Merge pull request #353 from prototaxites/master

Add busco_clean parameter

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#353](https://github.com/nf-core/mag/pull/353) - Added the busco_clean parameter to optionally clean each BUSCO directory after a successful
+
 ### `Changed`
 
 - [#340](https://github.com/nf-core/mag/pull/340) - Update to nf-core 2.6.1 `TEMPLATE`

conf/test.config

@@ -27,5 +27,6 @@ params {
     min_length_unbinned_contigs   = 1
     max_unbinned_contigs          = 2
     busco_reference               = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    busco_clean                   = true
     gtdb                          = false
 }

modules/local/busco.nf

@@ -32,6 +32,10 @@ process BUSCO {
     if (params.busco_reference)
         lineage_dataset_provided = "Y"
 
+    def busco_clean = "N"
+    if (params.busco_clean)
+        busco_clean = "Y"
+
     def p = "--auto-lineage"
     if (params.busco_reference){
         p = "--lineage_dataset dataset/${db}"
@@ -181,6 +185,13 @@ process BUSCO {
         mv BUSCO/logs/prodigal_out.log "${bin}_prodigal.gff"
     fi
 
+    # if needed delete temporary BUSCO files
+    if [ ${busco_clean} ]; then
+        find . -depth -type d -name "augustus_config" -execdir rm -rf "{}" \\;
+        find . -depth -type d -name "auto_lineage" -execdir rm -rf "{}" \\;
+        find . -depth -type d -name "run_*" -execdir rm -rf "{}" +
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version 2>&1 | sed 's/Python //g')

nextflow.config

@@ -97,6 +97,7 @@ params {
     busco_download_path                  = null
     busco_auto_lineage_prok              = false
     save_busco_reference                 = false
+    busco_clean                          = false
 
     // Reproducibility options
     megahit_fix_cpu_1                    = false

nextflow_schema.json

@@ -641,6 +641,11 @@
                     "description": "Specify which binning output is sent for downstream annotation, taxonomic classification, bin quality control etc.",
                     "help_text": "`raw_bins_only`: only bins (and unbinned contigs) from the binners.\n`refined_bins_only`:  only bins (and unbinned contigs) from the bin refinement step .\n`both`: bins and unbinned contigs from both the binning and bin refinement steps.",
                     "enum": ["raw_bins_only", "refined_bins_only", "both"]
+                },
+                "busco_clean": {
+                    "type": "boolean",
+                    "description": "Enable clean-up of temporary files created during BUSCO runs.",
+                    "help_text": "By default, BUSCO creates a large number of intermediate files every run. This may cause problems on some clusters which have file number limits in plate, particularly with large numbers of bins. Enabling this option cleans these files, reducing the total file count of the work directory."
                 }
             }
         },