From 7e551e52fc2707384640c2d1ec4aa46a32d72a90 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Fri, 15 Mar 2024 10:00:30 -0600
Subject: [PATCH] Update github_actions.config

---
 .github/workflows/github_actions.config | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/github_actions.config b/.github/workflows/github_actions.config
index 4f83c1e..4e32005 100755
--- a/.github/workflows/github_actions.config
+++ b/.github/workflows/github_actions.config
@@ -131,6 +131,12 @@ process {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:panaroo {
+		publishDir = { 
+			params.outdir, 
+			mode: 'link', 
+			saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+			pattern: "panaroo/core_gene_alignment.aln"
+			}
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:pbptyper {
@@ -143,6 +149,12 @@ process {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:prokka {
+		publishDir = { 
+			params.outdir, 
+			mode: 'link', 
+			saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+			pattern: "gff/*.gff"
+			}
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:quast {
@@ -175,4 +187,4 @@ process {
 	withName:versions {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-}
\ No newline at end of file
+}