Update module: Gecco fix to no file generated if no hits found (#1930)

* Make gene and cluster TSVs optional output in case no hits found

* update indicating optional output

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

modules/gecco/run/main.nf

@@ -13,9 +13,9 @@ process GECCO_RUN {
 
 
     output:
-    tuple val(meta), path("*.genes.tsv")           , emit: genes
-    tuple val(meta), path("*.features.tsv")        , emit: features
-    tuple val(meta), path("*.clusters.tsv") , emit: clusters
+    tuple val(meta), path("*.genes.tsv")    , optional: true, emit: genes
+    tuple val(meta), path("*.features.tsv")                 , emit: features
+    tuple val(meta), path("*.clusters.tsv") , optional: true, emit: clusters
     tuple val(meta), path("*_cluster_*.gbk"), optional: true, emit: gbk
     tuple val(meta), path("*.json")         , optional: true, emit: json
 

modules/gecco/run/meta.yml

@@ -44,7 +44,7 @@ output:
       pattern: "versions.yml"
   - genes:
       type: file
-      description: TSV file containing detected/predicted genes with BGC probability scores
+      description: TSV file containing detected/predicted genes with BGC probability scores. Will not be generated if no hits are found.
       pattern: "*.genes.tsv"
   - features:
       type: file
@@ -52,15 +52,15 @@ output:
       pattern: "*.features.tsv"
   - clusters:
       type: file
-      description: TSV file containing coordinates of predicted clusters and BGC types
+      description: TSV file containing coordinates of predicted clusters and BGC types.  Will not be generated if no hits are found.
       pattern: "*.clusters.tsv"
   - gbk:
       type: file
-      description: Per cluster GenBank file (if found) containing sequence with annotations
+      Description: Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found.
       pattern: "*.gbk"
   - json:
       type: file
-      description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied
+      description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found.
       pattern: "*.gbk"
 
 authors: