fixed config file

UPHL-BioNGS · Mar 15, 2024 · 113e3ec · 113e3ec
1 parent ebdc5c4
commit 113e3ec
Showing 1 changed file with 14 additions and 14 deletions.
diff --git a/.github/workflows/github_actions.config b/.github/workflows/github_actions.config
@@ -9,21 +9,21 @@ process {
 	}
 	withLabel:process_low {
 		cpus   = { 2     * task.attempt }
-	        memory = { 12.GB * task.attempt }
-	        time   = { 2.h   * task.attempt }
+	    memory = { 12.GB * task.attempt }
+	    time   = { 2.h   * task.attempt }
 	}
 	withLabel:process_medium {
 		cpus   = { 2     * task.attempt }
-	        memory = { 12.GB * task.attempt }
-        	time   = { 4.h   * task.attempt }
-    	}
-    	withLabel:process_high {
-        	cpus   = { 2    * task.attempt }
-        	memory = { 12.GB * task.attempt }
-        	time   = { 16.h  * task.attempt }
-    	}
-    	withLabel:process_long {
-        	time   = { 20.h  * task.attempt }
+	    memory = { 12.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
+    }
+    withLabel:process_high {
+        cpus   = { 2     * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
+    }
+    withLabel:process_long {
+        time   = { 20.h  * task.attempt }
 	}
 	withLabel:process_high_memory {
 		memory = { 12.GB * task.attempt }
@@ -132,7 +132,7 @@ process {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:panaroo {
-		publishDir = { params.outdir, mode: 'link', pattern: "panaroo/core_gene_alignment.aln"}
+		publishDir = [ path: "grandeur", mode: 'link', pattern: "panaroo/core_gene_alignment.aln"]
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:pbptyper {
@@ -145,7 +145,7 @@ process {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:prokka {
-		publishDir = { params.outdir, mode: 'link', pattern: "gff/*.gff" }
+		publishDir = [ path: "grandeur", mode: 'link', pattern: "gff/*.gff" ]
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:quast {