diff --git a/modules/nf-core/bwamem3/index/.conda-lock/linux_amd64-bd-b56ccc800b165a7e_1.txt b/modules/nf-core/bwamem3/index/.conda-lock/linux_amd64-bd-dfd4e361b022ff06_1.txt
similarity index 94%
rename from modules/nf-core/bwamem3/index/.conda-lock/linux_amd64-bd-b56ccc800b165a7e_1.txt
rename to modules/nf-core/bwamem3/index/.conda-lock/linux_amd64-bd-dfd4e361b022ff06_1.txt
index 2dc7fdd7050e..14b4de65fe2a 100644
--- a/modules/nf-core/bwamem3/index/.conda-lock/linux_amd64-bd-b56ccc800b165a7e_1.txt
+++ b/modules/nf-core/bwamem3/index/.conda-lock/linux_amd64-bd-dfd4e361b022ff06_1.txt
@@ -10,7 +10,7 @@ environments:
     packages:
       linux-64:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-8_kmp_llvm.conda
-      - conda: https://conda.anaconda.org/bioconda/linux-64/bwa-mem3-0.16.0-h8d53bd0_0.conda
+      - conda: https://conda.anaconda.org/bioconda/linux-64/bwa-mem3-0.17.0-h8d53bd0_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_10.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.9-hebe6cf0_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.10.23-hbd8a1cb_0.conda
@@ -30,10 +30,10 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-h6154650_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-16.2.0-h934c35e_7.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-23.1.4-h7148c6a_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-23.1.5-h7148c6a_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.5-h781a0a9_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h3cf9a74_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/which-2.25-h171cf75_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_7.conda
 packages:
@@ -47,9 +47,9 @@ packages:
   license_family: BSD
   size: 8050
   timestamp: 1788046427177
-- conda: https://conda.anaconda.org/bioconda/linux-64/bwa-mem3-0.16.0-h8d53bd0_0.conda
-  sha256: 27f8517c7fd4a01f233c804cbcb93905fbe65eadee94b07a12c4db91d1d5bb5c
-  md5: 06ad30c15183aed3f027c85bf4cb62b2
+- conda: https://conda.anaconda.org/bioconda/linux-64/bwa-mem3-0.17.0-h8d53bd0_0.conda
+  sha256: 94c5456e96d44d24b1940a94d72fd39790bfc7a6903c42c2b7d1f1b51fdf072f
+  md5: d3c2a5b8b4485b96987146d26f05e162
   depends:
   - __glibc >=2.17,<3.0.a0
   - _openmp_mutex * *_llvm
@@ -61,11 +61,11 @@ packages:
   - libsais >=2.12.0,<3.0a0
   - libstdcxx >=15
   - libzlib >=1.3.2,<2.0a0
-  - llvm-openmp >=23.1.4
+  - llvm-openmp >=23.1.5
   license: MIT AND Apache-2.0 AND Zlib
   license_family: MIT
-  size: 2306287
-  timestamp: 1793601053589
+  size: 2403678
+  timestamp: 1794194551017
 - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_10.conda
   sha256: 1a0d382c515ebf55f8ee1f38c8b81bc95af5c2acc42ad53b66bc5df932032f96
   md5: e675fabcf81499adc7edf58124fb1e01
@@ -292,18 +292,18 @@ packages:
   license_family: Other
   size: 63713
   timestamp: 1785362952714
-- conda: https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-23.1.4-h7148c6a_0.conda
-  sha256: 7de1204abbcf20aa8cb62c8a1385177ded2b7ca536b79c409866e46f30b0242f
-  md5: ad441557f951f09d7e4c79731a6a34dc
+- conda: https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-23.1.5-h7148c6a_0.conda
+  sha256: f4b1e7295d81a34f604cc2a16d620cc39b3e190618f0df50a1c654bd59764dc8
+  md5: 9cce0e7f4ded5b077718d11f9ccb5fa3
   depends:
   - __glibc >=2.17,<3.0.a0
   constrains:
   - intel-openmp <0.0a0
-  - openmp 23.1.4|23.1.4.*
+  - openmp 23.1.5|23.1.5.*
   license: Apache-2.0 WITH LLVM-exception
   license_family: APACHE
-  size: 6130038
-  timestamp: 1792567140233
+  size: 6118953
+  timestamp: 1793827614239
 - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_1.conda
   sha256: 5d46557214ed184381dafe835b7c94a474a1c3b307a08a250b1ea4779b44ffb3
   md5: ee6c0cd80a60961a1f48aa3e0b91f986
@@ -324,17 +324,17 @@ packages:
   license_family: Apache
   size: 3195299
   timestamp: 1791098052301
-- conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda
-  sha256: 4ce2e1ee31a6217998f78c31ce7dc0a3e0557d9238b51d49dd20c52d467a126d
-  md5: f2c23a77b25efcad57d377b34bd84941
+- conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h3cf9a74_1.conda
+  sha256: 1906df348defb547906fc612ab8594485454d011a22c4ca3922cd544f94a9f75
+  md5: fbe1312b64a74fb69c6a1866cf930daf
   depends:
   - __glibc >=2.17,<3.0.a0
-  - libgcc >=14
-  - ncurses >=6.5,<7.0a0
+  - libgcc >=15
+  - ncurses >=6.6,<7.0a0
   license: GPL-2.0-or-later AND LGPL-2.0-or-later
   license_family: GPL
-  size: 593603
-  timestamp: 1769710381284
+  size: 593790
+  timestamp: 1794091094920
 - conda: https://conda.anaconda.org/conda-forge/linux-64/which-2.25-h171cf75_0.conda
   sha256: 2bf9a40d86d29fd5c30d0febec99d06398143ddeece9ebb175cc5a6d20279943
   md5: f16d4aec5e8135e8e7bba02ef600149e
diff --git a/modules/nf-core/bwamem3/index/.conda-lock/linux_arm64-bd-d9c39c7fb055095e_1.txt b/modules/nf-core/bwamem3/index/.conda-lock/linux_arm64-bd-b1708a369edc0a4b_1.txt
similarity index 94%
rename from modules/nf-core/bwamem3/index/.conda-lock/linux_arm64-bd-d9c39c7fb055095e_1.txt
rename to modules/nf-core/bwamem3/index/.conda-lock/linux_arm64-bd-b1708a369edc0a4b_1.txt
index 7e62fe43fcd5..8d7d69b65df9 100644
--- a/modules/nf-core/bwamem3/index/.conda-lock/linux_arm64-bd-d9c39c7fb055095e_1.txt
+++ b/modules/nf-core/bwamem3/index/.conda-lock/linux_arm64-bd-b1708a369edc0a4b_1.txt
@@ -10,7 +10,7 @@ environments:
     packages:
       linux-aarch64:
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-8_kmp_llvm.conda
-      - conda: https://conda.anaconda.org/bioconda/linux-aarch64/bwa-mem3-0.16.0-h9200417_0.conda
+      - conda: https://conda.anaconda.org/bioconda/linux-aarch64/bwa-mem3-0.17.0-h9200417_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_10.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/c-ares-1.34.9-h29ee22c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.10.23-hbd8a1cb_0.conda
@@ -30,10 +30,10 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libssh2-1.11.1-h7572e3e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-16.2.0-hef695bb_7.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/llvm-openmp-23.1.4-hde6636f_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/llvm-openmp-23.1.5-hde6636f_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-h2b6f883_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.5-he6ad1d5_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h9388cd8_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/which-2.25-hdc560ac_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h9d15635_7.conda
 packages:
@@ -47,9 +47,9 @@ packages:
   license_family: BSD
   size: 8050
   timestamp: 1788046407214
-- conda: https://conda.anaconda.org/bioconda/linux-aarch64/bwa-mem3-0.16.0-h9200417_0.conda
-  sha256: 249fb5b1b65813e35beb9c961ff6415b6e8ad0edb3c92d78a568435f022b7ed5
-  md5: 8472e56ac58ed4814a34233ff000f9f2
+- conda: https://conda.anaconda.org/bioconda/linux-aarch64/bwa-mem3-0.17.0-h9200417_0.conda
+  sha256: de819c0675d80ad01fc9ce36ad14778f4b08c3cebd48e4fbad2dc7e1d9b451ca
+  md5: a73b7c85bac380d629639ef8f404e8b4
   depends:
   - _openmp_mutex * *_llvm
   - _openmp_mutex >=4.5
@@ -60,11 +60,11 @@ packages:
   - libsais >=2.12.0,<3.0a0
   - libstdcxx >=15
   - libzlib >=1.3.2,<2.0a0
-  - llvm-openmp >=23.1.4
+  - llvm-openmp >=23.1.5
   license: MIT AND Apache-2.0 AND Zlib
   license_family: MIT
-  size: 2236965
-  timestamp: 1793600705175
+  size: 2289268
+  timestamp: 1794194578344
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_10.conda
   sha256: 24eacc8a20fd7c4616566178562bef7f9344eb4a8700cfc3180fa75a6ff9d39f
   md5: fd544ef1c672d645bf78e5819cbb8f91
@@ -272,16 +272,16 @@ packages:
   license_family: Other
   size: 70108
   timestamp: 1785276540870
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/llvm-openmp-23.1.4-hde6636f_0.conda
-  sha256: 46eb282d04f311a2b465271c707c0477d165c7eb7012fa16b743a50477f34222
-  md5: 4cee2df4f3f12d25e17510142d8cd5fe
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/llvm-openmp-23.1.5-hde6636f_0.conda
+  sha256: 2660021f326065c2b6c4a977e26a05db4b34a2e04258abcb93ade156289fa226
+  md5: 42c4b10d36a07e86441d101610253cff
   constrains:
   - intel-openmp <0.0a0
-  - openmp 23.1.4|23.1.4.*
+  - openmp 23.1.5|23.1.5.*
   license: Apache-2.0 WITH LLVM-exception
   license_family: APACHE
-  size: 5826449
-  timestamp: 1792567126282
+  size: 5850031
+  timestamp: 1793827560360
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-h2b6f883_1.conda
   sha256: d69a04914139627f0a6bfd19412d6c7f1e37edc896af84a6011e07e8bc1e69fa
   md5: c3b4349171ca987ff33a1de61f7b3f96
@@ -300,16 +300,16 @@ packages:
   license_family: Apache
   size: 3716078
   timestamp: 1791097887829
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda
-  sha256: e9cbcbc94e151ada3d6dc365380aaaf591f65012c16d9a2abaea4b9b90adc402
-  md5: ab7288cc39545556d1bc5e71ab2df9a9
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h9388cd8_1.conda
+  sha256: f078969c025382c10e15f20192e10ba98db50e1b11ebd1edabbb4a55660ac0e5
+  md5: 4b9f497179d9c274c0cee68b48cc655c
   depends:
-  - libgcc >=14
-  - ncurses >=6.5,<7.0a0
+  - libgcc >=15
+  - ncurses >=6.6,<7.0a0
   license: GPL-2.0-or-later AND LGPL-2.0-or-later
   license_family: GPL
-  size: 636733
-  timestamp: 1769712412683
+  size: 640148
+  timestamp: 1794091075625
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/which-2.25-hdc560ac_0.conda
   sha256: 720691eb59b86f11ceb21b236b9402d59c47d156183375d2b24c53a201dd874b
   md5: 6dc4b55fc391a3d51ff12a6fed979562
diff --git a/modules/nf-core/bwamem3/index/environment.yml b/modules/nf-core/bwamem3/index/environment.yml
index 02eab67dca66..94f47fab1de8 100644
--- a/modules/nf-core/bwamem3/index/environment.yml
+++ b/modules/nf-core/bwamem3/index/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   # renovate: datasource=conda depName=bioconda/bwa-mem3
-  - "bioconda::bwa-mem3=0.16.0"
+  - "bioconda::bwa-mem3=0.17.0"
diff --git a/modules/nf-core/bwamem3/index/main.nf b/modules/nf-core/bwamem3/index/main.nf
index 50f2fe16207f..87fc59209705 100644
--- a/modules/nf-core/bwamem3/index/main.nf
+++ b/modules/nf-core/bwamem3/index/main.nf
@@ -9,8 +9,8 @@ process BWAMEM3_INDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/98/98b0f53f5aed4a3743c17acf6fe59bb0587228a320a6bbe01b3ff3e9ccf85d43/data'
-        : 'community.wave.seqera.io/library/bwa-mem3:0.16.0--b56ccc800b165a7e'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fa/fa51b6d8b6924f5ccb76a0b6d5380899901edbe821bf1440a3517029f198593a/data'
+        : 'community.wave.seqera.io/library/bwa-mem3:0.17.0--dfd4e361b022ff06'}"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/bwamem3/index/meta.yml b/modules/nf-core/bwamem3/index/meta.yml
index 366956afb964..edb636d4bafb 100644
--- a/modules/nf-core/bwamem3/index/meta.yml
+++ b/modules/nf-core/bwamem3/index/meta.yml
@@ -71,24 +71,24 @@ maintainers:
 containers:
   docker:
     linux/arm64:
-      name: community.wave.seqera.io/library/bwa-mem3:0.16.0--d9c39c7fb055095e
-      build_id: bd-d9c39c7fb055095e_1
-      scan_id: sc-2da9986395531902_1
+      name: community.wave.seqera.io/library/bwa-mem3:0.17.0--b1708a369edc0a4b
+      build_id: bd-b1708a369edc0a4b_1
+      scan_id: sc-31a62c0d7d3f953d_1
     linux/amd64:
-      name: community.wave.seqera.io/library/bwa-mem3:0.16.0--b56ccc800b165a7e
-      build_id: bd-b56ccc800b165a7e_1
-      scan_id: sc-57ddb57e00375a8c_1
+      name: community.wave.seqera.io/library/bwa-mem3:0.17.0--dfd4e361b022ff06
+      build_id: bd-dfd4e361b022ff06_1
+      scan_id: sc-1c1d837e52a8e73c_1
   singularity:
-    linux/amd64:
-      name: oras://community.wave.seqera.io/library/bwa-mem3:0.16.0--17e1d29274d441bb
-      build_id: bd-17e1d29274d441bb_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/98/98b0f53f5aed4a3743c17acf6fe59bb0587228a320a6bbe01b3ff3e9ccf85d43/data
     linux/arm64:
-      name: oras://community.wave.seqera.io/library/bwa-mem3:0.16.0--6b818219a81b827f
-      build_id: bd-6b818219a81b827f_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6c/6c07549c04bd7c7c8fc6b1d63eed3707b98996ca5c9ac1a0a99c6ac9ca71f9ad/data
+      name: oras://community.wave.seqera.io/library/bwa-mem3:0.17.0--f0b577e015f4da29
+      build_id: bd-f0b577e015f4da29_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/19/197c726992576ee3cb8a1f5c1e7efc48884f355691176fd9beea1b0c63d90ff3/data
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/bwa-mem3:0.17.0--81afc3b4105fd554
+      build_id: bd-81afc3b4105fd554_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fa/fa51b6d8b6924f5ccb76a0b6d5380899901edbe821bf1440a3517029f198593a/data
   conda:
     linux/amd64:
-      lock_file: modules/nf-core/bwamem3/index/.conda-lock/linux_amd64-bd-b56ccc800b165a7e_1.txt
+      lock_file: modules/nf-core/bwamem3/index/.conda-lock/linux_amd64-bd-dfd4e361b022ff06_1.txt
     linux/arm64:
-      lock_file: modules/nf-core/bwamem3/index/.conda-lock/linux_arm64-bd-d9c39c7fb055095e_1.txt
+      lock_file: modules/nf-core/bwamem3/index/.conda-lock/linux_arm64-bd-b1708a369edc0a4b_1.txt
diff --git a/modules/nf-core/bwamem3/index/tests/main.nf.test.snap b/modules/nf-core/bwamem3/index/tests/main.nf.test.snap
index 96da5e14b62c..ea954d28f752 100644
--- a/modules/nf-core/bwamem3/index/tests/main.nf.test.snap
+++ b/modules/nf-core/bwamem3/index/tests/main.nf.test.snap
@@ -22,12 +22,12 @@
                     [
                         "BWAMEM3_INDEX",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-11-11T16:20:38.60350813",
+        "timestamp": "2026-11-12T20:22:23.03530456",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -53,12 +53,12 @@
                     [
                         "BWAMEM3_INDEX",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-11-09T09:27:11.538896",
+        "timestamp": "2026-11-12T20:22:18.931836037",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -87,12 +87,12 @@
                     [
                         "BWAMEM3_INDEX",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-11-11T16:20:46.756059088",
+        "timestamp": "2026-11-12T20:22:31.145562099",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -121,12 +121,12 @@
                     [
                         "BWAMEM3_INDEX",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-11-11T16:20:42.686281819",
+        "timestamp": "2026-11-12T20:22:27.108078838",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -152,15 +152,15 @@
                     [
                         "BWAMEM3_INDEX",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-11-04T10:37:45.14069",
+        "timestamp": "2026-11-12T20:22:14.909505444",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.10.5"
+            "nextflow": "25.10.4"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bwamem3/mem/.conda-lock/linux_amd64-bd-f271e572b6aa004b_1.txt b/modules/nf-core/bwamem3/mem/.conda-lock/linux_amd64-bd-ac58207ad8b29268_1.txt
similarity index 95%
rename from modules/nf-core/bwamem3/mem/.conda-lock/linux_amd64-bd-f271e572b6aa004b_1.txt
rename to modules/nf-core/bwamem3/mem/.conda-lock/linux_amd64-bd-ac58207ad8b29268_1.txt
index 2edb32efefdb..015b460e8c41 100644
--- a/modules/nf-core/bwamem3/mem/.conda-lock/linux_amd64-bd-f271e572b6aa004b_1.txt
+++ b/modules/nf-core/bwamem3/mem/.conda-lock/linux_amd64-bd-ac58207ad8b29268_1.txt
@@ -11,7 +11,7 @@ environments:
     packages:
       linux-64:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-8_kmp_llvm.conda
-      - conda: https://conda.anaconda.org/bioconda/linux-64/bwa-mem3-0.16.0-h8d53bd0_0.conda
+      - conda: https://conda.anaconda.org/bioconda/linux-64/bwa-mem3-0.17.0-h8d53bd0_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_10.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.9-hebe6cf0_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.10.23-hbd8a1cb_0.conda
@@ -33,10 +33,10 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-16.2.0-h934c35e_7.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.38-h280c20c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-23.1.4-h7148c6a_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-23.1.5-h7148c6a_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.5-h781a0a9_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h3cf9a74_1.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/samtools-1.25-h9dcdb79_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/which-2.25-h171cf75_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_7.conda
@@ -51,9 +51,9 @@ packages:
   license_family: BSD
   size: 8050
   timestamp: 1788046427177
-- conda: https://conda.anaconda.org/bioconda/linux-64/bwa-mem3-0.16.0-h8d53bd0_0.conda
-  sha256: 27f8517c7fd4a01f233c804cbcb93905fbe65eadee94b07a12c4db91d1d5bb5c
-  md5: 06ad30c15183aed3f027c85bf4cb62b2
+- conda: https://conda.anaconda.org/bioconda/linux-64/bwa-mem3-0.17.0-h8d53bd0_0.conda
+  sha256: 94c5456e96d44d24b1940a94d72fd39790bfc7a6903c42c2b7d1f1b51fdf072f
+  md5: d3c2a5b8b4485b96987146d26f05e162
   depends:
   - __glibc >=2.17,<3.0.a0
   - _openmp_mutex * *_llvm
@@ -65,11 +65,11 @@ packages:
   - libsais >=2.12.0,<3.0a0
   - libstdcxx >=15
   - libzlib >=1.3.2,<2.0a0
-  - llvm-openmp >=23.1.4
+  - llvm-openmp >=23.1.5
   license: MIT AND Apache-2.0 AND Zlib
   license_family: MIT
-  size: 2306287
-  timestamp: 1793601053589
+  size: 2403678
+  timestamp: 1794194551017
 - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_10.conda
   sha256: 1a0d382c515ebf55f8ee1f38c8b81bc95af5c2acc42ad53b66bc5df932032f96
   md5: e675fabcf81499adc7edf58124fb1e01
@@ -315,18 +315,18 @@ packages:
   license_family: Other
   size: 63713
   timestamp: 1785362952714
-- conda: https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-23.1.4-h7148c6a_0.conda
-  sha256: 7de1204abbcf20aa8cb62c8a1385177ded2b7ca536b79c409866e46f30b0242f
-  md5: ad441557f951f09d7e4c79731a6a34dc
+- conda: https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-23.1.5-h7148c6a_0.conda
+  sha256: f4b1e7295d81a34f604cc2a16d620cc39b3e190618f0df50a1c654bd59764dc8
+  md5: 9cce0e7f4ded5b077718d11f9ccb5fa3
   depends:
   - __glibc >=2.17,<3.0.a0
   constrains:
   - intel-openmp <0.0a0
-  - openmp 23.1.4|23.1.4.*
+  - openmp 23.1.5|23.1.5.*
   license: Apache-2.0 WITH LLVM-exception
   license_family: APACHE
-  size: 6130038
-  timestamp: 1792567140233
+  size: 6118953
+  timestamp: 1793827614239
 - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_1.conda
   sha256: 5d46557214ed184381dafe835b7c94a474a1c3b307a08a250b1ea4779b44ffb3
   md5: ee6c0cd80a60961a1f48aa3e0b91f986
@@ -347,17 +347,17 @@ packages:
   license_family: Apache
   size: 3195299
   timestamp: 1791098052301
-- conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda
-  sha256: 4ce2e1ee31a6217998f78c31ce7dc0a3e0557d9238b51d49dd20c52d467a126d
-  md5: f2c23a77b25efcad57d377b34bd84941
+- conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h3cf9a74_1.conda
+  sha256: 1906df348defb547906fc612ab8594485454d011a22c4ca3922cd544f94a9f75
+  md5: fbe1312b64a74fb69c6a1866cf930daf
   depends:
   - __glibc >=2.17,<3.0.a0
-  - libgcc >=14
-  - ncurses >=6.5,<7.0a0
+  - libgcc >=15
+  - ncurses >=6.6,<7.0a0
   license: GPL-2.0-or-later AND LGPL-2.0-or-later
   license_family: GPL
-  size: 593603
-  timestamp: 1769710381284
+  size: 593790
+  timestamp: 1794091094920
 - conda: https://conda.anaconda.org/bioconda/linux-64/samtools-1.25-h9dcdb79_0.conda
   sha256: 92282894edc9e5c1ae4d0ea21a6e4e58257716ee0b4ad81d6fc8b0dc89d35692
   md5: 653e70a5ed974a5b25775bfee26430b8
diff --git a/modules/nf-core/bwamem3/mem/.conda-lock/linux_arm64-bd-e73cbc14b9a6cced_1.txt b/modules/nf-core/bwamem3/mem/.conda-lock/linux_arm64-bd-1b8229347711c377_1.txt
similarity index 94%
rename from modules/nf-core/bwamem3/mem/.conda-lock/linux_arm64-bd-e73cbc14b9a6cced_1.txt
rename to modules/nf-core/bwamem3/mem/.conda-lock/linux_arm64-bd-1b8229347711c377_1.txt
index 5af5c50504f8..df68fd8a4160 100644
--- a/modules/nf-core/bwamem3/mem/.conda-lock/linux_arm64-bd-e73cbc14b9a6cced_1.txt
+++ b/modules/nf-core/bwamem3/mem/.conda-lock/linux_arm64-bd-1b8229347711c377_1.txt
@@ -11,7 +11,7 @@ environments:
     packages:
       linux-aarch64:
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-8_kmp_llvm.conda
-      - conda: https://conda.anaconda.org/bioconda/linux-aarch64/bwa-mem3-0.16.0-h9200417_0.conda
+      - conda: https://conda.anaconda.org/bioconda/linux-aarch64/bwa-mem3-0.17.0-h9200417_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_10.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/c-ares-1.34.9-h29ee22c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.10.23-hbd8a1cb_0.conda
@@ -33,10 +33,10 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-16.2.0-hef695bb_7.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libxcrypt-4.4.38-h80f16a2_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/llvm-openmp-23.1.4-hde6636f_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/llvm-openmp-23.1.5-hde6636f_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-h2b6f883_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.5-he6ad1d5_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h9388cd8_1.conda
       - conda: https://conda.anaconda.org/bioconda/linux-aarch64/samtools-1.25-h391949c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/which-2.25-hdc560ac_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h9d15635_7.conda
@@ -51,9 +51,9 @@ packages:
   license_family: BSD
   size: 8050
   timestamp: 1788046407214
-- conda: https://conda.anaconda.org/bioconda/linux-aarch64/bwa-mem3-0.16.0-h9200417_0.conda
-  sha256: 249fb5b1b65813e35beb9c961ff6415b6e8ad0edb3c92d78a568435f022b7ed5
-  md5: 8472e56ac58ed4814a34233ff000f9f2
+- conda: https://conda.anaconda.org/bioconda/linux-aarch64/bwa-mem3-0.17.0-h9200417_0.conda
+  sha256: de819c0675d80ad01fc9ce36ad14778f4b08c3cebd48e4fbad2dc7e1d9b451ca
+  md5: a73b7c85bac380d629639ef8f404e8b4
   depends:
   - _openmp_mutex * *_llvm
   - _openmp_mutex >=4.5
@@ -64,11 +64,11 @@ packages:
   - libsais >=2.12.0,<3.0a0
   - libstdcxx >=15
   - libzlib >=1.3.2,<2.0a0
-  - llvm-openmp >=23.1.4
+  - llvm-openmp >=23.1.5
   license: MIT AND Apache-2.0 AND Zlib
   license_family: MIT
-  size: 2236965
-  timestamp: 1793600705175
+  size: 2289268
+  timestamp: 1794194578344
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_10.conda
   sha256: 24eacc8a20fd7c4616566178562bef7f9344eb4a8700cfc3180fa75a6ff9d39f
   md5: fd544ef1c672d645bf78e5819cbb8f91
@@ -293,16 +293,16 @@ packages:
   license_family: Other
   size: 70108
   timestamp: 1785276540870
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/llvm-openmp-23.1.4-hde6636f_0.conda
-  sha256: 46eb282d04f311a2b465271c707c0477d165c7eb7012fa16b743a50477f34222
-  md5: 4cee2df4f3f12d25e17510142d8cd5fe
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/llvm-openmp-23.1.5-hde6636f_0.conda
+  sha256: 2660021f326065c2b6c4a977e26a05db4b34a2e04258abcb93ade156289fa226
+  md5: 42c4b10d36a07e86441d101610253cff
   constrains:
   - intel-openmp <0.0a0
-  - openmp 23.1.4|23.1.4.*
+  - openmp 23.1.5|23.1.5.*
   license: Apache-2.0 WITH LLVM-exception
   license_family: APACHE
-  size: 5826449
-  timestamp: 1792567126282
+  size: 5850031
+  timestamp: 1793827560360
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-h2b6f883_1.conda
   sha256: d69a04914139627f0a6bfd19412d6c7f1e37edc896af84a6011e07e8bc1e69fa
   md5: c3b4349171ca987ff33a1de61f7b3f96
@@ -321,16 +321,16 @@ packages:
   license_family: Apache
   size: 3716078
   timestamp: 1791097887829
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda
-  sha256: e9cbcbc94e151ada3d6dc365380aaaf591f65012c16d9a2abaea4b9b90adc402
-  md5: ab7288cc39545556d1bc5e71ab2df9a9
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h9388cd8_1.conda
+  sha256: f078969c025382c10e15f20192e10ba98db50e1b11ebd1edabbb4a55660ac0e5
+  md5: 4b9f497179d9c274c0cee68b48cc655c
   depends:
-  - libgcc >=14
-  - ncurses >=6.5,<7.0a0
+  - libgcc >=15
+  - ncurses >=6.6,<7.0a0
   license: GPL-2.0-or-later AND LGPL-2.0-or-later
   license_family: GPL
-  size: 636733
-  timestamp: 1769712412683
+  size: 640148
+  timestamp: 1794091075625
 - conda: https://conda.anaconda.org/bioconda/linux-aarch64/samtools-1.25-h391949c_0.conda
   sha256: 1d13ec33fa8c8d5d07e3d82cf6bffd50382eeaf93739b409541ee485016b9bfb
   md5: e3e7166bd162704e3f39049069c613d8
diff --git a/modules/nf-core/bwamem3/mem/environment.yml b/modules/nf-core/bwamem3/mem/environment.yml
index bc67cfbc84a9..f556f68d1a64 100644
--- a/modules/nf-core/bwamem3/mem/environment.yml
+++ b/modules/nf-core/bwamem3/mem/environment.yml
@@ -5,7 +5,7 @@ channels:
   - bioconda
 dependencies:
   # renovate: datasource=conda depName=bioconda/bwa-mem3
-  - bioconda::bwa-mem3=0.16.0
+  - bioconda::bwa-mem3=0.17.0
   - bioconda::htslib=1.25
   - bioconda::samtools=1.25
   - conda-forge::findutils=4.10.0
diff --git a/modules/nf-core/bwamem3/mem/main.nf b/modules/nf-core/bwamem3/mem/main.nf
index 2bc085f372e8..6d6c85d5f7b4 100644
--- a/modules/nf-core/bwamem3/mem/main.nf
+++ b/modules/nf-core/bwamem3/mem/main.nf
@@ -7,8 +7,8 @@ process BWAMEM3_MEM {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ff/ffd9362ddd396e0eb431def1812e02a274552b162355b242d974af65fcf83167/data'
-        : 'community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:f271e572b6aa004b'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6c/6c7e01f3fbb256f4cb63f77d5630fe44f9c41557cd25abccf1da96fd693bbbf8/data'
+        : 'community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:ac58207ad8b29268'}"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/bwamem3/mem/meta.yml b/modules/nf-core/bwamem3/mem/meta.yml
index 5ec60abf86b6..aa1872f7b220 100644
--- a/modules/nf-core/bwamem3/mem/meta.yml
+++ b/modules/nf-core/bwamem3/mem/meta.yml
@@ -54,7 +54,9 @@ input:
           for TAPS; the `=` is required) needs an index built with `bwa-mem3 index --meth`,
           which adds the `*.meth.*` seed index. Aligning against a `--meth` index needs about
           1.7x the memory of a plain index (measured on human chr21 with bwa-mem3 0.16.0);
-          for a human genome that is tens of GB.
+          for a human genome that is tens of GB. Since bwa-mem3 0.17.0, bare `--meth`
+          (bisulfite/EM-seq) scores mismatches as `--meth-scoring genomic`; pass
+          `--meth-scoring collapsed` to keep the 0.16.0 scores, MAPQ and placements.
         pattern: "Directory containing bwa-mem3 index *.{amb,ann,bwt.2bit.64,pac}"
         ontologies:
           - edam: "http://edamontology.org/data_3210"
@@ -151,25 +153,25 @@ maintainers:
   - "@nh13"
 containers:
   docker:
-    linux/arm64:
-      name: community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:e73cbc14b9a6cced
-      build_id: bd-e73cbc14b9a6cced_1
-      scan_id: sc-88dd26a648f84e35_1
     linux/amd64:
-      name: community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:f271e572b6aa004b
-      build_id: bd-f271e572b6aa004b_1
-      scan_id: sc-f2ead31ae29e9b64_1
-  singularity:
+      name: community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:ac58207ad8b29268
+      build_id: bd-ac58207ad8b29268_1
+      scan_id: sc-0581889347908187_1
     linux/arm64:
-      name: oras://community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:6b077b9587af43f7
-      build_id: bd-6b077b9587af43f7_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f3/f32caea810da83646cb7c62800d7952f4246ca68799f53fa6b0e1a02e19009b5/data
+      name: community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:1b8229347711c377
+      build_id: bd-1b8229347711c377_1
+      scan_id: sc-113843aa1a9c1b59_1
+  singularity:
     linux/amd64:
-      name: oras://community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:9ae3c28116c5de4c
-      build_id: bd-9ae3c28116c5de4c_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ff/ffd9362ddd396e0eb431def1812e02a274552b162355b242d974af65fcf83167/data
+      name: oras://community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:faf85ebedc129476
+      build_id: bd-faf85ebedc129476_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6c/6c7e01f3fbb256f4cb63f77d5630fe44f9c41557cd25abccf1da96fd693bbbf8/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:a93f66d3bd891ac5
+      build_id: bd-a93f66d3bd891ac5_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/26/2620fede02f2bcc887412dbb17f5d0b7658fee3f9bc94f4bb3fdcef97fdd35b3/data
   conda:
     linux/amd64:
-      lock_file: modules/nf-core/bwamem3/mem/.conda-lock/linux_amd64-bd-f271e572b6aa004b_1.txt
+      lock_file: modules/nf-core/bwamem3/mem/.conda-lock/linux_amd64-bd-ac58207ad8b29268_1.txt
     linux/arm64:
-      lock_file: modules/nf-core/bwamem3/mem/.conda-lock/linux_arm64-bd-e73cbc14b9a6cced_1.txt
+      lock_file: modules/nf-core/bwamem3/mem/.conda-lock/linux_arm64-bd-1b8229347711c377_1.txt
diff --git a/modules/nf-core/bwamem3/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem3/mem/tests/main.nf.test.snap
index 95fdee362bd1..3a508136aff3 100644
--- a/modules/nf-core/bwamem3/mem/tests/main.nf.test.snap
+++ b/modules/nf-core/bwamem3/mem/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -30,10 +30,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-04T10:39:51.353815",
+        "timestamp": "2026-11-12T20:22:55.269724684",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.10.5"
+            "nextflow": "25.10.4"
         }
     },
     "sarscov2 - fastq, meth index, fasta, true - taps": {
@@ -55,7 +55,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -67,10 +67,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-04T10:40:23.46103",
+        "timestamp": "2026-11-12T20:23:11.855782441",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.10.5"
+            "nextflow": "25.10.4"
         }
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, true, bai": {
@@ -98,7 +98,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -110,7 +110,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-09T09:25:57.02971",
+        "timestamp": "2026-11-12T20:23:22.717616427",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -135,7 +135,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -147,7 +147,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-09T09:29:57.18716",
+        "timestamp": "2026-11-12T20:23:44.087790306",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -172,7 +172,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -184,10 +184,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-04T10:40:34.21552",
+        "timestamp": "2026-11-12T20:23:17.195510099",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.10.5"
+            "nextflow": "25.10.4"
         }
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, true": {
@@ -209,7 +209,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -221,10 +221,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-04T10:40:02.110772",
+        "timestamp": "2026-11-12T20:23:00.877046912",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.10.5"
+            "nextflow": "25.10.4"
         }
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, true, bai - stub": {
@@ -252,7 +252,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -264,7 +264,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-09T09:26:30.157855",
+        "timestamp": "2026-11-12T20:23:38.699650171",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -289,7 +289,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -301,10 +301,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-04T10:39:29.905685",
+        "timestamp": "2026-11-12T20:22:44.719015293",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.10.5"
+            "nextflow": "25.10.4"
         }
     },
     "sarscov2 - fastq, index, fasta, true": {
@@ -326,7 +326,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -338,10 +338,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-04T10:39:40.444158",
+        "timestamp": "2026-11-12T20:22:49.756816728",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.10.5"
+            "nextflow": "25.10.4"
         }
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, true, csi": {
@@ -369,7 +369,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -381,7 +381,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-09T09:26:08.787671",
+        "timestamp": "2026-11-12T20:23:28.282214136",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -406,7 +406,7 @@
                     [
                         "BWAMEM3_MEM",
                         "bwamem3",
-                        "0.16.0"
+                        "0.17.0"
                     ]
                 ],
                 "versions_samtools": [
@@ -418,7 +418,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-11-11T16:28:59.913310606",
+        "timestamp": "2026-11-12T20:23:06.395661068",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"