feat: Add save_dbs param to save diamond_db to output (#18)

dalmolingroup · Jul 17, 2023 · c728ac5 · c728ac5
1 parent 79305c7
commit c728ac5
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Showing 3 changed files with 16 additions and 1 deletion.
diff --git a/conf/modules.config b/conf/modules.config
@@ -103,6 +103,16 @@ process {
         ]
     }
 
+    if (params.save_dbs) {
+        withName: DIAMOND_MAKEDB {
+            publishDir = [
+                path: { "${params.outdir}/diamond_db/" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+    }
+
     withName: "FASTQC*" {
         ext.args = '--quiet'
     }

diff --git a/nextflow.config b/nextflow.config
@@ -21,6 +21,7 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     igenomes_ignore            = false
+    save_dbs                   = false
 
     // Assembly
     assembly_based             = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -39,6 +39,10 @@
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
+                },
+                "save_dbs": {
+                    "type": "boolean",
+                    "description": "Save DIAMOND db to results directory after construction"
                 }
             }
         },
@@ -169,7 +173,7 @@
                 },
                 "fasta": {
                     "type": "string",
-                    "default": null
+                    "default": "None"
                 }
             }
         },