Like in the genome note pipeline, use the work directory instead of /tmp

sanger-tol · Nov 25, 2023 · 2f3c372 · 2f3c372
1 parent 4497965
commit 2f3c372
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Showing 3 changed files with 22 additions and 1 deletion.
diff --git a/conf/modules.config b/conf/modules.config
@@ -28,7 +28,7 @@ process {
     }
 
     withName: SAMTOOLS_COLLATE {
-        ext.prefix = { "${meta.id}.collate" }
+        ext.prefix = { "${meta.id}.collate" + (params.use_work_dir_as_temp ? " -T." : "") }
     }
 
     withName: SAMTOOLS_FIXMATE {

diff --git a/nextflow.config b/nextflow.config
@@ -15,6 +15,9 @@ params {
     bwamem2_index              = null
     fasta                      = null
 
+    // Execution options
+    use_work_dir_as_temp        = false
+
 
     // Boilerplate options
     outdir                     = "./results"

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -67,6 +67,21 @@
                 }
             }
         },
+        "execution": {
+            "title": "Execution",
+            "type": "object",
+            "description": "Control the execution of the pipeline.",
+            "default": "",
+            "properties": {
+                "use_work_dir_as_temp": {
+                    "type": "boolean",
+                    "description": "Set to true to make tools (e.g. sort, FastK, MerquryFK) use the work directory for their temporary files, rather than the system default.",
+                    "fa_icon": "fas fa-arrow-circle-down",
+                    "hidden": true
+                }
+            },
+            "fa_icon": "fas fa-running"
+        },
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",
@@ -236,6 +251,9 @@
         {
             "$ref": "#/definitions/reference_genome_options"
         },
+        {
+            "$ref": "#/definitions/execution"
+        },
         {
             "$ref": "#/definitions/institutional_config_options"
         },