Update to include tmpdir

CHANGELOG.md

@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - The pipeline now stops on Busco failures (#194)
 - Update resource requirements for BLASTN modules (#191) and BLOBTOOLKIT_WINDOWSTATS
 - Fixed the `test_full` profile (Sanger only)
+- Addition of `--tmpdir` to Diamond blast modules (#200)
+- `--use_work_dir_as_temp` is no longer a hidden param.
 - Fixed some documentation (#193 and #197)
 - Made GENERATE_CONFIG more resilient to network errors (#197)
 

conf/modules.config

@@ -105,11 +105,11 @@ process {
     }
 
     withName: "DIAMOND_BLASTP" {
-        ext.args = "--evalue 1.0e-25  --max-target-seqs 10 --max-hsps 1"
+        ext.args = { "--evalue 1.0e-25  --max-target-seqs 10 --max-hsps 1" + ( params.use_work_dir_as_temp ? " --tmpdir ./blastp_tmp/" : "" ) }
     }
 
     withName: "DIAMOND_BLASTX" {
-        ext.args = "--evalue 1.0e-25  --max-target-seqs 10 --max-hsps 1"
+        ext.args = { "--evalue 1.0e-25  --max-target-seqs 10 --max-hsps 1" + ( params.use_work_dir_as_temp ? " --tmpdir ./blastx_tmp/" : "" ) }
     }
 
     withName: "BLOBTK_DEPTH" {
@@ -178,4 +178,3 @@ process {
     }
 
 }
-

nextflow.config

@@ -38,7 +38,7 @@ params {
     skip_taxon_filtering       = false
 
     // Execution options
-    use_work_dir_as_temp        = false
+    use_work_dir_as_temp       = false
 
     // MultiQC options
     multiqc_config             = null

nextflow_schema.json

@@ -175,9 +175,9 @@
             "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.",
+                    "description": "Set to true to make tools (e.g. sort, FastK, MerquryFK, BLASTP, BLASTX) use the work directory for their temporary files, rather than the system default.",
                     "fa_icon": "fas fa-arrow-circle-down",
-                    "hidden": true
+                    "hidden": false
                 }
             },
             "fa_icon": "fas fa-running"