"Dont split paralogs option" (-s) added to roary

metashot · Apr 22, 2021 · c55d062 · c55d062
1 parent 4b20dbd
commit c55d062
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/modules/roary.nf b/modules/roary.nf
@@ -22,6 +22,8 @@ process roary {
     else {
         param_translation = '-t 11'
     }
+
+    param_dont_split_paralogs = params.dont_split_paralogs ? '-s' : ''
     """
     roary \
         -e -n \
@@ -30,6 +32,7 @@ process roary {
         -f roary \
         -i ${params.min_ident} \
         -cd ${params.min_prev_core} \
+        ${param_dont_split_paralogs} \
         ${gffs}
     """
 }

diff --git a/nextflow.config b/nextflow.config
@@ -11,6 +11,7 @@ params {
     /* Roary options */
     min_ident = 95                    // minimum percentage identity
     min_prev_core = 99                // minimum prevalence of a gene to be consideded core
+    dont_split_paralogs = false       // dont split paralogs
 
     /* Core tree and RAxML options */
     skip_core_tree = false            // if true, skip tree inference with RAxML from the core alignment. Use
@@ -46,7 +47,7 @@ manifest {
     homePage = 'metashot.github.io'
     description = 'Pan genome analysis of closely related prokariotic genomes'
     mainScript = 'main.nf'
-    version = '1.1.0'
+    version = '1.2.0'
 }