nf-cmgg · matthdsm · Jun 4, 2026 · Jun 4, 2026 · Jun 4, 2026 · Jun 4, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,10 @@
 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).
 
+## v1.13.3
+
+- Bump bcftools modules to fix [topic channel errors when using the `nomad` executor](https://github.com/nf-cmgg/smallvariants/issues/337).
+
 ## v1.13.2
 
 A small patch release to re-add the default for `--genome`

diff --git a/conf/modules.config b/conf/modules.config
@@ -33,6 +33,11 @@ process {
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     */
 
+    withName: "^.*SMALLVARIANTS:BCFTOOLS_GETSAMPLES\$" {
+        ext.args = "--list-samples"
+        ext.suffix = "txt"
+    }
+
     withName: "^.*SMALLVARIANTS:BCFTOOLS_STATS\$" {
         ext.prefix = { "${meta.id}.${meta.caller}"}
     }

diff --git a/modules.json b/modules.json
@@ -7,52 +7,53 @@
                 "nf-core": {
                     "bcftools/annotate": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/filter": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
-                        "installed_by": ["modules"]
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/bcftools/filter/bcftools-filter.diff"
                     },
                     "bcftools/norm": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/pluginscatter": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/query": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/reheader": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/sort": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/stats": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/view": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "feef37435aea56816adf4b3bde1fc76aac327a8d",
                         "installed_by": ["modules"]
                     },
                     "bedtools/merge": {

diff --git a/modules/local/bcftools/filter/environment.yml b/modules/local/bcftools/filter/environment.yml
diff --git a/modules/local/bcftools/filter/main.nf b/modules/local/bcftools/filter/main.nf
diff --git a/modules/local/bcftools/filter/tests/main.nf.test b/modules/local/bcftools/filter/tests/main.nf.test
diff --git a/modules/local/bcftools/filter/tests/main.nf.test.snap b/modules/local/bcftools/filter/tests/main.nf.test.snap
diff --git a/modules/local/bcftools/filter/tests/one_filter.config b/modules/local/bcftools/filter/tests/one_filter.config
diff --git a/modules/local/bcftools/filter/tests/three_filters.config b/modules/local/bcftools/filter/tests/three_filters.config
diff --git a/modules/local/bcftools/filter/tests/two_filters.config b/modules/local/bcftools/filter/tests/two_filters.config
diff --git a/modules/local/bcftools/getsamples/environment.yml b/modules/local/bcftools/getsamples/environment.yml