Important! Template update for nf-core/tools v4.1.0

.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')

.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."

.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"

.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

.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 }}

.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
 

.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 }}
 

.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"

.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

.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

CHANGELOG.md

@@ -3,16 +3,23 @@
 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`
 
 - [#110](https://github.com/nf-core/proteinannotator/pull/110) - Added KOfamScan for KEGG Ortholog functional annotation, including automatic database download and local database support. (by @Yixuan39)
 
 ### `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`

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/)

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 }
     }

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' } }

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' } }

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' } }

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' } }

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' } }

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' } }

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' } }

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' } }

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
         ]
     }
 

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
 

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.

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.