add optional boostrap tree output for gubbins

bactopia · Apr 25, 2024 · 9a532ac · 9a532ac
1 parent 60b8053
commit 9a532ac
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Showing 4 changed files with 12 additions and 0 deletions.
diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf
@@ -29,6 +29,7 @@ process GUBBINS {
     tuple val(meta), path("*.branch_base_reconstruction.embl.gz"), emit: embl_branch
     tuple val(meta), path("*.final_tree.tre")                    , emit: tree
     tuple val(meta), path("*.node_labelled.final_tree.tre")      , emit: tree_labelled
+    tuple val(meta), path("*.final_bootstrapped_tree.tre")       , emit: bootstrap_tree, optional: true
     path "*.{log,err}"                           , optional: true, emit: logs
     path ".command.*"                                            , emit: nf_logs
     path "versions.yml"                                          , emit: versions

diff --git a/modules/nf-core/gubbins/meta.yml b/modules/nf-core/gubbins/meta.yml
@@ -62,5 +62,9 @@ output:
       type: file
       description: Recombination removed RAxML phylogenetic tree (nodes labelled)
       pattern: "*.{node_labelled.final_tree.tre}"
+  - bootstrap_tree:
+      type: file
+      description: Recombination removed RAxML phylogenetic tree with bootstrap values
+      pattern: "*.{final_tree.tre}"
 authors:
   - "@avantonder"
diff --git a/modules/nf-core/mlst/params.config b/modules/nf-core/mlst/params.config
@@ -9,4 +9,5 @@ params {
     mincov = 10
     minscore = 50
     nopath = false
+    mlst_db = ""
 }
diff --git a/modules/nf-core/mlst/params.json b/modules/nf-core/mlst/params.json
@@ -41,6 +41,12 @@
                     "default": false,
                     "description": "Strip filename paths from FILE column",
                     "fa_icon": "fas fa-expand-arrows-alt"
+                },
+                "mlst_db": {
+                    "type": "string",
+                    "default": "",
+                    "description": "A custom MLST database to use. Contents should be within a directory called 'mlstdb'",
+                    "fa_icon": "fas fa-expand-arrows-alt"
                 }
             }
         }