add nwk tree

nf-core · Dec 20, 2024 · 1a2e039 · 1a2e039
1 parent 945c946
commit 1a2e039
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Showing 3 changed files with 10 additions and 9 deletions.
diff --git a/subworkflows/local/qiime2_diversity.nf b/subworkflows/local/qiime2_diversity.nf
@@ -27,7 +27,8 @@ workflow QIIME2_DIVERSITY {
     ch_versions_qiime2_diversity = Channel.empty()
 
     //Phylogenetic tree for beta & alpha diversities
-    if (!ch_tree) {
+    produce_tree = !ch_tree ? true : false
+    if (produce_tree) {
         QIIME2_TREE ( ch_seq )
         ch_versions_qiime2_diversity = ch_versions_qiime2_diversity.mix(QIIME2_TREE.out.versions)
         ch_tree = QIIME2_TREE.out.qza
@@ -82,6 +83,8 @@ workflow QIIME2_DIVERSITY {
     }
 
     emit:
+    tree_qza = ch_tree
+    tree_nwk = produce_tree ? QIIME2_TREE.out.nwk : []
     depth    = !skip_diversity_indices ? QIIME2_DIVERSITY_CORE.out.depth : []
     alpha    = !skip_diversity_indices ? QIIME2_DIVERSITY_ALPHA.out.alpha : []
     beta     = !skip_diversity_indices ? QIIME2_DIVERSITY_BETA.out.beta : []

diff --git a/subworkflows/local/robject_workflow.nf b/subworkflows/local/robject_workflow.nf
@@ -11,7 +11,7 @@ workflow ROBJECT_WORKFLOW {
     ch_tax
     ch_tsv
     ch_meta
-    ch_tree
+    ch_robject_intree
     run_qiime2
 
     main:
@@ -23,12 +23,6 @@ workflow ROBJECT_WORKFLOW {
         ch_robject_inmeta = []
     }
 
-    if ( params.pplace_tree ) {
-        ch_robject_intree = ch_tree.map { it = it[1] }.first()
-    } else {
-        ch_robject_intree = []
-    }
-
     if ( run_qiime2 ) {
         if ( params.exclude_taxa != "none" || params.min_frequency != 1 || params.min_samples != 1 ) {
             ch_robject_inasv = PHYLOSEQ_INASV ( ch_tsv ).tsv

diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
@@ -870,7 +870,11 @@ workflow AMPLISEQ {
     //
     if ( !params.skip_taxonomy && ( !params.skip_phyloseq || !params.skip_tse ) ) {
         if ( params.pplace_tree ) {
-            ch_tree_for_robject = FASTA_NEWICK_EPANG_GAPPA.out.grafted_phylogeny
+            ch_tree_for_robject = FASTA_NEWICK_EPANG_GAPPA.out.grafted_phylogeny.map { it = it[1] }.first()
+        } else if (params.multiregion) {
+            ch_tree_for_robject = SIDLE_WF.out.tree_nwk
+        } else if ( params.metadata && (!params.skip_alpha_rarefaction || !params.skip_diversity_indices) ) {
+            ch_tree_for_robject = QIIME2_DIVERSITY.out.tree_nwk
         } else {
             ch_tree_for_robject = []
         }