From f0a74af4ae4ca2690a1bdc2c80ab4980bac46dbf Mon Sep 17 00:00:00 2001
From: Priyanka Surana <ps22@sanger.ac.uk>
Date: Thu, 21 Dec 2023 23:23:04 +0000
Subject: [PATCH] push busco results

---
 bin/update_versions.py |  2 --
 conf/modules.config    | 10 ++++++++++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/bin/update_versions.py b/bin/update_versions.py
index 43f95f93..0978393c 100755
--- a/bin/update_versions.py
+++ b/bin/update_versions.py
@@ -35,8 +35,6 @@ def update_meta(meta, software):
     del new_dict["sanger-tol/blobtoolkit"]
     infile["settings"]["software_versions"] = new_dict
 
-    del infile["settings"]["tmp"]
-
     return infile
 
 
diff --git a/conf/modules.config b/conf/modules.config
index 15ad7fcd..155111ab 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -64,6 +64,11 @@ process {
         scratch = true
         // Overridden in the test profile, see at the end of this file
         ext.args = "--force"
+        publishDir = [
+            path: { "${params.outdir}/BUSCO" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
+        ]
     }
 
     withName: "DIAMOND_BLASTP" {
@@ -173,6 +178,11 @@ profiles {
             withName: BUSCO {
                 // Note: BUSCO *must* see the double-quotes around the parameters
                 ext.args = '--force --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
+                publishDir = [
+                    path: { "${params.outdir}/BUSCO" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
+                ]
             }
         }
     }