small pangolin improv

replikation · May 5, 2020 · 611a1f0 · 611a1f0
1 parent 6fd5241
commit 611a1f0
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/modules/pangolin.nf b/modules/pangolin.nf
@@ -4,11 +4,14 @@ process pangolin {
   input:
     tuple val(name), path(fasta)
   output:
-    tuple val(name), path("lineage_report_${name}.csv")
-    path("lineage_report_${name}.csv")
+    tuple val(name), path("lineage_report_${name}.csv") optional true
+    path("lineage_report_${name}.csv") optional true
   script:
     """
     pangolin -t ${task.cpus} ${fasta}
+
     mv lineage_report.csv lineage_report_${name}.csv
+
+    find . -name "*.csv" -size  0 -print -delete
     """
   }