Update github_actions.config

UPHL-BioNGS · Mar 15, 2024 · 7e551e5 · 7e551e5
1 parent 396b5b7
commit 7e551e5
Showing 1 changed file with 13 additions and 1 deletion.
diff --git 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'}
 	}
-}
+}