feat: Add param to skip the pan/phylo subwf (#132)

beiko-lab · Jun 16, 2023 · 3f3f5b2 · 3f3f5b2
1 parent 78a8c92
commit 3f3f5b2
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Showing 3 changed files with 16 additions and 5 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -26,6 +26,7 @@ params {
     accessory_similarity       = 99
 
     // Phylogenomics parameters
+    skip_phylo                 = false
     use_ppanggolin             = false
     use_full_alignment         = false
     use_fasttree               = true

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -118,7 +118,8 @@
                 },
                 "skip_phispy": {
                     "type": "boolean",
-                    "fa_icon": "fas fa-virus"
+                    "fa_icon": "fas fa-virus",
+                    "description": "Skip PhiSpy phage detection tool"
                 }
             }
         },
@@ -129,6 +130,11 @@
             "default": "",
             "fa_icon": "fab fa-pagelines",
             "properties": {
+                "skip_phylo": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-forward",
+                    "description": "Skip Pangenomics and Phylogenomics subworkflow"
+                },
                 "use_ppanggolin": {
                     "type": "boolean",
                     "fa_icon": "fas fa-expand",

diff --git a/workflows/arete.nf b/workflows/arete.nf
@@ -197,8 +197,10 @@ workflow ARETE {
     ch_software_versions = ch_software_versions.mix(ASSEMBLE_SHORTREADS.out.assembly_software)
 
     ////////////////////////// PANGENOME /////////////////////////////////////
-    PHYLOGENOMICS(gffs, use_full_alignment, use_fasttree)
-    ch_software_versions = ch_software_versions.mix(PHYLOGENOMICS.out.phylo_software)
+    if (!params.skip_phylo) {
+        PHYLOGENOMICS(gffs, use_full_alignment, use_fasttree)
+        ch_software_versions = ch_software_versions.mix(PHYLOGENOMICS.out.phylo_software)
+    }
 
     ch_software_versions
         .map { it -> if (it) [ it.baseName, it ] }
@@ -387,8 +389,10 @@ workflow ANNOTATION {
     }
 
     ////////////////////////// PANGENOME /////////////////////////////////////
-    PHYLOGENOMICS(gffs, use_full_alignment, use_fasttree)
-    ch_software_versions = ch_software_versions.mix(PHYLOGENOMICS.out.phylo_software)
+    if (!params.skip_phylo) {
+        PHYLOGENOMICS(gffs, use_full_alignment, use_fasttree)
+        ch_software_versions = ch_software_versions.mix(PHYLOGENOMICS.out.phylo_software)
+    }
 
     ch_software_versions
         .map { it -> if (it) [ it.baseName, it ] }