Merge pull request #85 from sanger-tol/1.3.1-H1

Change bai to csi for more flexible indexing

Author: DLBPointon

.nf-core.yml

@@ -48,4 +48,4 @@ template:
     - seqera_platform
     - multiqc
     - rocrate
-  version: 1.3.0
+  version: 1.3.1

CHANGELOG.md

@@ -3,6 +3,13 @@
 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).
 
+## [[1.3.1](https://github.com/sanger-tol/curationpretext/releases/tag/1.3.1)] - UNSC Pillar-of-Autumn (H1) - [2025-04-02]
+
+### Added and Fixed
+
+- Changed the index format from `bai` to `csi` to be more flexible with large amount of mapping.
+- Correction to CHANGELOG entry on software versions for [[1.3.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.3.0)]
+
 ## [[1.3.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.3.0)] - UNSC Pillar-of-Autumn - [2025-02-27]
 
 ### Added and Fixed
@@ -33,15 +40,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
 
-| Module                             | Old Version | New Versions               |
-| ---------------------------------- | ----------- | -------------------------- |
-| `gawk`                             | -           | 5.3.0                      |
-| `rename_ids` ( coreutils )         | 9.1         | REMOVED                    |
-| `replace_dots` ( coreutils )       | 9.1         | REMOVED                    |
-| `gap_length` ( coreutils )         | 9.1         | REMOVED                    |
-| `reformat_intersect` ( coreutils ) | 9.1         | REMOVED                    |
-| `generate_genome_file` (coreutils) | 9.1         | REMOVED                    |
-| `custom_dumpsoftwareversions`      | -           | Python 3.11.7 + yaml 5.4.1 |
+| Module                             | Old Version                | New Versions |
+| ---------------------------------- | -------------------------- | ------------ |
+| `gawk`                             | -                          | 5.3.0        |
+| `rename_ids` ( coreutils )         | 9.1                        | REMOVED      |
+| `replace_dots` ( coreutils )       | 9.1                        | REMOVED      |
+| `gap_length` ( coreutils )         | 9.1                        | REMOVED      |
+| `reformat_intersect` ( coreutils ) | 9.1                        | REMOVED      |
+| `generate_genome_file` (coreutils) | 9.1                        | REMOVED      |
+| `custom_dumpsoftwareversions`      | Python 3.11.7 + yaml 5.4.1 | REMOVED      |
 
 ## [[1.2.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.2.0)] - UNSC Spirit-of-Fire - [2025-02-28]
 

CITATION.cff

@@ -18,6 +18,6 @@ identifiers:
     value: 10.5281/zenodo.12773958
 repository-code: "https://github.com/sanger-tol/curationpretext"
 license: MIT
-version: 1.3.0
+version: 1.3.1
 date-released: "2024-12-13"
 url: "https://pipelines.tol.sanger.ac.uk/curationpretext"

nextflow.config

@@ -237,7 +237,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.3.0'
+    version         = '1.3.1'
     doi             = '10.5281/zenodo.12773958'
 }
 

subworkflows/local/longread_coverage/main.nf

@@ -45,7 +45,7 @@ workflow LONGREAD_COVERAGE {
             ch_reads_path,
             reference_tuple.collect(),
             true,
-            "bai",
+            "csi",
             false,
             false,
     )

tests/main.nf.test.snap

@@ -134,7 +134,7 @@
                     "windowmasker": "1.0.0"
                 },
                 "Workflow": {
-                    "sanger-tol/curationpretext": "v1.3.0"
+                    "sanger-tol/curationpretext": "v1.3.1"
                 }
             },
             [
@@ -146,7 +146,7 @@
             ],
             5,
             [
-                
+
             ],
             0,
             2,
@@ -160,4 +160,4 @@
         },
         "timestamp": "2025-03-31T14:22:54.921071"
     }
-}
+}