made some files optional

UPHL-BioNGS · Nov 2, 2023 · 40391a8 · 40391a8
1 parent de69a45
commit 40391a8
Showing 1 changed file with 3 additions and 4 deletions.
diff --git a/modules/freyja.nf b/modules/freyja.nf
@@ -19,7 +19,7 @@ process freyja_variants {
 
   output:
   tuple val(sample), file("freyja/${sample}_{depths,variants}.tsv"), optional: true, emit: variants
-  path "freyja/${sample}*", emit: files
+  path "freyja/${sample}*",                                          optional: true, emit: files
   path "logs/${task.process}/${sample}.${workflow.sessionId}.log"
 
   shell:
@@ -60,7 +60,7 @@ process freyja_demix {
 
   output:
   path "freyja/${sample}_demix.tsv", optional: true, emit: demix
-  path "freyja/${sample}*",                          emit: files
+  path "freyja/${sample}*",          optional: true, emit: files
   path "logs/${task.process}/${sample}.${workflow.sessionId}.log"
 
   shell:
@@ -120,7 +120,6 @@ process freyja_boot {
   '''
 }
 
-
 process freyja_aggregate {
   tag        "Aggregating results from freyja"
   label      "process_single"
@@ -144,7 +143,7 @@ process freyja_aggregate {
   output:
   path "freyja/aggregated*",                                                   emit: files
   path "freyja/aggregated-freyja.tsv",                                         emit: aggregated_freyja_file
-  path "freyja/*mqc.png",                                                       emit: for_multiqc
+  path "freyja/*mqc.png",                                                      emit: for_multiqc
   path "freyja/*png"
   path "logs/${task.process}/${task.process}.${workflow.sessionId}.log"