diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 81f8f1e..1f41b48 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -32,12 +32,12 @@ runs:
         path: ./subworkflows
         depth: 10
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+      uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
       with:
         python-version: "3.14"
 
@@ -49,7 +49,7 @@ runs:
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 172de6f..b694012 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index a7bf4fc..ca2eb82 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -39,15 +39,15 @@ jobs:
     needs: configure
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
           architecture: "x64"
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index 3d6fa6c..254c304 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,12 +32,12 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
         continue-on-error: true
 
       # indication that the linting has finished
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index bc32219..277f12f 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,30 +11,30 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Run prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
           architecture: "x64"
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
 
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
@@ -46,7 +46,7 @@ jobs:
         run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
+        if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 4de681a..e363215 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 
@@ -85,7 +85,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index ee102f7..149e285 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.hooks/block_pipeline_outdir.sh b/.hooks/block_pipeline_outdir.sh
new file mode 100755
index 0000000..e9ba4f9
--- /dev/null
+++ b/.hooks/block_pipeline_outdir.sh
@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+# This hook is used to block commits if they include staged files inside a directory
+# which also contains a subdirectory called `pipeline_info`. The purpose of this is to
+# prevent users from inadvertently committing output from pipeline test runs inside the
+# development directory.
+
+set -e
+
+status=0
+seen_dirs=""
+
+while IFS= read -r file; do
+    # The offending output bundle's root is the ancestor directory that has
+    # `pipeline_info` as an immediate child, so callers can restore it in one go.
+    if [[ "$file" == pipeline_info/* ]]; then
+        top_dir="pipeline_info"
+    elif [[ "$file" == */pipeline_info/* ]]; then
+        top_dir="${file%%/pipeline_info/*}"
+    else
+        top_dir=""
+        dir=$(dirname "$file")
+        while [[ "$dir" != "." && "$dir" != "/" ]]; do
+            if [[ -d "$dir/pipeline_info" ]]; then
+                top_dir="$dir"
+                break
+            fi
+            dir=$(dirname "$dir")
+        done
+    fi
+
+    if [[ -n "$top_dir" ]]; then
+        echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file"
+        status=1
+        case "$seen_dirs" in
+            *"|$top_dir|"*) ;;
+            *)
+                echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area."
+                seen_dirs="$seen_dirs|$top_dir|"
+                ;;
+        esac
+    fi
+done < <(git diff --cached --name-only)
+
+exit "$status"
diff --git a/.nf-core.yml b/.nf-core.yml
index 6fad993..594af75 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -11,7 +11,7 @@ lint:
     - .github/PULL_REQUEST_TEMPLATE.md
     - .github/workflows/branch.yml
     - .github/workflows/linting.yml
-nf_core_version: 4.0.2
+nf_core_version: 4.1.0
 repository_type: pipeline
 template:
   author: Olga Botvinnik, Evangelos Karatzas
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f51e1a2..e9503db 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.8.3
+          - prettier@3.9.6
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -25,9 +25,26 @@ repos:
               subworkflows/(?!local/).*|
               .*\.snap$
           )$
+      - id: check-added-large-files
+        args: [--maxkb=5000]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              .*\.snap$|
+              lib/nfcore_external_java_deps.jar$|
+              docs/.*\.(svg|pdf)$|
+              assets/.*$
+          )$
+      - id: check-merge-conflict
   - repo: https://github.com/seqeralabs/nf-lint-pre-commit
     rev: v0.3.0
     hooks:
       - id: nextflow-lint
         files: '\.nf$|nextflow\.config$'
         args: ["-output", "json"]
+  - repo: local
+    hooks:
+      - id: block-pipeline-outdir
+        name: Prevent committing output from pipeline test runs to the pipeline code itself
+        entry: ./.hooks/block_pipeline_outdir.sh
+        language: script
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7a65002..7b1633f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.2.0dev - [date]
+## v1.2.0dev - [unreleased]
 
 ### `Added`
 
@@ -11,8 +11,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#111](https://github.com/nf-core/proteinannotator/pull/111) - nf-core tools template update to 4.1.0. (by @vagkaratzas)
 - [#106](https://github.com/nf-core/proteinannotator/pull/106) - nf-core tools template update to 4.0.3. (by @vagkaratzas)
 
+### `Dependencies`
+
+| Tool   | Previous version | New version |
+| ------ | ---------------- | ----------- |
+| seqkit | 2.9.0            | 2.13.0      |
+
 ## v1.1.0 - [2026/05/07]
 
 ### `Added`
diff --git a/README.md b/README.md
index 63080c6..aef4bed 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/conf/base.config b/conf/base.config
index 7212d70..4152257 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -49,6 +49,9 @@ process {
     withLabel:process_long {
         time   = { 20.h  * task.attempt }
     }
+    withLabel:process_low_memory {
+        memory = { 1.GB * task.attempt }
+    }
     withLabel:process_high_memory {
         memory = { 200.GB * task.attempt }
     }
diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
index f487ba4..eb32fe5 100644
--- a/conf/containers_conda_lock_files_amd64.config
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
+process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
index e9a3fed..3733ddf 100644
--- a/conf/containers_conda_lock_files_arm64.config
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
+process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } }
diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config
index 01b59df..ea18c3f 100644
--- a/conf/containers_docker_amd64.config
+++ b/conf/containers_docker_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } }
diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config
index 7785cb1..369f743 100644
--- a/conf/containers_docker_arm64.config
+++ b/conf/containers_docker_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } }
diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config
index 754821b..932fc7c 100644
--- a/conf/containers_singularity_https_amd64.config
+++ b/conf/containers_singularity_https_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } }
diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config
index 93071de..4f79532 100644
--- a/conf/containers_singularity_https_arm64.config
+++ b/conf/containers_singularity_https_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } }
diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config
index 952881d..2fa065b 100644
--- a/conf/containers_singularity_oras_amd64.config
+++ b/conf/containers_singularity_oras_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } }
diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config
index 498ec50..84f0792 100644
--- a/conf/containers_singularity_oras_arm64.config
+++ b/conf/containers_singularity_oras_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } }
diff --git a/conf/modules.config b/conf/modules.config
index cd716c8..f0d270f 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -233,8 +233,7 @@ process {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
index 9be0942..23db927 100644
--- a/docs/CONTRIBUTING.md
+++ b/docs/CONTRIBUTING.md
@@ -40,12 +40,12 @@ The nf-core stance on the use of AI and LLMs is that humans are still ultimately
 
 If you’re using AI tools, try to stick by these guidelines:
 
-- Keep PRs as small and focussed as possible
+- Keep PRs as small and focused as possible
 - Avoid any unnecessary changes, such as moving or refactoring code (unless that is the explicit intention of the PR)
 - Review all generated code yourself before opening a PR, and ensure that you understand it
 - Engage with the community review process and expect to make revisions
 
-For more detail, see the the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team.
+For more detail, see the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team.
 
 ### Getting help
 
@@ -128,7 +128,7 @@ Please also refer to the [pipeline-specific contribution guidelines](#pipeline-s
 - [ ] Perform local tests to validate that the new code works as expected.
   - [ ] If applicable, add a new test in the `tests` directory.
 - [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate.
-- [ ] [Lint](lint) the code with nf-core/tools.
+- [ ] [Lint](#lint-tests) the code with nf-core/tools.
 - [ ] Update any diagrams or pipeline images as necessary.
 - [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order.
 - [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module.
@@ -166,7 +166,7 @@ Specify these with generic `withLabel:` selectors, so they can be shared across
 nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config).
 These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements.
 
-Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
+Values assigned within these labels can be dynamically passed to a tool using the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
 
 #### Nextflow version bumping
 
diff --git a/docs/output.md b/docs/output.md
index 6b1be55..7caea22 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -422,4 +422,4 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 
 </details>
 
-[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
+[Nextflow](https://docs.seqera.io/platform-cloud/reports/overview) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
diff --git a/docs/usage.md b/docs/usage.md
index c8fd402..83cb471 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -186,7 +186,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `wave`
-  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
diff --git a/modules.json b/modules.json
index 1d4df10..4bcf981 100644
--- a/modules.json
+++ b/modules.json
@@ -33,7 +33,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
+                        "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
                         "installed_by": ["modules"]
                     },
                     "s4pred/runmodel": {
@@ -43,22 +43,22 @@
                     },
                     "seqfu/stats": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "e0c07e2169e7569da58d8d8c3ca71023fc6a217e",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/replace": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "d07a945f421a4a91ce4e5a22db63e0e7f8741607",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/rmdup": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "d07a945f421a4a91ce4e5a22db63e0e7f8741607",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/seq": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "d07a945f421a4a91ce4e5a22db63e0e7f8741607",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "untar": {
@@ -72,7 +72,7 @@
                 "nf-core": {
                     "faa_seqfu_seqkit": {
                         "branch": "master",
-                        "git_sha": "bf70cbf44b42ff4a81afcb673fcef604f5ef3a85",
+                        "git_sha": "d07a945f421a4a91ce4e5a22db63e0e7f8741607",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
@@ -87,7 +87,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "ce3424257de288c0ca25f097a68d3a289da23f12",
+                        "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
similarity index 75%
rename from modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
rename to modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
index 7619030..2a91c22 100644
--- a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
@@ -14,120 +14,118 @@ linux-64:
 - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.5.0-py314h680f03e_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.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-2026.2.25-hbd8a1cb_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.6-pyhd8ed1ab_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.5.20-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.5.20-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.0-pyhc90fa1f_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.4-hecca717_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.5-py314hd8ed1ab_100.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.8.1-hecca717_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
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 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.17.1-h27c8c51_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.18.0-h27c8c51_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.15-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-9.0.0-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/kaleido-core-0.2.1-h3644ca4_0.tar.bz2
-- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.18-h0c24ade_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.19.1-h0c24ade_0.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/lerc-4.1.0-hdb68285_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-5_h4a7cf45_openblas.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-5_h0358290_openblas.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-7_h4a7cf45_openblas.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-7_h0358290_openblas.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-h17f619e_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.4-hecca717_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.1-hecca717_0.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/libfreetype-2.14.3-ha770c72_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.3-h73754d4_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.2-hb03c661_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-5_h47877c9_openblas.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_19.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.4.1-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-7_h47877c9_openblas.conda
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.18.1-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.35-pyhdfd78af_1.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314h2b28147_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/pillow-12.1.1-py314h8ec4b1a_0.conda
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 noarch: generic
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 license_family: MIT
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 md5: a360c33a5abe61c07959e449fa1453eb
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 license: GPL-2.0-only OR FTL
 size: 384575
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 constrains:
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-- libgomp 15.2.0 he0feb66_18
+- libgcc-ng ==15.2.0=*_19
+- libgomp 15.2.0 he0feb66_19
 license: GPL-3.0-only WITH GCC-exception-3.1
 license_family: GPL
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 constrains:
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+- libgfortran-ng ==15.2.0=*_19
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 license_family: GPL
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 constrains:
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 license: IJG AND BSD-3-Clause AND Zlib
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 constrains:
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-- liblapacke 3.11.0   5*_openblas
-- libcblas   3.11.0   5*_openblas
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 license: BSD-3-Clause
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 depends:
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 constrains:
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+- xz 5.8.3.*
 license: 0BSD
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 md5: 2c21e66f50753a083cbe6b80f38268fa
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 license_family: BSD
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 timestamp: 1769482286018
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 constrains:
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 license: BSD-3-Clause
 license_family: BSD
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 license: zlib-acknowledgement
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-- libgcc 15.2.0 he0feb66_18
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 constrains:
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+- libstdcxx-ng ==15.2.0=*_19
 license: GPL-3.0-only WITH GCC-exception-3.1
 license_family: GPL
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 md5: cd5a90476766d53e901500df9215e927
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 license_family: BSD
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 sha256: 3aed21ab28eddffdaf7f804f49be7a7d701e8f0e46c856d801270b470820a37b
 md5: aea31d2e5b1091feca96fcfe945c3cf9
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 license_family: BSD
 size: 85893
 timestamp: 1770694658918
-- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda
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-md5: 5b5203189eb668f042ac2b0826244964
+- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.2.0-pyhd8ed1ab_0.conda
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 license: MIT
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 md5: 9a17c4307d23318476d7fbf0fedc0cde
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 depends:
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@@ -870,10 +856,11 @@ depends:
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+- polars-runtime-compat >=1.34.0
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-- python >=3.8,!=3.14.1
+- python >=3.9,!=3.14.1
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-- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.18.1-pyhcf101f3_1.conda
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 license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
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-- libgcc >=13
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 md5: a2c1eeadae7a309daed9d62c96012a2b
@@ -956,24 +944,24 @@ license: MPL-2.0
 license_family: MOZILLA
 size: 2057773
 timestamp: 1763485556350
-- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314h2b28147_0.conda
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-md5: 36f5b7eb328bdc204954a2225cf908e2
+- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.6-py314h2b28147_0.conda
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 depends:
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-- python_abi 3.14.* *_cp314
-- libcblas >=3.9.0,<4.0a0
 - liblapack >=3.9.0,<4.0a0
+- python_abi 3.14.* *_cp314
 - libblas >=3.9.0,<4.0a0
+- libcblas >=3.9.0,<4.0a0
 constrains:
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 license: BSD-3-Clause
 license_family: BSD
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 md5: 11b3379b191f63139e29c0d19dee24cd
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 license_family: BSD
 size: 355400
 timestamp: 1758489294972
-- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda
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-md5: f61eb8cd60ff9057122a3d338b99c00f
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda
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 depends:
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 constrains:
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 depends:
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 depends:
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 license: Python-2.0
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 depends:
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 license: MIT
 license_family: MIT
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@@ -1519,16 +1493,16 @@ license: MIT
 license_family: MIT
 size: 85189
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 license_family: MIT
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
deleted file mode 100644
index a55a4d4..0000000
--- a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
+++ /dev/null
@@ -1,126 +0,0 @@
-
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt
similarity index 74%
rename from modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
rename to modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt
index a58231a..3d5b93d 100644
--- a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
+++ b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt
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-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.52.0-hf1c7be2_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.1-he8854b5_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda
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-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda
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 packages:
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 license_family: MIT
 size: 64927
 timestamp: 1773935801332
-- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.5.0-py314h680f03e_0.conda
 noarch: generic
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 license: BSD-3-Clause AND MIT AND EPL-2.0
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 md5: a1b5c571a0923a205d663d8678df4792
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 license_family: BSD
 size: 192412
 timestamp: 1771350241232
-- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
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-md5: 4492fd26db29495f0ba23f146cd5638d
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.5.20-hbd8a1cb_0.conda
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 license: ISC
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 license: ISC
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 license: MIT
 license_family: MIT
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-- python >=3.10
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+- python >=3.10
 license: BSD-3-Clause
 license_family: BSD
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 sha256: 8021c76eeadbdd5784b881b165242db9449783e12ce26d6234060026fd6a8680
 md5: b866ff7007b934d564961066c8195983
@@ -263,26 +261,26 @@ license: BSD-3-Clause
 license_family: BSD
 size: 39326
 timestamp: 1735759976140
-- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.5-py314hd8ed1ab_100.conda
 noarch: generic
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 license: Python-2.0
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 depends:
-- libexpat 2.7.4 hfae3067_0
+- libexpat 2.8.1 hfae3067_0
 - libgcc >=14
 license: MIT
 license_family: MIT
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 md5: 0c96522c6bdaed4b1566d11387caaf45
@@ -311,20 +309,20 @@ license: LicenseRef-Ubuntu-Font-Licence-Version-1.0
 license_family: Other
 size: 1620504
 timestamp: 1727511233259
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/fontconfig-2.17.1-hba86a56_0.conda
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 depends:
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-- libfreetype >=2.14.1
-- libfreetype6 >=2.14.1
+- libexpat >=2.8.1,<3.0a0
+- libfreetype >=2.14.3
+- libfreetype6 >=2.14.3
 - libgcc >=14
-- libuuid >=2.41.3,<3.0a0
-- libzlib >=1.3.1,<2.0a0
+- libuuid >=2.42.1,<3.0a0
+- libzlib >=1.3.2,<2.0a0
 license: MIT
 license_family: MIT
-size: 279044
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 sha256: 54eea8469786bc2291cc40bca5f46438d3e062a399e8f53f013b6a9f50e98333
 md5: a7970cd949a077b7cb9696379d338681
@@ -386,36 +384,26 @@ license: MIT
 license_family: MIT
 size: 17397
 timestamp: 1737618427549
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 depends:
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 license: BSD-3-Clause
 license_family: BSD
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 depends:
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 license: Apache-2.0
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 md5: 04558c96691bed63104678757beb4f8d
@@ -469,17 +457,17 @@ license: MIT
 license_family: MIT
 size: 65750397
 timestamp: 1615199465742
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda
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-md5: bb960f01525b5e001608afef9d47b79c
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 depends:
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-- libjpeg-turbo >=3.1.2,<4.0a0
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 license: MIT
 license_family: MIT
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 md5: a21644fc4a83da26452a718dc9468d5f
@@ -501,37 +489,37 @@ license: Apache-2.0
 license_family: Apache
 size: 240444
 timestamp: 1773114901155
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-5_haddc8a3_openblas.conda
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 depends:
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-- libopenblas >=0.3.30,<1.0a0
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+- libopenblas >=0.3.33,<1.0a0
 constrains:
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-- liblapack  3.11.0   5*_openblas
-- liblapacke 3.11.0   5*_openblas
-- blas 2.305   openblas
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+- libcblas   3.11.0   7*_openblas
+- mkl <2027
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+- liblapacke 3.11.0   7*_openblas
 license: BSD-3-Clause
 license_family: BSD
-size: 18369
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-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-5_hd72aa62_openblas.conda
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 constrains:
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-- liblapacke 3.11.0   5*_openblas
-- blas 2.305   openblas
+- liblapack  3.11.0   7*_openblas
+- blas 2.307   openblas
+- liblapacke 3.11.0   7*_openblas
 license: BSD-3-Clause
 license_family: BSD
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 md5: a9138815598fe6b91a1d6782ca657b0c
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 license_family: MIT
 size: 71117
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 depends:
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 constrains:
-- expat 2.7.4.*
+- expat 2.8.1.*
 license: MIT
 license_family: MIT
-size: 76564
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 md5: 2f364feefb6a7c00423e80dcb12db62a
@@ -581,90 +569,90 @@ constrains:
 license: GPL-2.0-only OR FTL
 size: 422941
 timestamp: 1774301093473
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda
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 depends:
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 constrains:
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-- libgomp 15.2.0 h8acb6b2_18
+- libgomp 15.2.0 h8acb6b2_19
+- libgcc-ng ==15.2.0=*_19
 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/libgcc-ng-15.2.0-he9431aa_18.conda
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 depends:
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 md5: 3e9427ee186846052e81fadde8ebe96a
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 license_family: MIT
 size: 5251872
 timestamp: 1772628857717
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 depends:
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 constrains:
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 license: MIT
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 noarch: python
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 depends:
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 license: MIT
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 noarch: python
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 depends:
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-- libgcc >=14
 - libstdcxx >=14
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 - _python_abi3_support 1.*
 - cpython >=3.10
 constrains:
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 license: MIT
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 md5: ab7288cc39545556d1bc5e71ab2df9a9
@@ -1104,24 +1079,23 @@ license: MIT
 license_family: MIT
 size: 14645
 timestamp: 1736766960536
-- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.12.5-pyhcf101f3_1.conda
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-md5: c3946ed24acdb28db1b5d63321dbca7d
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 depends:
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-- typing-extensions >=4.6.1
 - annotated-types >=0.6.0
-- pydantic-core ==2.41.5
+- pydantic-core ==2.46.4
 - python
 license: MIT
 license_family: MIT
-size: 340482
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-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.41.5-py314h451b6cc_1.conda
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 depends:
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@@ -1132,17 +1106,17 @@ constrains:
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 license: MIT
 license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.2-pyhd8ed1ab_0.conda
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 depends:
-- python >=3.9
+- python >=3.10
 license: BSD-2-Clause
 license_family: BSD
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 - conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda
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 md5: 461219d1a5bd61342293efa2c0c90eac
@@ -1153,31 +1127,31 @@ license: BSD-3-Clause
 license_family: BSD
 size: 21085
 timestamp: 1733217331982
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.3-hb06a95a_101_cp314.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.5-hfd9ac0a_100_cp314.conda
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 depends:
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 - ld_impl_linux-aarch64 >=2.36.1
-- libexpat >=2.7.3,<3.0a0
+- libexpat >=2.8.0,<3.0a0
 - libffi >=3.5.2,<3.6.0a0
 - libgcc >=14
-- liblzma >=5.8.2,<6.0a0
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 - libmpdec >=4.0.0,<5.0a0
-- libsqlite >=3.51.2,<4.0a0
-- libuuid >=2.41.3,<3.0a0
-- libzlib >=1.3.1,<2.0a0
-- ncurses >=6.5,<7.0a0
-- openssl >=3.5.5,<4.0a0
+- libsqlite >=3.53.1,<4.0a0
+- libuuid >=2.42.1,<3.0a0
+- libzlib >=1.3.2,<2.0a0
+- ncurses >=6.6,<7.0a0
+- openssl >=3.5.6,<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: 37305578
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+size: 37510439
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 python_site_packages_path: lib/python3.14/site-packages
 - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda
 sha256: 74e417a768f59f02a242c25e7db0aa796627b5bc8c818863b57786072aeb85e5
@@ -1188,15 +1162,15 @@ license: BSD-3-Clause
 license_family: BSD
 size: 27848
 timestamp: 1772388605021
-- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda
-sha256: 233aebd94c704ac112afefbb29cf4170b7bc606e22958906f2672081bc50638a
-md5: 235765e4ea0d0301c75965985163b5a1
+- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.5-h4df99d1_100.conda
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 depends:
-- cpython 3.14.3.*
+- cpython 3.14.5.*
 - python_abi * *_cp314
 license: Python-2.0
-size: 50062
-timestamp: 1770674497152
+size: 50212
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 - conda: https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2
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 md5: 310259a5b03ff02289d7705f39e2b1d2
@@ -1253,9 +1227,9 @@ license: MIT
 license_family: MIT
 size: 51788
 timestamp: 1760379115194
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.2.28-py314h51f160d_0.conda
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-md5: 818aa2c9f6b3c808da5e7be22a9a424c
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.5.9-py314h51f160d_0.conda
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+md5: 34ed7bc9febeca70f55b757ca09c354d
 depends:
 - libgcc >=14
 - python >=3.14,<3.15.0a0
@@ -1263,27 +1237,27 @@ depends:
 - python_abi 3.14.* *_cp314
 license: Apache-2.0 AND CNRI-Python
 license_family: PSF
-size: 408097
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-- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.34.2-pyhcf101f3_0.conda
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 depends:
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-- certifi >=2017.4.17
+- certifi >=2023.5.7
 - charset-normalizer >=2,<4
 - idna >=2.5,<4
-- urllib3 >=1.21.1,<3
+- urllib3 >=1.26,<3
 - python
 constrains:
-- chardet >=3.0.2,<6
+- chardet >=3.0.2,<8
 license: Apache-2.0
 license_family: APACHE
-size: 63602
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-- conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda
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+md5: 0242025a3c804966bf71aa04eee82f66
 depends:
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 - pygments >=2.13.0,<3.0.0
@@ -1292,8 +1266,8 @@ depends:
 - python
 license: MIT
 license_family: MIT
-size: 208472
-timestamp: 1771572730357
+size: 208577
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 - conda: https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda
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 md5: 0c20a8ebcddb24a45da89d5e917e6cb9
@@ -1331,19 +1305,18 @@ license: MIT
 license_family: MIT
 size: 22284
 timestamp: 1735770589188
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.52.0-hf1c7be2_0.conda
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-md5: d9634079df93a65ee045b3c75f35cae1
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.1-he8854b5_0.conda
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 depends:
-- icu >=78.2,<79.0a0
 - libgcc >=14
-- libsqlite 3.52.0 h10b116e_0
-- libzlib >=1.3.1,<2.0a0
-- ncurses >=6.5,<7.0a0
+- libsqlite 3.53.1 h022381a_0
+- libzlib >=1.3.2,<2.0a0
+- ncurses >=6.6,<7.0a0
 - readline >=8.3,<9.0a0
 license: blessing
-size: 209416
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 md5: 55bf7b559202236157b14323b40f19e6
@@ -1382,20 +1355,20 @@ depends:
 license: MPL-2.0 and MIT
 size: 94132
 timestamp: 1770153424136
-- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda
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-md5: 260af1b0a94f719de76b4e14094e9a3b
+- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.2-pyhcf101f3_0.conda
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-- importlib-metadata >=3.6
-- python >=3.10
-- typing-extensions >=4.10.0
 - typing_extensions >=4.14.0
+- python >=3.10
+- importlib-metadata >=3.6
+- python
 constrains:
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 license: MIT
 license_family: MIT
-size: 36838
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 - conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda
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 md5: edd329d7d3a4ab45dcf905899a7a6115
@@ -1405,16 +1378,17 @@ license: PSF-2.0
 license_family: PSF
 size: 91383
 timestamp: 1756220668932
-- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda
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-md5: a0a4a3035667fc34f29bfbd5c190baa6
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda
+sha256: 8b90d2f19f9458b8c58a55e1fcdc1d90c1603a847a47654d8a454549413ba60a
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 license_family: MIT
-size: 18923
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 - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda
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 md5: 0caa1af407ecff61170c9437a808404d
@@ -1431,9 +1405,9 @@ md5: ad659d0a2b3e47e38d829aa8cad2d610
 license: LicenseRef-Public-Domain
 size: 119135
 timestamp: 1767016325805
-- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda
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-md5: 9272daa869e03efe68833e3dc7a02130
+- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda
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@@ -1442,8 +1416,8 @@ depends:
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 license: MIT
 license_family: MIT
-size: 103172
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+size: 103560
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 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda
 sha256: e9f6e931feeb2f40e1fdbafe41d3b665f1ab6cb39c5880a1fcf9f79a3f3c84a5
 md5: 1c246e1105000c3660558459e2fd6d43
@@ -1471,16 +1445,16 @@ license: MIT
 license_family: MIT
 size: 88088
 timestamp: 1753484092643
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
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-md5: 30cd29cb87d819caead4d55184c1d115
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
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 license: MIT
 license_family: MIT
-size: 24194
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 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda
 sha256: 638a3a41a4fbfed52d3c60c8ef5a3693b3f12a5b1a3f58fa29f5698d0a0702e2
 md5: f731af71c723065d91b4c01bb822641b
diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
deleted file mode 100644
index f787dbe..0000000
--- a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
+++ /dev/null
@@ -1,125 +0,0 @@
-
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: linux-aarch64
-@EXPLICIT
-https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda#4faa39bf919939602e594253bd673958
-https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda#468fd3bb9e1f671d36c2cbc677e56f1d
-https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda#552567ea2b61e3a3035759b2fdb3f9a6
-https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda#840d8fc0d7b3209be93080bc20e07f2d
-https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda#502006882cf5461adced436e410046d1
-https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda#c3655f82dcea2aa179b291e7099c1fcc
-https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_102.conda#a21644fc4a83da26452a718dc9468d5f
-https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.7.5-hfae3067_0.conda#05d1e0b30acd816a192c03dc6e164f4d
-https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.5.2-h376a255_0.conda#2f364feefb6a7c00423e80dcb12db62a
-https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.3-he30d5cf_0.conda#76298a9e6d71ee6e832a8d0d7373b261
-https://conda.anaconda.org/conda-forge/linux-aarch64/libmpdec-4.0.0-he30d5cf_1.conda#7b9813e885482e3ccb1fa212b86d7fd0
-https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.53.0-h022381a_0.conda#86db4036fd08bf34e991bf48a8af405d
-https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.42-h1022ec0_0.conda#a0b5de740d01c390bdbb46d7503c9fab
-https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.5-ha32ae93_3.conda#182afabe009dc78d8b73100255ee6868
-https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73
-https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.2-h546c87b_0.conda#3b129669089e4d6a5c6871dbb4669b99
-https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda#0539938c55b6b1a59b560e843ad864a4
-https://conda.anaconda.org/conda-forge/linux-aarch64/readline-8.3-hb682ff5_0.conda#3d49cad61f829f4f0e0611547a9cda12
-https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.13-noxft_h0dc03b3_103.conda#7fc6affb9b01e567d2ef1d05b84aa6ed
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610
-https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.4-hfd9ac0a_100_cp314.conda#3cfbe780f0f51cc8cba41db9f8a28bfe
-https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda#f111d4cfaf1fe9496f386bc98ae94452
-https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda#e4e60721757979d01d3964122f674959
-https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda#aaa2a381ccc56eac91d63b6c1240312f
-https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda#0caa1af407ecff61170c9437a808404d
-https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda#edd329d7d3a4ab45dcf905899a7a6115
-https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda#2934f256a8acfe48f6ebb4fce6cde29c
-https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda#c6b0543676ecb1fb2d7643941fe375f2
-https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda#a2ac7763a9ac75055b68f325d3255265
-https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-15.2.0-hef695bb_18.conda#f56573d05e3b735cb03efeb64a15f388
-https://conda.anaconda.org/conda-forge/linux-aarch64/brotli-python-1.2.0-py314h352cb57_1.conda#a1b5c571a0923a205d663d8678df4792
-https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda#929471569c93acefb30282a22060dcd5
-https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda#a9167b9571f3baa9d448faa2139d1089
-https://conda.anaconda.org/conda-forge/noarch/click-8.3.2-pyhc90fa1f_0.conda#4d18bc3af7cfcea97bd817164672a08c
-https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda#7fe569c10905402ed47024fc481bb371
-https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda#b866ff7007b934d564961066c8195983
-https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda#a2c1eeadae7a309daed9d62c96012a2b
-https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran5-15.2.0-h1b7bec0_18.conda#574d88ce3348331e962cfa5ed451b247
-https://conda.anaconda.org/conda-forge/linux-aarch64/libgfortran-15.2.0-he9431aa_18.conda#41f261f5e4e2e8cbd236c2f1f15dae1b
-https://conda.anaconda.org/conda-forge/linux-aarch64/libopenblas-0.3.32-pthreads_h9d3fd7e_0.conda#5d2ce5cf40443d055ec6d33840192265
-https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-6_haddc8a3_openblas.conda#652bb20bb4618cacd11e17ae070f47ce
-https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-6_hd72aa62_openblas.conda#939e300b110db241a96a1bed438c315b
-https://conda.anaconda.org/conda-forge/linux-aarch64/liblapack-3.11.0-6_h88aeb00_openblas.conda#e23a27b52fb320687239e2c5ae4d7540
-https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.4.3-py314haac167e_0.conda#25d896c331481145720a21e5145fad65
-https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda#071cf7b0ce333c81718b054066c15102
-https://conda.anaconda.org/conda-forge/linux-aarch64/expat-2.7.5-hfae3067_0.conda#d2bb0c889d94f2fdc5856392c3002976
-https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
-https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
-https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
-https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7
-https://conda.anaconda.org/conda-forge/linux-aarch64/libpng-1.6.58-h1abf092_0.conda#f51503ac45a4888bce71af9027a2ecc9
-https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype6-2.14.3-hdae7a39_0.conda#b99ed99e42dafb27889483b3098cace7
-https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype-2.14.3-h8af1aa0_0.conda#a229e22d4d8814a07702b0919d8e6701
-https://conda.anaconda.org/conda-forge/linux-aarch64/fontconfig-2.17.1-hba86a56_0.conda#0fed1ff55f4938a65907f3ecf62609db
-https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda#a7970cd949a077b7cb9696379d338681
-https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda#0a802cb9888dd14eeefc611f05c40b6e
-https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda#8e6923fc12f1fe8f8c4e5c9f343256ac
-https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda#164fc43f0b53b6e3a7bc7dce5e4f1dc9
-https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda#daddf757c3ecd6067b9af1df1f25d89e
-https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda#fb7130c190f9b4ec91219840a05ba3ac
-https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.1-pyhcf101f3_0.conda#e1c36c6121a7c9c76f2f148f1e83b983
-https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda#080594bf4493e6bae2607e65390c520a
-https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-3.0.3-py314hb76de3f_1.conda#e5de3c36dd548b35ff2a8aa49208dcb3
-https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda#04558c96691bed63104678757beb4f8d
-https://conda.anaconda.org/conda-forge/linux-aarch64/rpds-py-0.30.0-py314h02b7a91_0.conda#e7f6ed9e60043bb5cbcc527764897f0d
-https://conda.anaconda.org/conda-forge/noarch/referencing-0.37.0-pyhcf101f3_0.conda#870293df500ca7e18bedefa5838a22ab
-https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda#439cd0f567d697b20a8f45cb70a1005a
-https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda#ada41c863af263cc4c5fcbaff7c3e4dc
-https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_18.conda#4feebd0fbf61075a1a9c2e9b3936c257
-https://conda.anaconda.org/conda-forge/linux-aarch64/mathjax-2.7.7-h8af1aa0_3.tar.bz2#7b08314a6867a9d5648a1c3265e9eb8e
-https://conda.anaconda.org/conda-forge/linux-aarch64/nspr-4.38-h3ad9384_0.conda#6dd4f07147774bf720075a210f8026b9
-https://conda.anaconda.org/conda-forge/linux-aarch64/nss-3.118-h544fa81_0.conda#4540f9570d12db2150f42ba036154552
-https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.0-he8854b5_0.conda#ad8164bdeece883b825c50639c0c4725
-https://conda.anaconda.org/conda-forge/linux-aarch64/kaleido-core-0.2.1-he5a581e_0.tar.bz2#4f0d284f5d11e04277b552eb1c172c7f
-https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.4.1-he30d5cf_0.conda#a85ba48648f6868016f2741fd9170250
-https://conda.anaconda.org/conda-forge/linux-aarch64/lerc-4.1.0-h52b7260_0.conda#d13423b06447113a90b5b1366d4da171
-https://conda.anaconda.org/conda-forge/linux-aarch64/libdeflate-1.25-h1af38f5_0.conda#a9138815598fe6b91a1d6782ca657b0c
-https://conda.anaconda.org/conda-forge/linux-aarch64/libwebp-base-1.6.0-ha2e29f5_0.conda#24e92d0942c799db387f5c9d7b81f1af
-https://conda.anaconda.org/conda-forge/linux-aarch64/libtiff-4.7.1-hdb009f0_1.conda#8c6fd84f9c87ac00636007c6131e457d
-https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda#bb960f01525b5e001608afef9d47b79c
-https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda#bb5a90c93e3bac3d5690acf76b4a6386
-https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda#1c246e1105000c3660558459e2fd6d43
-https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda#bff06dcde4a707339d66d45d96ceb2e2
-https://conda.anaconda.org/conda-forge/linux-aarch64/libxcb-1.17.0-h262b8f6_0.conda#cd14ee5cca2464a425b1dbfc24d90db2
-https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda#ba0a9221ce1063f31692c07370d062f3
-https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda#592132998493b3ff25fd7479396e8351
-https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda#5b5203189eb668f042ac2b0826244964
-https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda#e941e85e273121222580723010bd4fa2
-https://conda.anaconda.org/conda-forge/noarch/packaging-26.1-pyhc364b38_0.conda#b8ae38639d323d808da535fb71e31be8
-https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda#cea962410e327262346d48d01f05936c
-https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda#f731af71c723065d91b4c01bb822641b
-https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda#87d58d103b47c4a8567b3d7666647684
-https://conda.anaconda.org/conda-forge/noarch/narwhals-2.20.0-pyhcf101f3_0.conda#6cac1a50359219d786453c6fef819f98
-https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda#3e9427ee186846052e81fadde8ebe96a
-https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.0-py310hff09b76_0.conda#d5628a33ce7652511e38fc98643dc910
-https://conda.anaconda.org/conda-forge/noarch/polars-1.40.0-pyh58ad624_0.conda#fd16be490f5403adfbf27dd4901bbe34
-https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.40.0-py310hf00a4a2_0.conda#a82af0fcbb72db253dc89a7a45279372
-https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda#ef0340e75068ac8ff96462749b5c98e7
-https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda#032d8030e4a24fe1f72c74423a46fb88
-https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda#9ae2c92975118058bd720e9ba2bb7c58
-https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda#e17be1016bcc3516827b836cd3e4d9dc
-https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.3-py314h451b6cc_0.conda#1a2cb55be9a153ad6203bff6b787c240
-https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6
-https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98
-https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c
-https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2
-https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac
-https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130
-https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59
-https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0
-https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66
-https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9
-https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a
-https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864
-https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6
-https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206
-https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b
-https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873
-https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f
-https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 37e7612..7a970e2 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.34
+  - bioconda::multiqc=1.35
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index e80e8cd..c4bc715 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -4,8 +4,8 @@ process MULTIQC {
 
     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/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data'
-        : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data'
+        : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}"
 
     input:
     tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 2facc62..27ce18d 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -110,24 +110,24 @@ maintainers:
 containers:
   conda:
     linux/amd64:
-      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
     linux/arm64:
-      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt
   docker:
     linux/amd64:
-      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
-      build_id: bd-db7c73dae76bc9e6_1
-      scan_id: sc-66fc7138dbf1cf48_1
+      name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc
+      build_id: bd-c17fb751507e9dfc_1
+      scan_id: sc-3b1b3932f9846892_1
     linux/arm64:
-      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
-      build_id: bd-d167b8012595a136_1
-      scan_id: sc-ac701dfa631a2af9_1
+      name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5
+      build_id: bd-5c84a5000a226ab5_1
+      scan_id: sc-0d39df41e9737bbd_1
   singularity:
     linux/amd64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
-      build_id: bd-4fc8657c816047c0_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2
+      build_id: bd-c680f2aea25ccec2_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data
     linux/arm64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
-      build_id: bd-7fbd82d945c06726_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81
+      build_id: bd-c0468833d65b2f81_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7c2f370..4489921 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -81,7 +81,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -175,7 +175,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -221,7 +221,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -314,7 +314,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -408,7 +408,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml
index 856e6f7..a172cc5 100644
--- a/modules/nf-core/seqfu/stats/meta.yml
+++ b/modules/nf-core/seqfu/stats/meta.yml
@@ -12,6 +12,11 @@ tools:
       documentation: "https://telatin.github.io/seqfu2/"
       tool_dev_url: "https://github.com/telatin/seqfu2"
       doi: "10.3390/bioengineering8050059"
+      publication:
+        author: "Telatin A., Fariselli P. & Birolo G."
+        year: 2021
+        title: "SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files"
+        source: "Bioengineering"
       licence:
         - "GPL v3"
       identifier: biotools:seqfu
diff --git a/modules/nf-core/seqkit/replace/environment.yml b/modules/nf-core/seqkit/replace/environment.yml
index b26fb1e..09abb79 100644
--- a/modules/nf-core/seqkit/replace/environment.yml
+++ b/modules/nf-core/seqkit/replace/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.9.0
+  - bioconda::seqkit=2.13.0
diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf
index 6abbd14..18a1b99 100644
--- a/modules/nf-core/seqkit/replace/main.nf
+++ b/modules/nf-core/seqkit/replace/main.nf
@@ -4,11 +4,12 @@ process SEQKIT_REPLACE {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
-        : 'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fe272ab9a519cf418160471a485b5ef50ea3f571a8e4555a826f70a4d8243ae/data'
+        : 'community.wave.seqera.io/library/seqkit:2.13.0--05c0a96bf9fb2751'}"
 
     input:
     tuple val(meta), path(fastx)
+    val out_ext
 
     output:
     tuple val(meta), path("*.fast*"), emit: fastx
@@ -28,7 +29,7 @@ process SEQKIT_REPLACE {
     if ("${fastx}" ==~ /.+\.gz/) {
         isgz = ".gz"
     }
-    def endswith = task.ext.suffix ?: "${extension}${isgz}"
+    def endswith = out_ext ?: "${extension}${isgz}"
     """
     seqkit \\
         replace \\
@@ -39,14 +40,22 @@ process SEQKIT_REPLACE {
     """
 
     stub:
+    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def extension = "fastq"
-    if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) {
+    if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.faa|.+\.faa.gz/) {
         extension = "fasta"
     }
-    def endswith = task.ext.suffix ?: "${extension}.gz"
+    def isgz = ""
+    if ("${fastx}" ==~ /.+\.gz/) {
+        isgz = ".gz"
+    }
+    def endswith = out_ext ?: "${extension}${isgz}"
 
+    def create_cmd = endswith.endsWith('gz') ? "echo '' | gzip >" : "touch"
     """
-    echo "" | gzip > ${prefix}.${endswith}
+    echo ${args}
+
+    ${create_cmd} ${prefix}.${endswith}
     """
 }
diff --git a/modules/nf-core/seqkit/replace/meta.yml b/modules/nf-core/seqkit/replace/meta.yml
index ed1e818..e8ef679 100644
--- a/modules/nf-core/seqkit/replace/meta.yml
+++ b/modules/nf-core/seqkit/replace/meta.yml
@@ -27,6 +27,11 @@ input:
         pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*"
         ontologies:
           - edam: http://edamontology.org/format_1930 # FASTQ
+  - out_ext:
+      type: string
+      description: >
+        Output file extension. Leave empty to auto-detect from input (for example
+        `.fasta`, `.fasta.gz`)
 output:
   fastx:
     - - meta:
diff --git a/modules/nf-core/seqkit/replace/tests/main.nf.test b/modules/nf-core/seqkit/replace/tests/main.nf.test
index 15fb7d3..679312e 100644
--- a/modules/nf-core/seqkit/replace/tests/main.nf.test
+++ b/modules/nf-core/seqkit/replace/tests/main.nf.test
@@ -9,97 +9,103 @@ nextflow_process {
     tag "seqkit"
     tag "seqkit/replace"
 
-    test("sarscov2 - fasta - replace") {
-
-        config "./replace.config"
+    config "./nextflow.config"
 
+    test("sarscov2 - fasta - replace") {
         when {
+            params {
+                modules_args = "-s -p 'A' -r 'N'"
+            }
             process {
                 """
-                    input[0] = [ [ id:'test' ],   // meta map
-                                 [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) ]
-                    ]
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true)
+                ]
+                input[1] = ''
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
-
     test("sarscov2 - fasta - replace - uncompressed") {
-
-        config "./replace.config"
-
         when {
+            params {
+                modules_args = "-s -p 'A' -r 'N'"
+            }
             process {
                 """
-                    input[0] = [ [ id:'test' ],   // meta map
-                                 [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-                    ]
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[1] = ''
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
     test("sarscov2 - fasta - uncomp - custom") {
-
-        config "./uncomp.config"
-
         when {
+            params {
+                modules_args = "-s -p 'T' -r 'N'"
+            }
             process {
                 """
-                    input[0] = [ [ id:'test' ],   // meta map
-                                 [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-                    ]
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[1] = 'fasta'
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
     test("sarscov2 - fasta - stub") {
-
-        options "-stub"
+        options '-stub'
 
         when {
+            params {
+                modules_args = ""
+            }
             process {
                 """
-                    input[0] = [ [ id:'test' ],   // meta map
-                                 [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-                    ]
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[1] = ''
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
index fdae3eb..02bace1 100644
--- a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
@@ -2,62 +2,32 @@
     "sarscov2 - fasta - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_REPLACE",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions_seqkit": [
                     [
                         "SEQKIT_REPLACE",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-06-13T12:47:21.226842064",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T14:51:31.369966565"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
     },
     "sarscov2 - fasta - replace - uncompressed": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta:md5,b1518908253a4997fcad98270751112e"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_REPLACE",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -70,76 +40,46 @@
                     [
                         "SEQKIT_REPLACE",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-06-12T17:26:01.449665395",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T14:51:20.851601162"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
     },
     "sarscov2 - fasta - uncomp - custom": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test..fasta:md5,05d3294a62c72f5489f067c1da3c2f6c"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_REPLACE",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
                             "id": "test"
                         },
-                        "test..fasta:md5,05d3294a62c72f5489f067c1da3c2f6c"
+                        "test.fasta:md5,05d3294a62c72f5489f067c1da3c2f6c"
                     ]
                 ],
                 "versions_seqkit": [
                     [
                         "SEQKIT_REPLACE",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-06-13T12:54:19.323281146",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T14:51:26.121667583"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
     },
     "sarscov2 - fasta - replace": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta.gz:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_REPLACE",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -152,15 +92,15 @@
                     [
                         "SEQKIT_REPLACE",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-06-12T17:25:54.471016576",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T14:51:15.520168225"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/replace/tests/nextflow.config b/modules/nf-core/seqkit/replace/tests/nextflow.config
new file mode 100644
index 0000000..09856f3
--- /dev/null
+++ b/modules/nf-core/seqkit/replace/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: SEQKIT_REPLACE {
+        ext.args = params.modules_args ?: ''
+    }
+}
diff --git a/modules/nf-core/seqkit/replace/tests/replace.config b/modules/nf-core/seqkit/replace/tests/replace.config
deleted file mode 100644
index 8766447..0000000
--- a/modules/nf-core/seqkit/replace/tests/replace.config
+++ /dev/null
@@ -1,5 +0,0 @@
- process {
-    withName: 'SEQKIT_REPLACE' {
-        ext.args   = "-s -p 'A' -r 'N'"
-    }
- }
diff --git a/modules/nf-core/seqkit/replace/tests/uncomp.config b/modules/nf-core/seqkit/replace/tests/uncomp.config
deleted file mode 100644
index dbd892b..0000000
--- a/modules/nf-core/seqkit/replace/tests/uncomp.config
+++ /dev/null
@@ -1,6 +0,0 @@
- process {
-    withName: 'SEQKIT_REPLACE' {
-        ext.args          = "-s -p 'T' -r 'N'"
-        ext.suffix        = ".fasta"
-    }
- }
diff --git a/modules/nf-core/seqkit/rmdup/environment.yml b/modules/nf-core/seqkit/rmdup/environment.yml
index b26fb1e..09abb79 100644
--- a/modules/nf-core/seqkit/rmdup/environment.yml
+++ b/modules/nf-core/seqkit/rmdup/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.9.0
+  - bioconda::seqkit=2.13.0
diff --git a/modules/nf-core/seqkit/rmdup/main.nf b/modules/nf-core/seqkit/rmdup/main.nf
index 22f3b1a..7f86538 100644
--- a/modules/nf-core/seqkit/rmdup/main.nf
+++ b/modules/nf-core/seqkit/rmdup/main.nf
@@ -1,54 +1,62 @@
 process SEQKIT_RMDUP {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
     // File IO can be a bottleneck. See: https://bioinf.shenwei.me/seqkit/usage/#parallelization-of-cpu-intensive-jobs
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
-        'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fe272ab9a519cf418160471a485b5ef50ea3f571a8e4555a826f70a4d8243ae/data'
+        : 'community.wave.seqera.io/library/seqkit:2.13.0--05c0a96bf9fb2751'}"
 
     input:
     tuple val(meta), path(fastx)
 
     output:
-    tuple val(meta), path("${prefix}.${extension}") , emit: fastx
-    tuple val(meta), path("*.log")                  , emit: log
+    tuple val(meta), path("${prefix}.${extension}"), emit: fastx
+    tuple val(meta), path("*.log"), emit: log
     tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/^.*v//'"), emit: versions_seqkit, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args        = task.ext.args ?: ''
-    prefix          = task.ext.prefix ?: "${meta.id}"
-    extension       = "fastq"
-    if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
-        extension   = "fasta"
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    extension = "fastq"
+    if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
+        extension = "fasta"
     }
-    extension       = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
+    extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
     // SeqKit/rmdup takes care of compressing the output: https://bioinf.shenwei.me/seqkit/usage/#rmdup
-    if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("${prefix}.${extension}" == "${fastx}") {
+        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+    }
     """
     seqkit \\
         rmdup \\
-        --threads $task.cpus \\
-        $args \\
-        $fastx \\
+        --threads ${task.cpus} \\
+        ${args} \\
+        ${fastx} \\
         -o ${prefix}.${extension} \\
         2>| >(tee ${prefix}.log >&2)
     """
 
     stub:
-    prefix          = task.ext.prefix ?: "${meta.id}"
-    extension       = "fastq"
-    if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
-        extension   = "fasta"
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    extension = "fastq"
+    if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
+        extension = "fasta"
     }
     extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
-    if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("${prefix}.${extension}" == "${fastx}") {
+        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+    }
+    def create_cmd = extension.endsWith('gz') ? "echo '' | gzip >" : "touch"
     """
-    touch ${prefix}.${extension}
+    echo ${args}
+
+    ${create_cmd} ${prefix}.${extension}
     echo \\
         '[INFO] 0 duplicated records removed' \\
         > ${prefix}.log
diff --git a/modules/nf-core/seqkit/rmdup/tests/main.nf.test b/modules/nf-core/seqkit/rmdup/tests/main.nf.test
index beac3a4..411a2dd 100644
--- a/modules/nf-core/seqkit/rmdup/tests/main.nf.test
+++ b/modules/nf-core/seqkit/rmdup/tests/main.nf.test
@@ -22,13 +22,12 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
                 { assert path(process.out.log[0][1]).text.contains('0 duplicated records removed') }
             )
         }
-
     }
 
     test("repeated-fasta") {
@@ -47,13 +46,12 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
                 { assert path(process.out.log[0][1]).text.contains('1 duplicated records removed') }
             )
         }
-
     }
 
     test("sarscov2-genome_fasta_gz") {
@@ -69,13 +67,12 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
                 { assert path(process.out.log[0][1]).text.contains('0 duplicated records removed') }
             )
         }
-
     }
 
     test("sarscov2-test_1_fastq_gz") {
@@ -91,13 +88,12 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
                 { assert path(process.out.log[0][1]).text.contains('0 duplicated records removed') }
             )
         }
-
     }
 
     test("file_name_conflict-fail_with_error") {
@@ -113,16 +109,14 @@ nextflow_process {
         }
 
         then {
+            assert process.failed
             assertAll(
-                { assert !process.success },
                 { assert process.stdout.toString().contains("Input and output names are the same") }
             )
         }
-
     }
 
     test("sarscov2-genome_fasta-stub") {
-
         options '-stub'
 
         when {
@@ -137,13 +131,12 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
                 { assert path(process.out.log[0][1]).text.contains('0 duplicated records removed') }
             )
         }
-
     }
 
     test("file_name_conflict-fail_with_error-stub") {
@@ -161,12 +154,10 @@ nextflow_process {
         }
 
         then {
+            assert process.failed
             assertAll(
-                { assert !process.success },
                 { assert process.stdout.toString().contains("Input and output names are the same") }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap b/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap
index 764cd09..0bd79b3 100644
--- a/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap
@@ -2,29 +2,6 @@
     "sarscov2-genome_fasta-stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,cf833211befdf890bb6b2a3cd0b91853"
-                    ]
-                ],
-                "2": [
-                    [
-                        "SEQKIT_RMDUP",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -45,43 +22,20 @@
                     [
                         "SEQKIT_RMDUP",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-12T13:08:29.041177508",
+        "timestamp": "2026-06-12T17:26:48.435786445",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "sarscov2-test_1_fastq_gz": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
-                    ]
-                ],
-                "2": [
-                    [
-                        "SEQKIT_RMDUP",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -102,43 +56,20 @@
                     [
                         "SEQKIT_RMDUP",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-12T13:08:15.046237092",
+        "timestamp": "2026-06-12T17:26:39.040489053",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "sarscov2-genome_fasta": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta:md5,483f4a5dfe60171c86ee9b7e6dff908b"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
-                    ]
-                ],
-                "2": [
-                    [
-                        "SEQKIT_RMDUP",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -159,43 +90,20 @@
                     [
                         "SEQKIT_RMDUP",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-12T13:07:53.771340434",
+        "timestamp": "2026-06-12T17:26:21.035761383",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "repeated-fasta": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta:md5,7510a742291241e7d7556bf720caf65c"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,314c0aaef0f832a217a3f6ce3f8bc117"
-                    ]
-                ],
-                "2": [
-                    [
-                        "SEQKIT_RMDUP",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -216,43 +124,20 @@
                     [
                         "SEQKIT_RMDUP",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-12T13:08:00.578741348",
+        "timestamp": "2026-06-12T17:26:26.868734329",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "sarscov2-genome_fasta_gz": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
-                    ]
-                ],
-                "2": [
-                    [
-                        "SEQKIT_RMDUP",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -273,15 +158,15 @@
                     [
                         "SEQKIT_RMDUP",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-12T13:08:07.836784907",
+        "timestamp": "2026-06-12T17:26:33.522032009",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/seq/environment.yml b/modules/nf-core/seqkit/seq/environment.yml
index b26fb1e..09abb79 100644
--- a/modules/nf-core/seqkit/seq/environment.yml
+++ b/modules/nf-core/seqkit/seq/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.9.0
+  - bioconda::seqkit=2.13.0
diff --git a/modules/nf-core/seqkit/seq/main.nf b/modules/nf-core/seqkit/seq/main.nf
index d78040a..3bade4e 100644
--- a/modules/nf-core/seqkit/seq/main.nf
+++ b/modules/nf-core/seqkit/seq/main.nf
@@ -5,8 +5,8 @@ process SEQKIT_SEQ {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
-        : 'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fe272ab9a519cf418160471a485b5ef50ea3f571a8e4555a826f70a4d8243ae/data'
+        : 'community.wave.seqera.io/library/seqkit:2.13.0--05c0a96bf9fb2751'}"
 
     input:
     tuple val(meta), path(fastx)
@@ -42,6 +42,8 @@ process SEQKIT_SEQ {
     """
 
     stub:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     def extension = "fastq"
     if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
@@ -51,7 +53,11 @@ process SEQKIT_SEQ {
     if ("${prefix}.${extension}" == "${fastx}") {
         error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
     }
+    def create_cmd = extension.endsWith('gz') ? "echo '' | gzip >" : "touch"
     """
-    touch ${prefix}.${extension}
+    echo ${args}
+    echo ${args2}
+
+    ${create_cmd} ${prefix}.${extension}
     """
 }
diff --git a/modules/nf-core/seqkit/seq/tests/main.nf.test b/modules/nf-core/seqkit/seq/tests/main.nf.test
index 9fd1c08..457be88 100644
--- a/modules/nf-core/seqkit/seq/tests/main.nf.test
+++ b/modules/nf-core/seqkit/seq/tests/main.nf.test
@@ -12,6 +12,9 @@ nextflow_process {
 
     test("sarscov2-genome_fasta") {
         when {
+            params {
+                modules_args2 = '-n'
+            }
             process {
                 """
                 input[0] = [
@@ -23,16 +26,18 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
     test("sarscov2-genome_fasta_gz") {
         when {
+            params {
+                modules_args2 = '-n'
+            }
             process {
                 """
                 input[0] = [
@@ -44,16 +49,18 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
     test("sarscov2-test_1_fastq_gz") {
         when {
+            params {
+                modules_args2 = '-n'
+            }
             process {
                 """
                 input[0] = [
@@ -65,16 +72,18 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
     test("file_name_conflict-fail_with_error") {
         when {
+            params {
+                modules_args2 = '-n'
+            }
             process {
                 """
                 input[0] = [
@@ -86,19 +95,20 @@ nextflow_process {
         }
 
         then {
+            assert process.failed
             assertAll(
-                { assert !process.success },
                 { assert process.stdout.toString().contains("Input and output names are the same") }
             )
         }
-
     }
 
     test("sarscov2-genome_fasta-stub") {
-
         options '-stub'
 
         when {
+            params {
+                modules_args2 = '-n'
+            }
             process {
                 """
                 input[0] = [
@@ -110,19 +120,20 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
     test("file_name_conflict-fail_with_error-stub") {
-
         options '-stub'
 
         when {
+            params {
+                modules_args2 = '-n'
+            }
             process {
                 """
                 input[0] = [
@@ -134,12 +145,10 @@ nextflow_process {
         }
 
         then {
+            assert process.failed
             assertAll(
-                { assert !process.success },
                 { assert process.stdout.toString().contains("Input and output names are the same") }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/seqkit/seq/tests/main.nf.test.snap b/modules/nf-core/seqkit/seq/tests/main.nf.test.snap
index bbcc995..d8e79f6 100644
--- a/modules/nf-core/seqkit/seq/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/seq/tests/main.nf.test.snap
@@ -2,21 +2,6 @@
     "sarscov2-genome_fasta-stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_SEQ",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -29,35 +14,20 @@
                     [
                         "SEQKIT_SEQ",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-12T13:09:25.839048434",
+        "timestamp": "2026-06-14T18:54:38.462339108",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "sarscov2-test_1_fastq_gz": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_SEQ",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -70,35 +40,20 @@
                     [
                         "SEQKIT_SEQ",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-12T13:09:12.72324007",
+        "timestamp": "2026-06-12T17:27:53.391265296",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "sarscov2-genome_fasta": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta:md5,483f4a5dfe60171c86ee9b7e6dff908b"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_SEQ",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -111,35 +66,20 @@
                     [
                         "SEQKIT_SEQ",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-12T13:08:58.152442646",
+        "timestamp": "2026-06-12T17:27:43.147566645",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "sarscov2-genome_fasta_gz": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fasta.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_SEQ",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
                 "fastx": [
                     [
                         {
@@ -152,15 +92,15 @@
                     [
                         "SEQKIT_SEQ",
                         "seqkit",
-                        "2.9.0"
+                        "2.13.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-12T13:09:05.344232955",
+        "timestamp": "2026-06-12T17:27:48.241605452",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/seq/tests/nextflow.config b/modules/nf-core/seqkit/seq/tests/nextflow.config
index d8e3c66..cd1f022 100644
--- a/modules/nf-core/seqkit/seq/tests/nextflow.config
+++ b/modules/nf-core/seqkit/seq/tests/nextflow.config
@@ -1,3 +1,5 @@
 process {
-    ext.args2 = '-n'
+    withName: SEQKIT_SEQ {
+        ext.args2 = params.modules_args2 ?: ''
+    }
 }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index bc6d5de..89380a6 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2026-07-24T12:36:11+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-proteinannotator_logo_dark.png\">\n    <img alt=\"nf-core/proteinannotator\" src=\"docs/images/nf-core-proteinannotator_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n<p>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/proteinannotator_metromap_dark.png\">\n    <img alt=\"nf-core/proteinannotator\" src=\"docs/images/proteinannotator_metromap_light.png\">\n  </picture>\n</p>\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n   such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/), [FunFam](https://download.cathdb.info/cath/releases/all-releases/), and [NMPFams and metagRoot](https://pavlopoulos-lab.org/envofams/databases/hmmer/)\n2. Functional annotation:\n   - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n   - ([`KOfamScan`](https://github.com/takaram/kofam_scan)) assigns KEGG Orthologs to protein sequences using profile HMMs and KO-specific score thresholds.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a FASTA file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/proteinannotator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\n- [Martin Beracochea](https://github.com/mberacochea)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-proteinannotator_logo_dark.png\">\n    <img alt=\"nf-core/proteinannotator\" src=\"docs/images/nf-core-proteinannotator_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n<p>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/proteinannotator_metromap_dark.png\">\n    <img alt=\"nf-core/proteinannotator\" src=\"docs/images/proteinannotator_metromap_light.png\">\n  </picture>\n</p>\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n   such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/), [FunFam](https://download.cathdb.info/cath/releases/all-releases/), and [NMPFams and metagRoot](https://pavlopoulos-lab.org/envofams/databases/hmmer/)\n2. Functional annotation:\n   - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n   - ([`KOfamScan`](https://github.com/takaram/kofam_scan)) assigns KEGG Orthologs to protein sequences using profile HMMs and KO-specific score thresholds.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a FASTA file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/proteinannotator/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\n- [Martin Beracochea](https://github.com/mberacochea)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#298e589a-490b-4612-aa89-ca4366da3a32"
+                    "@id": "#b1c0b828-9db5-4bbd-94a0-ffe1d7e49a89"
                 }
             ],
             "name": "nf-core/proteinannotator"
@@ -137,7 +137,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-07-24T12:36:11Z",
+            "dateModified": "2026-09-01T12:58:59Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -183,11 +183,11 @@
             "version": "!>=25.10.4"
         },
         {
-            "@id": "#298e589a-490b-4612-aa89-ca4366da3a32",
+            "@id": "#b1c0b828-9db5-4bbd-94a0-ffe1d7e49a89",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#ba41f42b-de31-45cc-b1f8-751ccec12108"
+                    "@id": "#6cd80838-6920-4883-a7a4-3e2bafb938f0"
                 }
             ],
             "mainEntity": {
@@ -196,7 +196,7 @@
             "name": "Test suite for nf-core/proteinannotator"
         },
         {
-            "@id": "#ba41f42b-de31-45cc-b1f8-751ccec12108",
+            "@id": "#6cd80838-6920-4883-a7a4-3e2bafb938f0",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/proteinannotator",
             "resource": "repos/nf-core/proteinannotator/actions/workflows/nf-test.yml",
diff --git a/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf b/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf
index b449a2d..76ae9c9 100644
--- a/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf
@@ -88,7 +88,7 @@ workflow PIPELINE_INITIALISATION {
         before_text,
         after_text,
         command,
-        null
+        false
     )
 
     //
diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/main.nf b/subworkflows/nf-core/faa_seqfu_seqkit/main.nf
index bd5b177..9a7ea77 100644
--- a/subworkflows/nf-core/faa_seqfu_seqkit/main.nf
+++ b/subworkflows/nf-core/faa_seqfu_seqkit/main.nf
@@ -18,7 +18,7 @@ workflow FAA_SEQFU_SEQKIT {
     if (!skip_preprocessing) {
         SEQKIT_SEQ(ch_fasta)
 
-        SEQKIT_REPLACE(SEQKIT_SEQ.out.fastx)
+        SEQKIT_REPLACE(SEQKIT_SEQ.out.fastx, 'fasta')
 
         SEQKIT_RMDUP(SEQKIT_REPLACE.out.fastx)
         ch_fasta = SEQKIT_RMDUP.out.fastx
diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap
index c09fb56..e39656c 100644
--- a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap
@@ -26,10 +26,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-12T14:44:03.010426069",
+        "timestamp": "2026-06-13T14:16:45.234475759",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "faa": {
@@ -59,10 +59,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-12T14:43:53.509896933",
+        "timestamp": "2026-06-13T14:16:37.15518591",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/tests/nextflow.config b/subworkflows/nf-core/faa_seqfu_seqkit/tests/nextflow.config
index 38af0eb..b0e7247 100644
--- a/subworkflows/nf-core/faa_seqfu_seqkit/tests/nextflow.config
+++ b/subworkflows/nf-core/faa_seqfu_seqkit/tests/nextflow.config
@@ -1,5 +1,4 @@
 process {
-
     withName: SEQFU_STATS_BEFORE {
         ext.prefix = { "${meta.id}_before" }
     }
@@ -21,8 +20,6 @@ process {
 
     withName: SEQKIT_REPLACE {
         ext.args   = '-p "/" -r "_"'
-        ext.suffix = "fasta"
         ext.prefix = "intermediate_seqkit_replace"
     }
-
 }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index 0d9d4e0..9ff0681 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -35,7 +35,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
             fullHelp: help_full,
         ]
         if(parameters_schema) {
-            help_options << [parametersSchema: parameters_schema]
+            help_options << [parameters_schema: parameters_schema]
         }
         log.info paramsHelp(
             help_options,
@@ -51,7 +51,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
 
     summary_options = [:]
     if(parameters_schema) {
-        summary_options << [parametersSchema: parameters_schema]
+        summary_options << [parameters_schema: parameters_schema]
     }
     log.info before_text
     log.info paramsSummaryLog(summary_options, input_workflow)
@@ -64,10 +64,10 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     if(validate_params) {
         validateOptions = [:]
         if(parameters_schema) {
-            validateOptions << [parametersSchema: parameters_schema]
+            validateOptions << [parameters_schema: parameters_schema]
         }
         if(cli_typecast != null) {
-            validateOptions << [cliTypecast: cli_typecast]
+            validateOptions << [cast_cli_params: cli_typecast]
         }
         validateParameters(validateOptions)
     }
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 724f8cc..3e4f17a 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -55,13 +55,13 @@
                     "seqfu": "1.22.3"
                 },
                 "SEQKIT_REPLACE": {
-                    "seqkit": "2.9.0"
+                    "seqkit": "2.13.0"
                 },
                 "SEQKIT_RMDUP": {
-                    "seqkit": "2.9.0"
+                    "seqkit": "2.13.0"
                 },
                 "SEQKIT_SEQ": {
-                    "seqkit": "2.9.0"
+                    "seqkit": "2.13.0"
                 },
                 "UNTAR_INTERPROSCAN": {
                     "untar": 1.34
@@ -451,10 +451,10 @@
                 "GI|225038609|EFDID|719595|FULL.ss2:md5,e7d8eaa84d46a6a714ffe00d7f21cdfb"
             ]
         ],
-        "timestamp": "2026-07-27T13:43:53.452281",
+        "timestamp": "2026-09-02T11:22:22.960095437",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
         }
     }
-}
+}
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 519bc8e..6084f9d 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -7,7 +7,8 @@
 // Or any resources requirements
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/proteinannotator/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinannotator/'
 }
 
+// Fixes S3 access issues on self-hosted runners
 aws.client.anonymous = true