nf-cmgg · matthdsm · Jul 14, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add `apple` profile to enable the use of Apple containers.
 - Drop `hook_url` parameter. To configure messaging services, use a custom config in tandem with the `nf-teams`/`nf-slack` plugin instead.
 - Drop `run_coverage` and add `qc_mode` parameter. Thorough coveage analysis is now included in the `qc_mode` parameter, which can be set to `basic` or `full`. Basic QC includes samtools flagstat, idxstats and mosdepth. Full QC includes samtools stats, samtools coverage, riker metrics and panel coverage in addition to basic QC.
+- Bump `samtools` module to 1.24.
+- Add UMI consensus subworkflow using `fgumi`.
 
 ## 3.0.2
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -182,7 +182,7 @@ process {
                 "-s",
                 "--json",
                 "-d 2500",
-                meta.umi_aware ? "--barcode-name" : "",
+                meta.umi_aware ? "--barcode-name --move-umi-to-tag" : "",
                 "--write-index",
                 "--output-fmt cram,version=3.0",
                 "--output-fmt-option archive",

diff --git a/modules.json b/modules.json
@@ -112,41 +112,41 @@
                     },
                     "samtools/convert": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/convert/samtools-convert.diff"
                     },
                     "samtools/coverage": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/coverage/samtools-coverage.diff"
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["modules"]
                     },
                     "samtools/sormadup": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/sormadup/samtools-sormadup.diff"
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/sort/samtools-sort.diff"
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/stats/samtools-stats.diff"
                     },

diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml
diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf
diff --git a/modules/nf-core/samtools/convert/samtools-convert.diff b/modules/nf-core/samtools/convert/samtools-convert.diff
diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test b/modules/nf-core/samtools/convert/tests/main.nf.test
diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap
diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml
diff --git a/modules/nf-core/samtools/coverage/main.nf b/modules/nf-core/samtools/coverage/main.nf
diff --git a/modules/nf-core/samtools/coverage/samtools-coverage.diff b/modules/nf-core/samtools/coverage/samtools-coverage.diff
diff --git a/modules/nf-core/samtools/coverage/tests/main.nf.test b/modules/nf-core/samtools/coverage/tests/main.nf.test
diff --git a/modules/nf-core/samtools/coverage/tests/main.nf.test.snap b/modules/nf-core/samtools/coverage/tests/main.nf.test.snap
diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml