Merge pull request #6 from artic-network/dev

Bump to 1.0.12
artic-network · Nov 11, 2024 · 266ab8f · 266ab8f
2 parents 6de92b4 + 3996299
commit 266ab8f
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Showing 3 changed files with 10 additions and 1 deletion.
diff --git a/main.nf b/main.nf
@@ -44,6 +44,8 @@ process squirrel {
         extra += " -bf bg.fa"
     if ( params.outgroups )
         extra += " --outgroups ${params.outgroups}"
+    if ( params.extra_flags )
+            extra += " ${params.extra_flags}"
 
     """
     export XDG_CACHE_HOME=\$PWD/.cache

diff --git a/nextflow.config b/nextflow.config
@@ -45,6 +45,7 @@ params {
     additional_background = null
     default_additional_background = "data/empty.fa"
     outgroups = null
+    extra_flags = null
 
     wf {
           example_cmd = [
@@ -64,7 +65,7 @@ manifest {
     description     = 'Some QUIck Rearranging to Resolve Evolutionary Links.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = '1.0.10'
+    version         = '1.0.12'
 }
 
 executor {

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -141,6 +141,12 @@
           "title": "Concatenate CDS ",
           "description": "Concatenate coding sequences for each genome, separated by `NNN`.",
           "help_text": "Default: write out as separate records."
+        },
+        "extra_flags": {
+          "type": "string",
+          "title": "Extra flags ",
+          "description": "Additional command line arguments to be passed to squirrel.",
+          "help_text": ""
         }
       }
     },