    // Create a branch of the channel to retrieve the normal counts when there is no variable selection.
-    ch_counts_cor.propr
-        .branch{
-            no_sel: it[0]["sel_method"] == null
-            sel:    it[0]["sel_method"] != null
-        }
-        .set { ch_counts_selection }
+    // ----------------------------------------------------
+    // Perform correlation analysis with propr
+    // ----------------------------------------------------
 
-    ch_propr = ch_counts_filtered.mix(ch_counts_selection.no_sel)
-
-    PROPR(ch_propr)
+    PROPR(ch_counts_cor.propr)
     ch_matrix = PROPR.out.matrix
     ch_adjacency = PROPR.out.adj
 
     emit:
     matrix = ch_matrix
     adjacency = ch_adjacency
-
 }

subworkflows/local/differential/main.nf

@@ -4,7 +4,6 @@
 include { PROPR_PROPD as PROPD } from "../../../modules/nf-core/propr/propd/main.nf"
 include { DESEQ2_DIFFERENTIAL  } from '../../../modules/nf-core/deseq2/differential/main'
 
-
 workflow DIFFERENTIAL {
     take:
     ch_contrasts    // [meta, contrast_variable, reference, target]
@@ -13,22 +12,30 @@ workflow DIFFERENTIAL {
     ch_tools
 
     main:
+
+    // initialize empty results channels
+    ch_results   = Channel.empty()
+    ch_adjacency = Channel.empty()
+
+    // branch tools to select the correct differential analysis method
     ch_tools
         .branch {
             propd:  it[0]["diff_method"] == "propd"
             deseq2: it[0]["diff_method"] == "deseq2"
         }
         .set { ch_tools_single }
 
+    // ----------------------------------------------------
+    // Perform differential analysis with propd
+    // ----------------------------------------------------
 
-    // Perform differential analysis with PROPD
     ch_counts
         .combine(ch_tools_single.propd)
         .combine(ch_contrasts)
         .map {
             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.args_diff = (meta.args_diff ?: "") + " --group_col $contrast_variable"  // TODO parse the toolsheet with the ext.arg from modules.config at the beginning of the experimental workflow
                 [ meta, counts ]
         }
         .unique()
@@ -38,10 +45,13 @@ workflow DIFFERENTIAL {
         ch_counts_propd,
         ch_samplesheet.first()
     )
-    ch_results   = PROPD.out.results
-    ch_adjacency = PROPD.out.adj
+    ch_results = ch_results.mix(PROPD.out.results)
+    ch_adjacency = ch_adjacency.mix(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 = [[],[]] }
@@ -64,5 +74,4 @@ workflow DIFFERENTIAL {
     emit:
     results   = ch_results
     adjacency = ch_adjacency
-
 }

subworkflows/local/experimental/main.nf

@@ -3,20 +3,21 @@
 //
 include { CORRELATION }         from '../correlation/main.nf'
 include { DIFFERENTIAL }        from '../differential/main.nf'
-include { VARIABLE_SELECTION }  from '../variable_selection/main.nf'
 include { ENRICHMENT }          from '../enrichment/main.nf'
 
-
 workflow EXPERIMENTAL {
     take:
     ch_contrasts
     ch_samplesheet
     ch_counts
     ch_tools
 
-
     main:
-    // Perform differential analysis
+
+    // ----------------------------------------------------
+    // DIFFERENTIAL ANALYSIS BLOCK
+    // ----------------------------------------------------
+
     DIFFERENTIAL(
         ch_contrasts,
         ch_samplesheet,
@@ -26,33 +27,41 @@ workflow EXPERIMENTAL {
     ch_diff_results = DIFFERENTIAL.out.results
     ch_diff_adjacency = DIFFERENTIAL.out.adjacency
 
-    // Perform variable selection
-    ch_counts_filtered = VARIABLE_SELECTION(ch_diff_adjacency, ch_counts)
+    // ----------------------------------------------------
+    // CORRELATION ANALYSIS BLOCK
+    // ----------------------------------------------------
 
-    // Perform correlation analysis
     CORRELATION(
         ch_counts,
-        ch_tools,
-        ch_counts_filtered
+        ch_tools
     )
-    ch_matrix = CORRELATION.out.matrix
-    ch_cor_adjacency = CORRELATION.out.adjacency
+    ch_corr_matrix = CORRELATION.out.matrix
+    ch_corr_adjacency = CORRELATION.out.adjacency
+
+    // ----------------------------------------------------
+    // FUNCTIONAL ENRICHMENT BLOCK
+    // ----------------------------------------------------
 
-    // Perform enrichment analysis
     ENRICHMENT(
         ch_diff_adjacency,
-        ch_cor_adjacency,
+        ch_corr_adjacency,
         ch_counts
     )
     ch_enriched_cor = ENRICHMENT.out.enriched_cor
     ch_enriched_diff = ENRICHMENT.out.enriched_diff
 
+    // ----------------------------------------------------
+    // VISUALIZATION BLOCK
+    // ----------------------------------------------------
+
+    // TODO: add visualization stuff here
+
+    // do we need to emit anything?
     emit:
-    diff_res    = ch_diff_results
-    diff_adj    = ch_diff_adjacency
-    var_count   = ch_counts_filtered
-    corr_matrix = ch_matrix
-    corr_adj    = ch_cor_adjacency
+    diff_res        = ch_diff_results
+    diff_adj        = ch_diff_adjacency
+    corr_matrix     = ch_corr_matrix
+    corr_adj        = ch_corr_adjacency
     enriched_cor    = ch_enriched_cor
     enriched_cor    = ch_enriched_diff
 }