Fix the staging the blast nt database

.nf-core.yml

@@ -43,4 +43,4 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 0.10.1
+  version: 0.10.2

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[0.10.2](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.10.2)] – Onix (patch 2) – [2026-06-15]
+
+### Enhancements & fixes
+
+- bugfix: stage the database with a custom name to avoid issues when it has colons or other unexpected characters
+
 ## [[0.10.1](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.10.1)] – Onix (patch 1) – [2026-03-30]
 
 ### Enhancements & fixes

CITATION.cff

@@ -75,7 +75,7 @@ license: MIT
 message: If you use this software, please cite it using the metadata from this file
   and all references from CITATIONS.md .
 repository-code: https://github.com/sanger-tol/blobtoolkit
-title: sanger-tol/blobtoolkit v0.10.1 - Onix (patch 1)
+title: sanger-tol/blobtoolkit v0.10.2 - Onix (patch 1)
 type: software
 url: https://pipelines.tol.sanger.ac.uk/blobtoolkit
-version: 0.10.1
+version: 0.10.2

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/sanger-tol/blobtoolkit/releases/tag/0.10.1" target="_blank">sanger-tol/blobtoolkit</a>
+  This report has been generated by the <a href="https://github.com/sanger-tol/blobtoolkit/releases/tag/0.10.2" target="_blank">sanger-tol/blobtoolkit</a>
   analysis pipeline.
 report_section_order:
   "sanger-tol-blobtoolkit-methods-description":

nextflow.config

@@ -9,7 +9,6 @@
 // Global default params, used in configs
 params {
 
-    // Specify your pipeline's command line flags
     // Input options
     input                      = null
     align                      = false
@@ -363,7 +362,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=25.04.0'
-    version         = '0.10.1'
+    version         = '0.10.2'
     doi             = '10.5281/zenodo.7949058'
 }
 

ro-crate-metadata.json

@@ -183,10 +183,10 @@
             },
             "url": [
                 "https://github.com/sanger-tol/blobtoolkit",
-                "https://pipelines.tol.sanger.ac.uk//blobtoolkit/0.10.1/"
+                "https://pipelines.tol.sanger.ac.uk//blobtoolkit/0.10.2/"
             ],
             "version": [
-                "0.10.1"
+                "0.10.2"
             ]
         },
         {

tests/default.nf.test.snap

@@ -81,7 +81,7 @@
                     "windowstats_input.py": "1.0.0"
                 },
                 "Workflow": {
-                    "sanger-tol/blobtoolkit": "v0.10.1"
+                    "sanger-tol/blobtoolkit": "v0.10.2"
                 }
             },
             [
@@ -524,7 +524,7 @@
                 "GCA_922984935.2_mononuc_windows.tsv.gz:md5,fcbad31a372540f6cf3765c872e5fdb4",
                 "GCA_922984935.2_tetranuc_windows.tsv.gz:md5,342780b7a1fee014b1cca48d7b52249b",
                 "GCA_922984935.2_trinuc_windows.tsv.gz:md5,6120169d675929da0fec1ec4e3e409e3",
-                "GCA_922984935.2.synonyms_synonyms.json.gz:md5,1da678113c2a1e368805c79a14ad0531",
+                "GCA_922984935.2.synonyms_synonyms.json.gz:md5,0ffb860b9a146602a84adeaa2690e1cd",
                 "archaea_odb10_busco.json.gz:md5,d720747c456c3a9d5f82a213f14c56c2",
                 "archaea_odb10_count.json.gz:md5,db3bfe371d6198e64cade978c5094222",
                 "archaea_odb10_count_windows.json.gz:md5,f6ec3d25d5f03f765ec1e46e4b55e358",
@@ -807,10 +807,10 @@
                 "mMelMel3_ont.coverage.1k.bed.gz:md5,3cd28f4bbfc849a30320715c23606406"
             ]
         ],
+        "timestamp": "2026-06-13T09:25:04.105203147",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-02-07T01:02:46.82860754"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }

tests/nobusco.nf.test.snap

@@ -81,7 +81,7 @@
                     "windowstats_input.py": "1.0.0"
                 },
                 "Workflow": {
-                    "sanger-tol/blobtoolkit": "v0.10.1"
+                    "sanger-tol/blobtoolkit": "v0.10.2"
                 }
             },
             [
@@ -452,7 +452,7 @@
                 "GCA_922984935.2_mononuc_windows.tsv.gz:md5,fcbad31a372540f6cf3765c872e5fdb4",
                 "GCA_922984935.2_tetranuc_windows.tsv.gz:md5,342780b7a1fee014b1cca48d7b52249b",
                 "GCA_922984935.2_trinuc_windows.tsv.gz:md5,6120169d675929da0fec1ec4e3e409e3",
-                "GCA_922984935.2.synonyms_synonyms.json.gz:md5,1da678113c2a1e368805c79a14ad0531",
+                "GCA_922984935.2.synonyms_synonyms.json.gz:md5,0ffb860b9a146602a84adeaa2690e1cd",
                 "archaea_odb10_busco.json.gz:md5,d720747c456c3a9d5f82a213f14c56c2",
                 "archaea_odb10_count.json.gz:md5,db3bfe371d6198e64cade978c5094222",
                 "archaea_odb10_count_windows.json.gz:md5,f6ec3d25d5f03f765ec1e46e4b55e358",
@@ -717,10 +717,10 @@
                 "mMelMel3_ont.coverage.1k.bed.gz:md5,3cd28f4bbfc849a30320715c23606406"
             ]
         ],
+        "timestamp": "2026-06-13T09:27:06.649796842",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-02-12T09:38:54.872279759"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }

tests/raw.nf.test.snap

@@ -86,7 +86,7 @@
                     "windowstats_input.py": "1.0.0"
                 },
                 "Workflow": {
-                    "sanger-tol/blobtoolkit": "v0.10.1"
+                    "sanger-tol/blobtoolkit": "v0.10.2"
                 }
             },
             [
@@ -424,7 +424,7 @@
                 "GCA_922984935.2_mononuc_windows.tsv.gz:md5,2ea0f8ff12a46ef6999c2b0941d38698",
                 "GCA_922984935.2_tetranuc_windows.tsv.gz:md5,c2a751c8242fd2b2cb2fbdbde1c728dc",
                 "GCA_922984935.2_trinuc_windows.tsv.gz:md5,1c1ee422d1ca25ead7bc3d911f861d93",
-                "GCA_922984935.2.synonyms_synonyms.json.gz:md5,1da678113c2a1e368805c79a14ad0531",
+                "GCA_922984935.2.synonyms_synonyms.json.gz:md5,0ffb860b9a146602a84adeaa2690e1cd",
                 "archaea_odb10_busco.json.gz:md5,d720747c456c3a9d5f82a213f14c56c2",
                 "archaea_odb10_count.json.gz:md5,db3bfe371d6198e64cade978c5094222",
                 "archaea_odb10_count_windows.json.gz:md5,f6ec3d25d5f03f765ec1e46e4b55e358",
@@ -661,10 +661,10 @@
                 "GCA_922984935.2.obinary:md5,571f465e27e107f6e4bb3fa2e833250b"
             ]
         ],
+        "timestamp": "2026-06-13T09:29:47.045310754",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-02-12T09:41:19.508904774"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }