Review and update of services.json for files and folders cleaning

CHANGELOG.md

@@ -80,6 +80,7 @@ Code contributions to the new version:
 - Fixed autoclean-sftp function. [#281](https://github.com/BU-ISCIII/buisciii-tools/pull/281)
 - Fixed bioinfo_doc.py. Modified it so that this module creates a .pdf file including new-line characters, without merging lines into one single line [#259](https://github.com/BU-ISCIII/buisciii-tools/pull/259).
 - PR [#288](https://github.com/BU-ISCIII/buisciii-tools/pull/288) Fixed updating service's state to in_progress multiple times, related with issue [#285](https://github.com/BU-ISCIII/buisciii-tools/issues/285)
+- Review and update of services.json for files and folders cleaning [#318](https://github.com/BU-ISCIII/buisciii-tools/pull/318).
 
 #### Changed
 

bu_isciii/templates/services.json

@@ -42,10 +42,10 @@
       "url": "https://github.com/BU-ISCIII/PikaVirus",
       "description": "PikaVirus, a mapping-based tool for metagenome analysis of virus.",
       "clean": {
-        "folders":[],
+        "folders":["virus_coverage/plots"],
         "files":[]
       },
-      "no_copy": ["RAW", "TMP"],
+      "no_copy": ["RAW", "TMP", "01-PikaVirus-results"],
       "last_folder":"REFERENCES",
       "delivery_md": "assets/reports/md/pikavirus.md",
       "results_md": "assets/reports/results/pikavirus.md"
@@ -60,7 +60,7 @@
       "description": "Plasmid identification tool based on mapping and assisted by assembly",
       "clean": {
         "folders":["01-preprocessing/trimmed_sequences"],
-        "files":[]
+        "files":["mapping/sample_name.sorted.bam", "kmer/database.msh"]
       },
       "no_copy": ["RAW", "TMP"],
       "delivery_md": "assets/reports/md/plasmidid.md",
@@ -76,7 +76,7 @@
         "description": "Multilocus sequence typing (MLST) using Taranis",
         "depends_on": "assembly_annotation",
         "clean": {
-          "folders":["03-assembly/trimming/trimmed", "01-preprocessing"],
+          "folders":[],
           "files":[]
         },
         "no_copy": ["RAW", "TMP"],
@@ -94,7 +94,7 @@
         "description": "Multilocus sequence typing (MLST) using chewBBACA",
         "depends_on": "assembly_annotation",
         "clean": {
-          "folders":["03-assembly/trimming/trimmed", "01-preprocessing/{sample_name}"],
+          "folders":[],
           "files":[]
         },
         "no_copy": ["RAW", "TMP"],
@@ -195,7 +195,7 @@
       "end": "",
       "description": "",
       "clean": {
-        "folders":[],
+        "folders":["01-preprocessing"],
         "files":[]
       },
       "no_copy": ["RAW", "TMP", "00-reads", "fasta_inputs"],