nf-core · kubranarci · Jan 22, 2026 · Jan 22, 2026 · Jan 22, 2026 · Jan 22, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,14 +8,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - RTGtools update to 3.13 [#261](https://github.com/nf-core/variantbenchmarking/issues/261)
+- Transforming local modules with bcftools and tabix to standard nf-core modules [#267](https://github.com/nf-core/variantbenchmarking/pull/267)
 
 ### `Fixed`
 
 ### `Dependencies`
 
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
-| rtgtools   | 3.12.1      | 3.13        |
+| Dependency        | Old version | New version |
+| ----------------- | ----------- | ----------- |
+| rtgtools          | 3.12.1      | 3.13        |
+| bcftools/reheader | 1.2         | 1.22        |
+| tabix             | 1.19.1      | 1.21        |
 
 ## 1.4.0
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -84,7 +84,7 @@ process {
         ]
     }
 
-    withName: BGZIP_TABIX {
+    withName: TABIX_BGZIPTABIX {
         publishDir = [
             enabled: false
         ]
@@ -117,7 +117,7 @@ process {
             enabled: false
         ]
     }
-    withName: BCFTOOLS_RENAME_CHR {
+    withName: BCFTOOLS_ANNOTATE {
         ext.prefix = {input.baseName - ".vcf" + ".renamechr"}
         ext.args   = {"--output-type z"}
         publishDir = [
@@ -452,6 +452,11 @@ process {
             pattern: "*{.vcf.gz,tbi,json}",
             mode: params.publish_dir_mode
         ]
+        containerOptions = {
+            workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer'
+                ? "--home ${launchDir}"
+                : null
+        }
     }
     withName: BEDTOOLS_INTERSECT_BENCH {
 

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bcftools/annotate": {
                         "branch": "master",
-                        "git_sha": "c1a7fa1c038061b344f2a41be71942061ec40d2e",
+                        "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6",
                         "installed_by": ["modules"]
                     },
                     "bcftools/filter": {
@@ -30,6 +30,11 @@
                         "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
+                    "bcftools/reheader": {
+                        "branch": "master",
+                        "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/sort": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
@@ -158,17 +163,17 @@
                     },
                     "tabix/bgzip": {
                         "branch": "master",
-                        "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9",
+                        "git_sha": "f2cfcf9d3f6a2d123e6c44aefa788aa232204a7a",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9",
+                        "git_sha": "61846a0d757ff9c0682ba3e28ab0441afd95ad7e",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9",
+                        "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a",
                         "installed_by": ["modules"]
                     },
                     "truvari/bench": {

diff --git a/modules/local/bcftools/reheader/environment.yml b/modules/local/bcftools/reheader/environment.yml
diff --git a/modules/local/bcftools/reheader/main.nf b/modules/local/bcftools/reheader/main.nf
diff --git a/modules/local/bcftools/rename_chr/environment.yml b/modules/local/bcftools/rename_chr/environment.yml
diff --git a/modules/local/bcftools/rename_chr/main.nf b/modules/local/bcftools/rename_chr/main.nf
diff --git a/modules/local/bgzip/tabix/environment.yml b/modules/local/bgzip/tabix/environment.yml
diff --git a/modules/local/bgzip/tabix/main.nf b/modules/local/bgzip/tabix/main.nf
diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml