From 941e336aae42728de76502a1144adbb02277e123 Mon Sep 17 00:00:00 2001
From: jvfe <jvfecav@gmail.com>
Date: Wed, 19 Jul 2023 14:43:31 -0300
Subject: [PATCH] refactor: Change prefixes for recombination processes

---
 conf/modules.config  | 3 ++-
 modules/local/ska.nf | 8 ++++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 438141f0..41d2a3e9 100755
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -411,6 +411,7 @@ process {
 
     // Recombination
     withName: VERTICALL_PAIRWISE {
+        ext.prefix = { "cluster_${cluster}" }
         publishDir = [
             path: { "${params.outdir}/recombination/verticall" },
             mode: params.publish_dir_mode,
@@ -429,7 +430,7 @@ process {
     withName: GUBBINS {
         ext.args = '--tree-builder fasttree'
         publishDir = [
-            path: { "${params.outdir}/recombination/gubbins/${cluster}" },
+            path: { "${params.outdir}/recombination/gubbins/cluster_${cluster}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/modules/local/ska.nf b/modules/local/ska.nf
index 6c6e7880..c833b482 100644
--- a/modules/local/ska.nf
+++ b/modules/local/ska.nf
@@ -12,8 +12,8 @@ process SKA2 {
     path assembly_files
 
     output:
-    tuple val(cluster), path("${cluster}_alignment.aln"), emit: aln
-    path "versions.yml"                                 , emit: versions
+    tuple val(cluster), path("${cluster}.aln"), emit: aln
+    path "versions.yml"                       , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,7 +27,7 @@ process SKA2 {
         $args \\
         --input $assemblies \\
         --reference $reference \\
-        --out ${cluster}_alignment.aln \\
+        --out ${cluster}.aln \\
         --threads $task.cpus
 
     cat <<-END_VERSIONS > versions.yml
@@ -38,7 +38,7 @@ process SKA2 {
     stub:
     def VERSION = '3.3.0'
     """
-    touch ${cluster}_alignment.aln
+    touch ${cluster}.aln
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":