Merge pull request #93 from sanger-tol/hotfix

Hotfixes for production
sanger-tol · Nov 21, 2023 · 273bdf5 · 273bdf5
2 parents 3a60381 + 65133a6
commit 273bdf5
Show file tree

Hide file tree

Showing 3 changed files with 28 additions and 3 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -24,12 +24,12 @@ process {
     }
 
     withName: BED_SORT {
-        ext.args   = { "-k4 --parallel=${task.cpus} -S${task.memory.giga}G" }
+        ext.args   = { "-k4 --parallel=${task.cpus} -S${task.memory.mega - 100}M" + (params.use_work_dir_as_temp ? " -T." : "") }
         ext.prefix = { "${meta.id}_sorted" }
     }
 
     withName: FILTER_SORT {
-        ext.args   = { "-k3,3d -k7,7d --parallel=${task.cpus} -S${task.memory.giga}G" }
+        ext.args   = { "-k3,3d -k7,7d --parallel=${task.cpus} -S${task.memory.mega - 100}M" + (params.use_work_dir_as_temp ? " -T." : "") }
         ext.prefix = { "${meta.id}_sorted" }
     }
 
@@ -62,7 +62,11 @@ process {
 
     withName: FASTK_FASTK {
         scratch    = false  // Disable scratch to get around bug https://github.com/nextflow-io/nextflow/issues/2983 - from genomeassembler
-        ext.args   = { "-t1 -k${params.kmer_size}" }
+        ext.args   = { "-t1 -k${params.kmer_size}" + (params.use_work_dir_as_temp ? " -P." : "") }
+    }
+
+    withName: MERQURYFK_MERQURYFK {
+        ext.args   = { (params.use_work_dir_as_temp ? "-P." : "") }
     }
 
     withName: CREATETABLE {

diff --git a/nextflow.config b/nextflow.config
@@ -22,6 +22,9 @@ params {
     // References
     fasta                       = null
 
+    // Execution options
+    use_work_dir_as_temp        = false
+
     // MultiQC options
     multiqc_config              = null
     multiqc_title               = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -92,6 +92,21 @@
             },
             "required": ["fasta"]
         },
+        "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",
@@ -290,6 +305,9 @@
         {
             "$ref": "#/definitions/reference_genome_options"
         },
+        {
+            "$ref": "#/definitions/execution"
+        },
         {
             "$ref": "#/definitions/institutional_config_options"
         },