diff --git a/CHANGELOG.md b/CHANGELOG.md
index f830efac..a5f5ff3b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Pipeline Updates
 
+- 🔧 Update Bismark to v3.1.0 ([#614](https://github.com/nf-core/methylseq/pull/614))
 - 🔧 Update Bismark to v3.0.0 and refresh the bismark, samtools, bwa, bwameth, methyldackel and parabricks nf-core modules and alignment subworkflows to their latest versions ([#610](https://github.com/nf-core/methylseq/pull/610))
   - Migrated module version reporting to Nextflow topic channels
   - Threaded a combined `[ meta, fasta, fai ]` channel through the alignment subworkflows
diff --git a/modules.json b/modules.json
index 83eaa0c3..a51859bf 100644
--- a/modules.json
+++ b/modules.json
@@ -12,37 +12,37 @@
                     },
                     "bismark/align": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/coverage2cytosine": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/deduplicate": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/genomepreparation": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
                     },
                     "bismark/methylationextractor": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/report": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/summary": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bwa/index": {
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new file mode 100644
index 00000000..da83b7d3
--- /dev/null
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+- libxcrypt >=4.4.36
+license: GPL-1.0-or-later OR Artistic-1.0-Perl
+size: 13338804
+timestamp: 1703310557094
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda
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+- ncurses >=6.5,<7.0a0
+license: GPL-2.0-or-later AND LGPL-2.0-or-later
+license_family: GPL
+size: 636733
+timestamp: 1769712412683
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.6-hc679e19_100_cp314.conda
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+- ld_impl_linux-aarch64 >=2.36.1
+- libexpat >=2.8.1,<3.0a0
+- libffi >=3.5.2,<3.6.0a0
+- libgcc >=14
+- liblzma >=5.8.3,<6.0a0
+- libmpdec >=4.0.0,<5.0a0
+- libsqlite >=3.53.2,<4.0a0
+- libuuid >=2.42.1,<3.0a0
+- libzlib >=1.3.2,<2.0a0
+- ncurses >=6.6,<7.0a0
+- openssl >=3.5.7,<4.0a0
+- python_abi 3.14.* *_cp314
+- readline >=8.3,<9.0a0
+- tk >=8.6.13,<8.7.0a0
+- tzdata
+- zstd >=1.5.7,<1.6.0a0
+license: Python-2.0
+size: 34900936
+timestamp: 1781254861576
+python_site_packages_path: lib/python3.14/site-packages
+- conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+build_number: 8
+sha256: ad6d2e9ac39751cc0529dd1566a26751a0bf2542adb0c232533d32e176e21db5
+md5: 0539938c55b6b1a59b560e843ad864a4
+constrains:
+- python 3.14.* *_cp314
+license: BSD-3-Clause
+license_family: BSD
+size: 6989
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+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/readline-8.3-hb682ff5_0.conda
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+- ncurses >=6.5,<7.0a0
+license: GPL-3.0-only
+license_family: GPL
+size: 357597
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+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.13-noxft_h0dc03b3_103.conda
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+license: TCL
+license_family: BSD
+size: 3368666
+timestamp: 1769464148928
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
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+md5: c3655f82dcea2aa179b291e7099c1fcc
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diff --git a/modules/nf-core/bismark/align/environment.yml b/modules/nf-core/bismark/align/environment.yml
index 7d85512c..dc444907 100644
--- a/modules/nf-core/bismark/align/environment.yml
+++ b/modules/nf-core/bismark/align/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bismark=3.0.0
+  - bioconda::bismark=3.1.0
diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf
index 4b6b1d95..ff7af322 100644
--- a/modules/nf-core/bismark/align/main.nf
+++ b/modules/nf-core/bismark/align/main.nf
@@ -4,8 +4,8 @@ process BISMARK_ALIGN {
 
     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/a6/a65c28a667a89edfb989e4e47a01246ce75577673e02e103ab1cd30fbca84d31/data' :
-        'community.wave.seqera.io/library/bismark:3.0.0--e50ebd38454e3a10' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data' :
+        'community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/bismark/align/meta.yml b/modules/nf-core/bismark/align/meta.yml
index 8f1b5cd9..1bd9fcd5 100644
--- a/modules/nf-core/bismark/align/meta.yml
+++ b/modules/nf-core/bismark/align/meta.yml
@@ -111,3 +111,27 @@ authors:
 maintainers:
   - "@phue"
   - "@sateeshperi"
+containers:
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4
+      build_id: bd-9557d6ab108a83e4_1
+      scan_id: sc-8d2a54959fbc873b_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--f83bc6617fa3cadd
+      build_id: bd-f83bc6617fa3cadd_1
+      scan_id: sc-cf3a320dd51a3a24_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--3abb485fce628c19
+      build_id: bd-3abb485fce628c19_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--4c41a9578c1f2001
+      build_id: bd-4c41a9578c1f2001_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b84d7ddbd3e0bb2240038ce3c9ff9979287d38bf09f2945256eaafba1450096/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/bismark/align/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/bismark/align/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt
diff --git a/modules/nf-core/bismark/align/tests/main.nf.test.snap b/modules/nf-core/bismark/align/tests/main.nf.test.snap
index eaf788d6..b4161134 100644
--- a/modules/nf-core/bismark/align/tests/main.nf.test.snap
+++ b/modules/nf-core/bismark/align/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     [
                         "BISMARK_ALIGN",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -34,7 +34,7 @@
                     [
                         "BISMARK_ALIGN",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -57,7 +57,7 @@
                     [
                         "BISMARK_ALIGN",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -80,7 +80,7 @@
                     [
                         "BISMARK_ALIGN",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -103,7 +103,7 @@
                     [
                         "BISMARK_ALIGN",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
diff --git a/modules/nf-core/bismark/coverage2cytosine/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt b/modules/nf-core/bismark/coverage2cytosine/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
new file mode 100644
index 00000000..da83b7d3
--- /dev/null
+++ b/modules/nf-core/bismark/coverage2cytosine/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
@@ -0,0 +1,432 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bismark-3.1.0-hfa8f182_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.5-ha27dd3b_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.6.17-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.2-h503566f_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/k8-1.2-he8db53b_6.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_9.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.1-hecca717_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.3-h0c1763c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.2-h5347b49_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/minimap2-2.31-h118bc1c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.3-h35e630c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.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/python-3.14.6-habeac84_100_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.28-h4ee821c_9.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
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diff --git a/modules/nf-core/bismark/coverage2cytosine/environment.yml b/modules/nf-core/bismark/coverage2cytosine/environment.yml
index 7d85512c..dc444907 100644
--- a/modules/nf-core/bismark/coverage2cytosine/environment.yml
+++ b/modules/nf-core/bismark/coverage2cytosine/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bismark=3.0.0
+  - bioconda::bismark=3.1.0
diff --git a/modules/nf-core/bismark/coverage2cytosine/main.nf b/modules/nf-core/bismark/coverage2cytosine/main.nf
index ccbaa13a..0370850b 100644
--- a/modules/nf-core/bismark/coverage2cytosine/main.nf
+++ b/modules/nf-core/bismark/coverage2cytosine/main.nf
@@ -4,8 +4,8 @@ process BISMARK_COVERAGE2CYTOSINE {
 
     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/a6/a65c28a667a89edfb989e4e47a01246ce75577673e02e103ab1cd30fbca84d31/data' :
-        'community.wave.seqera.io/library/bismark:3.0.0--e50ebd38454e3a10' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data' :
+        'community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4' }"
 
     input:
     tuple val(meta), path(coverage_file)
diff --git a/modules/nf-core/bismark/coverage2cytosine/meta.yml b/modules/nf-core/bismark/coverage2cytosine/meta.yml
index e00903a3..2cdbc5ef 100644
--- a/modules/nf-core/bismark/coverage2cytosine/meta.yml
+++ b/modules/nf-core/bismark/coverage2cytosine/meta.yml
@@ -114,3 +114,27 @@ authors:
 maintainers:
   - "@ewels"
   - "@sateeshperi"
+containers:
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4
+      build_id: bd-9557d6ab108a83e4_1
+      scan_id: sc-8d2a54959fbc873b_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--f83bc6617fa3cadd
+      build_id: bd-f83bc6617fa3cadd_1
+      scan_id: sc-cf3a320dd51a3a24_1
+  singularity:
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--4c41a9578c1f2001
+      build_id: bd-4c41a9578c1f2001_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b84d7ddbd3e0bb2240038ce3c9ff9979287d38bf09f2945256eaafba1450096/data
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--3abb485fce628c19
+      build_id: bd-3abb485fce628c19_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/bismark/coverage2cytosine/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/bismark/coverage2cytosine/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt
diff --git a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap
index d69f8c1c..3de9914e 100644
--- a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap
+++ b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap
@@ -27,7 +27,7 @@
                     [
                         "BISMARK_COVERAGE2CYTOSINE",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -66,7 +66,7 @@
                     [
                         "BISMARK_COVERAGE2CYTOSINE",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
diff --git a/modules/nf-core/bismark/deduplicate/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt b/modules/nf-core/bismark/deduplicate/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
new file mode 100644
index 00000000..da83b7d3
--- /dev/null
+++ b/modules/nf-core/bismark/deduplicate/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
@@ -0,0 +1,432 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bismark-3.1.0-hfa8f182_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.5-ha27dd3b_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.6.17-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.2-h503566f_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/k8-1.2-he8db53b_6.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_9.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.1-hecca717_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.3-h0c1763c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.2-h5347b49_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/minimap2-2.31-h118bc1c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.3-h35e630c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.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/python-3.14.6-habeac84_100_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.28-h4ee821c_9.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_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_6.conda
+packages:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+build_number: 20
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+- libgomp >=7.5.0
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+license: BSD-3-Clause
+license_family: BSD
+size: 28948
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diff --git a/modules/nf-core/bismark/deduplicate/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt b/modules/nf-core/bismark/deduplicate/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt
new file mode 100644
index 00000000..100bcafd
--- /dev/null
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diff --git a/modules/nf-core/bismark/deduplicate/environment.yml b/modules/nf-core/bismark/deduplicate/environment.yml
index 7d85512c..dc444907 100644
--- a/modules/nf-core/bismark/deduplicate/environment.yml
+++ b/modules/nf-core/bismark/deduplicate/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bismark=3.0.0
+  - bioconda::bismark=3.1.0
diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf
index cbdd374a..c29a6258 100644
--- a/modules/nf-core/bismark/deduplicate/main.nf
+++ b/modules/nf-core/bismark/deduplicate/main.nf
@@ -4,8 +4,8 @@ process BISMARK_DEDUPLICATE {
 
     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/a6/a65c28a667a89edfb989e4e47a01246ce75577673e02e103ab1cd30fbca84d31/data' :
-        'community.wave.seqera.io/library/bismark:3.0.0--e50ebd38454e3a10' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data' :
+        'community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/bismark/deduplicate/meta.yml b/modules/nf-core/bismark/deduplicate/meta.yml
index 5f563528..5dcc4ba6 100644
--- a/modules/nf-core/bismark/deduplicate/meta.yml
+++ b/modules/nf-core/bismark/deduplicate/meta.yml
@@ -83,3 +83,27 @@ authors:
 maintainers:
   - "@phue"
   - "@sateeshperi"
+containers:
+  docker:
+    linux/arm64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--f83bc6617fa3cadd
+      build_id: bd-f83bc6617fa3cadd_1
+      scan_id: sc-cf3a320dd51a3a24_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4
+      build_id: bd-9557d6ab108a83e4_1
+      scan_id: sc-8d2a54959fbc873b_1
+  singularity:
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--4c41a9578c1f2001
+      build_id: bd-4c41a9578c1f2001_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b84d7ddbd3e0bb2240038ce3c9ff9979287d38bf09f2945256eaafba1450096/data
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--3abb485fce628c19
+      build_id: bd-3abb485fce628c19_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/bismark/deduplicate/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/bismark/deduplicate/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt
diff --git a/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap b/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap
index b472349e..260c23d5 100644
--- a/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap
+++ b/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap
@@ -24,7 +24,7 @@
                     [
                         "BISMARK_DEDUPLICATE",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -52,7 +52,7 @@
                     [
                         "BISMARK_DEDUPLICATE",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
diff --git a/modules/nf-core/bismark/genomepreparation/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt b/modules/nf-core/bismark/genomepreparation/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
new file mode 100644
index 00000000..da83b7d3
--- /dev/null
+++ b/modules/nf-core/bismark/genomepreparation/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
@@ -0,0 +1,432 @@
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new file mode 100644
index 00000000..100bcafd
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+sha256: ad6d2e9ac39751cc0529dd1566a26751a0bf2542adb0c232533d32e176e21db5
+md5: 0539938c55b6b1a59b560e843ad864a4
+constrains:
+- python 3.14.* *_cp314
+license: BSD-3-Clause
+license_family: BSD
+size: 6989
+timestamp: 1752805904792
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/readline-8.3-hb682ff5_0.conda
+sha256: fe695f9d215e9a2e3dd0ca7f56435ab4df24f5504b83865e3d295df36e88d216
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+- libgcc >=14
+- ncurses >=6.5,<7.0a0
+license: GPL-3.0-only
+license_family: GPL
+size: 357597
+timestamp: 1765815673644
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.13-noxft_h0dc03b3_103.conda
+sha256: e25c314b52764219f842b41aea2c98a059f06437392268f09b03561e4f6e5309
+md5: 7fc6affb9b01e567d2ef1d05b84aa6ed
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+- libgcc >=14
+- libzlib >=1.3.1,<2.0a0
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+license: TCL
+license_family: BSD
+size: 3368666
+timestamp: 1769464148928
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
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+- libgcc >=14
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+license_family: GPL
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+md5: c3655f82dcea2aa179b291e7099c1fcc
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diff --git a/modules/nf-core/bismark/genomepreparation/environment.yml b/modules/nf-core/bismark/genomepreparation/environment.yml
index 7d85512c..dc444907 100644
--- a/modules/nf-core/bismark/genomepreparation/environment.yml
+++ b/modules/nf-core/bismark/genomepreparation/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bismark=3.0.0
+  - bioconda::bismark=3.1.0
diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf
index 1bd89814..bbd180ca 100644
--- a/modules/nf-core/bismark/genomepreparation/main.nf
+++ b/modules/nf-core/bismark/genomepreparation/main.nf
@@ -4,8 +4,8 @@ process BISMARK_GENOMEPREPARATION {
 
     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/a6/a65c28a667a89edfb989e4e47a01246ce75577673e02e103ab1cd30fbca84d31/data' :
-        'community.wave.seqera.io/library/bismark:3.0.0--e50ebd38454e3a10' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data' :
+        'community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4' }"
 
     input:
     tuple val(meta), path(fasta, name:"BismarkIndex/")
diff --git a/modules/nf-core/bismark/genomepreparation/meta.yml b/modules/nf-core/bismark/genomepreparation/meta.yml
index ed847bbb..6ef230e2 100644
--- a/modules/nf-core/bismark/genomepreparation/meta.yml
+++ b/modules/nf-core/bismark/genomepreparation/meta.yml
@@ -70,3 +70,27 @@ authors:
 maintainers:
   - "@phue"
   - "@sateeshperi"
+containers:
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4
+      build_id: bd-9557d6ab108a83e4_1
+      scan_id: sc-8d2a54959fbc873b_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--f83bc6617fa3cadd
+      build_id: bd-f83bc6617fa3cadd_1
+      scan_id: sc-cf3a320dd51a3a24_1
+  singularity:
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--4c41a9578c1f2001
+      build_id: bd-4c41a9578c1f2001_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b84d7ddbd3e0bb2240038ce3c9ff9979287d38bf09f2945256eaafba1450096/data
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--3abb485fce628c19
+      build_id: bd-3abb485fce628c19_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/bismark/genomepreparation/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/bismark/genomepreparation/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt
diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
index 27602125..6c8e392b 100644
--- a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
+++ b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
@@ -35,7 +35,7 @@
                     [
                         "BISMARK_GENOMEPREPARATION",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -83,7 +83,7 @@
                     [
                         "BISMARK_GENOMEPREPARATION",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
diff --git a/modules/nf-core/bismark/methylationextractor/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt b/modules/nf-core/bismark/methylationextractor/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
new file mode 100644
index 00000000..da83b7d3
--- /dev/null
+++ b/modules/nf-core/bismark/methylationextractor/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
@@ -0,0 +1,432 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bismark-3.1.0-hfa8f182_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.5-ha27dd3b_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.6.17-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.2-h503566f_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/k8-1.2-he8db53b_6.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_9.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.1-hecca717_1.conda
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+- conda: https://conda.anaconda.org/bioconda/linux-64/minimap2-2.31-h118bc1c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.3-h35e630c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.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/python-3.14.6-habeac84_100_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda
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index 00000000..100bcafd
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diff --git a/modules/nf-core/bismark/methylationextractor/environment.yml b/modules/nf-core/bismark/methylationextractor/environment.yml
index 7d85512c..dc444907 100644
--- a/modules/nf-core/bismark/methylationextractor/environment.yml
+++ b/modules/nf-core/bismark/methylationextractor/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bismark=3.0.0
+  - bioconda::bismark=3.1.0
diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf
index 39cb0504..d7a620b4 100644
--- a/modules/nf-core/bismark/methylationextractor/main.nf
+++ b/modules/nf-core/bismark/methylationextractor/main.nf
@@ -4,8 +4,8 @@ process BISMARK_METHYLATIONEXTRACTOR {
 
     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/a6/a65c28a667a89edfb989e4e47a01246ce75577673e02e103ab1cd30fbca84d31/data' :
-        'community.wave.seqera.io/library/bismark:3.0.0--e50ebd38454e3a10' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data' :
+        'community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/bismark/methylationextractor/meta.yml b/modules/nf-core/bismark/methylationextractor/meta.yml
index e7766c15..79ef0729 100644
--- a/modules/nf-core/bismark/methylationextractor/meta.yml
+++ b/modules/nf-core/bismark/methylationextractor/meta.yml
@@ -1,6 +1,5 @@
 name: bismark_methylationextractor
-description: Extracts methylation information for individual cytosines from
-  alignments.
+description: Extracts methylation information for individual cytosines from alignments.
 keywords:
   - bismark
   - consensus
@@ -52,8 +51,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.bedGraph.gz":
           type: file
-          description: Bismark output file containing coverage and methylation
-            metrics
+          description: Bismark output file containing coverage and methylation metrics
           pattern: "*.{bedGraph.gz}"
           ontologies: []
   methylation_calls:
@@ -64,8 +62,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.txt.gz":
           type: file
-          description: Bismark output file containing strand-specific methylation
-            calls
+          description: Bismark output file containing strand-specific methylation calls
           pattern: "*.{txt.gz}"
           ontologies: []
   coverage:
@@ -127,3 +124,27 @@ authors:
 maintainers:
   - "@phue"
   - "@sateeshperi"
+containers:
+  docker:
+    linux/arm64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--f83bc6617fa3cadd
+      build_id: bd-f83bc6617fa3cadd_1
+      scan_id: sc-cf3a320dd51a3a24_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4
+      build_id: bd-9557d6ab108a83e4_1
+      scan_id: sc-8d2a54959fbc873b_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--3abb485fce628c19
+      build_id: bd-3abb485fce628c19_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--4c41a9578c1f2001
+      build_id: bd-4c41a9578c1f2001_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b84d7ddbd3e0bb2240038ce3c9ff9979287d38bf09f2945256eaafba1450096/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/bismark/methylationextractor/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/bismark/methylationextractor/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt
diff --git a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap
index 92b5c4c9..f38d1b6b 100644
--- a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap
+++ b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap
@@ -58,7 +58,7 @@
                     [
                         "BISMARK_METHYLATIONEXTRACTOR",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -121,7 +121,7 @@
                     [
                         "BISMARK_METHYLATIONEXTRACTOR",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
diff --git a/modules/nf-core/bismark/report/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt b/modules/nf-core/bismark/report/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
new file mode 100644
index 00000000..da83b7d3
--- /dev/null
+++ b/modules/nf-core/bismark/report/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
@@ -0,0 +1,432 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bismark-3.1.0-hfa8f182_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.5-ha27dd3b_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.6.17-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.2-h503566f_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/k8-1.2-he8db53b_6.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_9.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.1-hecca717_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.3-h0c1763c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.2-h5347b49_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/minimap2-2.31-h118bc1c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.3-h35e630c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.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/python-3.14.6-habeac84_100_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.28-h4ee821c_9.conda
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+license: BSD-3-Clause
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+size: 28948
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index 00000000..100bcafd
--- /dev/null
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+license: GPL-3.0-only WITH GCC-exception-3.1
+license_family: GPL
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+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.42.2-h1022ec0_0.conda
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diff --git a/modules/nf-core/bismark/report/environment.yml b/modules/nf-core/bismark/report/environment.yml
index 7d85512c..dc444907 100644
--- a/modules/nf-core/bismark/report/environment.yml
+++ b/modules/nf-core/bismark/report/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bismark=3.0.0
+  - bioconda::bismark=3.1.0
diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf
index 10938788..f10da297 100644
--- a/modules/nf-core/bismark/report/main.nf
+++ b/modules/nf-core/bismark/report/main.nf
@@ -4,8 +4,8 @@ process BISMARK_REPORT {
 
     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/a6/a65c28a667a89edfb989e4e47a01246ce75577673e02e103ab1cd30fbca84d31/data' :
-        'community.wave.seqera.io/library/bismark:3.0.0--e50ebd38454e3a10' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data' :
+        'community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4' }"
 
     input:
     tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias)
diff --git a/modules/nf-core/bismark/report/meta.yml b/modules/nf-core/bismark/report/meta.yml
index 5f45c151..3ebd2e72 100644
--- a/modules/nf-core/bismark/report/meta.yml
+++ b/modules/nf-core/bismark/report/meta.yml
@@ -83,3 +83,27 @@ authors:
 maintainers:
   - "@phue"
   - "@sateeshperi"
+containers:
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4
+      build_id: bd-9557d6ab108a83e4_1
+      scan_id: sc-8d2a54959fbc873b_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--f83bc6617fa3cadd
+      build_id: bd-f83bc6617fa3cadd_1
+      scan_id: sc-cf3a320dd51a3a24_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--3abb485fce628c19
+      build_id: bd-3abb485fce628c19_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--4c41a9578c1f2001
+      build_id: bd-4c41a9578c1f2001_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b84d7ddbd3e0bb2240038ce3c9ff9979287d38bf09f2945256eaafba1450096/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/bismark/report/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/bismark/report/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt
diff --git a/modules/nf-core/bismark/report/tests/main.nf.test.snap b/modules/nf-core/bismark/report/tests/main.nf.test.snap
index 56c28d8e..747e601a 100644
--- a/modules/nf-core/bismark/report/tests/main.nf.test.snap
+++ b/modules/nf-core/bismark/report/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                     [
                         "BISMARK_REPORT",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -34,7 +34,7 @@
                     [
                         "BISMARK_REPORT",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
diff --git a/modules/nf-core/bismark/summary/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt b/modules/nf-core/bismark/summary/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
new file mode 100644
index 00000000..da83b7d3
--- /dev/null
+++ b/modules/nf-core/bismark/summary/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
@@ -0,0 +1,432 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bismark-3.1.0-hfa8f182_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.5-ha27dd3b_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.6.17-hbd8a1cb_0.conda
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diff --git a/modules/nf-core/bismark/summary/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt b/modules/nf-core/bismark/summary/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt
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index 00000000..100bcafd
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+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda
+sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75
+md5: c3655f82dcea2aa179b291e7099c1fcc
+depends:
+- libzlib >=1.3.1,<2.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/modules/nf-core/bismark/summary/environment.yml b/modules/nf-core/bismark/summary/environment.yml
index 7d85512c..dc444907 100644
--- a/modules/nf-core/bismark/summary/environment.yml
+++ b/modules/nf-core/bismark/summary/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bismark=3.0.0
+  - bioconda::bismark=3.1.0
diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf
index 8ea3933c..6e6bdd6e 100644
--- a/modules/nf-core/bismark/summary/main.nf
+++ b/modules/nf-core/bismark/summary/main.nf
@@ -3,8 +3,8 @@ process BISMARK_SUMMARY {
 
     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/a6/a65c28a667a89edfb989e4e47a01246ce75577673e02e103ab1cd30fbca84d31/data' :
-        'community.wave.seqera.io/library/bismark:3.0.0--e50ebd38454e3a10' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data' :
+        'community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4' }"
 
     input:
     val(bam)
diff --git a/modules/nf-core/bismark/summary/meta.yml b/modules/nf-core/bismark/summary/meta.yml
index 9a426404..f497e34e 100644
--- a/modules/nf-core/bismark/summary/meta.yml
+++ b/modules/nf-core/bismark/summary/meta.yml
@@ -1,6 +1,5 @@
 name: bismark_summary
-description: Uses Bismark report files of several samples in a run folder to
-  generate a graphical summary HTML report.
+description: Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report.
 keywords:
   - bismark
   - qc
@@ -80,3 +79,27 @@ authors:
 maintainers:
   - "@phue"
   - "@sateeshperi"
+containers:
+  docker:
+    linux/arm64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--f83bc6617fa3cadd
+      build_id: bd-f83bc6617fa3cadd_1
+      scan_id: sc-cf3a320dd51a3a24_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/bismark:3.1.0--9557d6ab108a83e4
+      build_id: bd-9557d6ab108a83e4_1
+      scan_id: sc-8d2a54959fbc873b_1
+  singularity:
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--4c41a9578c1f2001
+      build_id: bd-4c41a9578c1f2001_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b84d7ddbd3e0bb2240038ce3c9ff9979287d38bf09f2945256eaafba1450096/data
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/bismark:3.1.0--3abb485fce628c19
+      build_id: bd-3abb485fce628c19_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/bismark/summary/.conda-lock/linux_amd64-bd-9557d6ab108a83e4_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/bismark/summary/.conda-lock/linux_arm64-bd-f83bc6617fa3cadd_1.txt
diff --git a/modules/nf-core/bismark/summary/tests/main.nf.test.snap b/modules/nf-core/bismark/summary/tests/main.nf.test.snap
index 210ec907..51d1f3c3 100644
--- a/modules/nf-core/bismark/summary/tests/main.nf.test.snap
+++ b/modules/nf-core/bismark/summary/tests/main.nf.test.snap
@@ -6,7 +6,7 @@
                     [
                         "BISMARK_SUMMARY",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
@@ -30,7 +30,7 @@
                     [
                         "BISMARK_SUMMARY",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ],
                 "summary": [
@@ -43,7 +43,7 @@
                     [
                         "BISMARK_SUMMARY",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             },
@@ -52,7 +52,7 @@
                     [
                         "BISMARK_SUMMARY",
                         "bismark",
-                        "3.0.0"
+                        "3.1.0"
                     ]
                 ]
             }
diff --git a/tests/bismark_hisat_variants.nf.test.snap b/tests/bismark_hisat_variants.nf.test.snap
index e607f3ec..2a0fc9f6 100644
--- a/tests/bismark_hisat_variants.nf.test.snap
+++ b/tests/bismark_hisat_variants.nf.test.snap
@@ -11,19 +11,19 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_HISAT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -393,22 +393,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_HISAT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -837,22 +837,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_HISAT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
diff --git a/tests/bismark_variants.nf.test.snap b/tests/bismark_variants.nf.test.snap
index 55122d2b..abfa1e3e 100644
--- a/tests/bismark_variants.nf.test.snap
+++ b/tests/bismark_variants.nf.test.snap
@@ -14,22 +14,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -649,25 +649,25 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_COVERAGE2CYTOSINE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -1077,22 +1077,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -1297,22 +1297,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -1678,25 +1678,25 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_COVERAGE2CYTOSINE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -2082,22 +2082,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -2458,22 +2458,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -2800,19 +2800,19 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -3182,19 +3182,19 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -3564,22 +3564,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -3998,19 +3998,19 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -4274,22 +4274,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -4655,22 +4655,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "GUNZIP": {
                     "gunzip": 1.13
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 2b4b9a44..ad07dc2d 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -11,22 +11,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
diff --git a/tests/index_downloads.nf.test.snap b/tests/index_downloads.nf.test.snap
index 6e38fa39..54c5fefc 100644
--- a/tests/index_downloads.nf.test.snap
+++ b/tests/index_downloads.nf.test.snap
@@ -11,19 +11,19 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -63,22 +63,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_HISAT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -115,19 +115,19 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
diff --git a/tests/targeted_sequencing_variants.nf.test.snap b/tests/targeted_sequencing_variants.nf.test.snap
index e86342c1..14a16072 100644
--- a/tests/targeted_sequencing_variants.nf.test.snap
+++ b/tests/targeted_sequencing_variants.nf.test.snap
@@ -337,22 +337,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -742,22 +742,22 @@
                     "nf-core/methylseq": "v4.3.0dev"
                 },
                 "BISMARK_ALIGN": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_DEDUPLICATE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_GENOMEPREPARATION_BOWTIE": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_METHYLATIONEXTRACTOR": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_REPORT": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "BISMARK_SUMMARY": {
-                    "bismark": "3.0.0"
+                    "bismark": "3.1.0"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"