diff --git a/.editorconfig b/.editorconfig
deleted file mode 100644
index 6d9b74cc..00000000
--- a/.editorconfig
+++ /dev/null
@@ -1,37 +0,0 @@
-root = true
-
-[*]
-charset = utf-8
-end_of_line = lf
-insert_final_newline = true
-trim_trailing_whitespace = true
-indent_size = 4
-indent_style = space
-
-[*.{md,yml,yaml,html,css,scss,js}]
-indent_size = 2
-
-# These files are edited and tested upstream in nf-core/modules
-[/modules/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-[/subworkflows/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-
-[/assets/email*]
-indent_size = unset
-
-# ignore python and markdown
-[*.{py,md}]
-indent_style = unset
-
-# ignore ro-crate metadata files
-[**/ro-crate-metadata.json]
-insert_final_newline = unset
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 9421e534..711f925a 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -13,33 +13,14 @@ on:
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/hgtseq' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+    if: github.repository == 'nf-core/hgtseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
-      - name: Get PR reviews
-        uses: octokit/request-action@v2.x
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
@@ -50,16 +31,16 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/hgtseq/work-${{ github.sha }}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/hgtseq/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hgtseq/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hgtseq/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 83f3f29e..e3dba69c 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
deleted file mode 100644
index 403f8171..00000000
--- a/.github/workflows/ci.yml
+++ /dev/null
@@ -1,87 +0,0 @@
-name: nf-core CI
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-on:
-  push:
-    branches:
-      - dev
-  pull_request:
-  release:
-    types: [published]
-  workflow_dispatch:
-
-env:
-  NXF_ANSI_LOG: false
-  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
-  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
-  cancel-in-progress: true
-
-jobs:
-  test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hgtseq') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "24.04.2"
-          - "latest-everything"
-        profile:
-          - "conda"
-          - "docker"
-          - "singularity"
-        test_name:
-          - "test"
-        isMaster:
-          - ${{ github.base_ref == 'master' }}
-        # Exclude conda and singularity on dev
-        exclude:
-          - isMaster: false
-            profile: "conda"
-          - isMaster: false
-            profile: "singularity"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          fetch-depth: 0
-
-      - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Set up Apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up Miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          conda-solver: libmamba
-          channels: conda-forge,bioconda
-
-      - name: Set up Conda
-        if: matrix.profile == 'conda'
-        run: |
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 0b6b1f27..ac030fd5 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@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
         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 ab06316e..999bcc38 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -12,14 +12,6 @@ on:
         required: true
         default: "dev"
   pull_request:
-    types:
-      - opened
-      - edited
-      - synchronize
-    branches:
-      - main
-      - master
-  pull_request_target:
     branches:
       - main
       - master
@@ -52,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -120,6 +112,7 @@ jobs:
           echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
+        id: count_comparison
         run: |
           if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
             initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
@@ -132,3 +125,10 @@ jobs:
           else
             echo "The pipeline can be downloaded successfully!"
           fi
+
+      - name: Upload Nextflow logfile for debugging purposes
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: nextflow_logfile.txt
+          path: .nextflow.log*
+          include-hidden-files: true
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix_linting.yml
similarity index 96%
rename from .github/workflows/fix-linting.yml
rename to .github/workflows/fix_linting.yml
index 1327bf84..408ff617 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 69393343..a01b36ac 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -48,8 +48,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          tags: "cpu,cpu_conda"
-          max_shards: 15
+          max_shards: 7
 
       - name: debug
         run: |
@@ -63,7 +62,6 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
-      - disk=large
     strategy:
       fail-fast: false
       matrix:
@@ -80,6 +78,7 @@ jobs:
         NXF_VER:
           - "24.04.2"
           - "25.04.8"
+          - "24.10.5"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 76a9e67e..0f732495 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
+      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template-version-comment.yml
similarity index 95%
rename from .github/workflows/template_version_comment.yml
rename to .github/workflows/template-version-comment.yml
index 537529bc..beb5c77f 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -14,7 +14,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: nichmor/minimal-read-yaml@v0.0.2
+        uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
diff --git a/.nf-core.yml b/.nf-core.yml
index d4485392..f116ba4d 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -5,7 +5,7 @@ lint:
     - assets/analysis_report.Rmd
     - docs/images/nf-core-hgtseq_logo_dark.png
     - docs/images/nf-core-hgtseq_logo_light.png
-nf_core_version: 3.2.0
+nf_core_version: 3.3.2
 repository_type: pipeline
 template:
   author: Simone Carpanzano, Francesco Lescai
@@ -16,3 +16,8 @@ template:
   org: nf-core
   outdir: .
   version: 1.2.0dev
+update:
+  https://github.com/nf-core/modules.git:
+    nf-core:
+      fastqc: False
+      multiqc: False
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1dec8650..bb41beec 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,10 +4,24 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
-
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.1.2"
+          - prettier@3.6.2
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-      - id: editorconfig-checker
-        alias: ec
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
diff --git a/.vscode/settings.json b/.vscode/settings.json
index a33b527c..af2d783f 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,3 +1,4 @@
 {
-    "markdown.styles": ["public/vscode_markdown.css"]
+    "markdown.styles": ["public/vscode_markdown.css"],
+    "nextflow.telemetry.enabled": false
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3b7bbd0a..18eee565 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,18 @@
 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).
 
-## 1.2.0dev
+## v1.2.0dev - [11/11/2025]
+
+### `Added`
+
+- updated pipeline logo
+
+### `Fixed`
+
+- fixed an issue with pipeline config preventing loading on Seqera platform
+- template update to nf-core version 3.3.2
+- fixed null-pointer-exception triggered with Nextflow versions 25.x
+- [#51](https://github.com/nf-core/hgtseq/pull/56) - Fixed json schema to latest version
 
 ## [1.1.0](https://github.com/nf-core/hgtseq/releases/tag/1.1.0) - Beary Rose
 
diff --git a/README.md b/README.md
index 82f9c007..d0331f55 100644
--- a/README.md
+++ b/README.md
@@ -5,18 +5,18 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/hgtseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/hgtseq/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/hgtseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/hgtseq/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/hgtseq/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7244734-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7244734)
+[![GitHub Actions CI Status](https://github.com/nf-core/hgtseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/hgtseq/actions/workflows/nf-test.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/hgtseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/hgtseq/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/hgtseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7244734-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7244734)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
 [![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/)
 [![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/hgtseq)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hgtseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/hgtseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hgtseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/hgtseq)[![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)
 
 ## Introduction
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 7d1f4224..352dcd41 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/hgtseq/releases/tag/1.1.0" target="_blank">nf-core/hgtseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/hgtseq/tree/dev" target="_blank">nf-core/hgtseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/hgtseq/1.1.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/hgtseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-hgtseq-methods-description":
     order: -1000
diff --git a/assets/schema_input.json b/assets/schema_input.json
index db3b9590..dfb77654 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/hgtseq/master/assets/schema_input.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/hgtseq/main/assets/schema_input.json",
     "title": "nf-core/hgtseq pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",
@@ -16,7 +16,7 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
diff --git a/conf/base.config b/conf/base.config
index 3a29825e..6ce9dfc1 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -15,7 +15,7 @@ process {
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
@@ -60,4 +60,8 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+    withLabel: process_gpu {
+        ext.use_gpu = { workflow.profile.contains('gpu') }
+        accelerator = { workflow.profile.contains('gpu') ? 1 : null }
+    }
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index ef3f6683..282879ec 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -37,6 +37,5 @@ params {
     kronadb  = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
 
     // reporting only if Human data
-    taxonomy_id = "9606"
+    taxonomy_id = 9606
 }
-
diff --git a/modules.json b/modules.json
index 91a234cf..352966bc 100644
--- a/modules.json
+++ b/modules.json
@@ -17,7 +17,7 @@
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "15a93581f7f81d05c04b828954004a089360ea9b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
@@ -27,7 +27,7 @@
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "15a93581f7f81d05c04b828954004a089360ea9b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
@@ -37,32 +37,32 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "krona/ktimporttaxonomy": {
                         "branch": "master",
-                        "git_sha": "4789f43ab82b70a6719890d2ffe43685979960bd",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "krona/ktupdatetaxonomy": {
                         "branch": "master",
-                        "git_sha": "4789f43ab82b70a6719890d2ffe43685979960bd",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "qualimap/bamqc": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "samtools/fastq": {
@@ -72,27 +72,27 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
@@ -102,12 +102,12 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     }
                 }
@@ -116,17 +116,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
+                        "git_sha": "dcd088f483cede0c3df4034d405126f05a764cc7",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 033f4154..23e16634 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -29,7 +29,7 @@ process FASTQC {
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
     // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
-    def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null
+    def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 2b2e62b8..c8d9d025 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -29,9 +29,10 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
+        ontologies: []
 output:
-  - html:
-      - meta:
+  html:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -40,8 +41,9 @@ output:
           type: file
           description: FastQC report
           pattern: "*_{fastqc.html}"
-  - zip:
-      - meta:
+          ontologies: []
+  zip:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -50,11 +52,14 @@ output:
           type: file
           description: FastQC report archive
           pattern: "*_{fastqc.zip}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index c3b3413f..812fc4c5 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=1.27
+  - bioconda::multiqc=1.29
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 58d9313c..0ac3c369 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.29--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index b16c1879..ce30eb73 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -15,57 +15,71 @@ tools:
       licence: ["GPL-3.0-or-later"]
       identifier: biotools:multiqc
 input:
-  - - multiqc_files:
-        type: file
-        description: |
-          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - - multiqc_config:
-        type: file
-        description: Optional config yml for MultiQC
-        pattern: "*.{yml,yaml}"
-  - - extra_multiqc_config:
-        type: file
-        description: Second optional config yml for MultiQC. Will override common sections
-          in multiqc_config.
-        pattern: "*.{yml,yaml}"
-  - - multiqc_logo:
+  - multiqc_files:
+      type: file
+      description: |
+        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+      ontologies: []
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections
+        in multiqc_config.
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+      ontologies: []
+  - replace_names:
+      type: file
+      description: |
+        Optional two-column sample renaming file. First column a set of
+        patterns, second column a set of corresponding replacements. Passed via
+        MultiQC's `--replace-names` option.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+  - sample_names:
+      type: file
+      description: |
+        Optional TSV file with headers, passed to the MultiQC --sample_names
+        argument.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+output:
+  report:
+    - "*multiqc_report.html":
         type: file
-        description: Optional logo file for MultiQC
-        pattern: "*.{png}"
-  - - replace_names:
+        description: MultiQC report file
+        pattern: "multiqc_report.html"
+        ontologies: []
+  data:
+    - "*_data":
+        type: directory
+        description: MultiQC data dir
+        pattern: "multiqc_data"
+  plots:
+    - "*_plots":
         type: file
-        description: |
-          Optional two-column sample renaming file. First column a set of
-          patterns, second column a set of corresponding replacements. Passed via
-          MultiQC's `--replace-names` option.
-        pattern: "*.{tsv}"
-  - - sample_names:
+        description: Plots created by MultiQC
+        pattern: "*_data"
+        ontologies: []
+  versions:
+    - versions.yml:
         type: file
-        description: |
-          Optional TSV file with headers, passed to the MultiQC --sample_names
-          argument.
-        pattern: "*.{tsv}"
-output:
-  - report:
-      - "*multiqc_report.html":
-          type: file
-          description: MultiQC report file
-          pattern: "multiqc_report.html"
-  - data:
-      - "*_data":
-          type: directory
-          description: MultiQC data dir
-          pattern: "multiqc_data"
-  - plots:
-      - "*_plots":
-          type: file
-          description: Plots created by MultiQC
-          pattern: "*_data"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7b7c1322..88e90571 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:29:57.631982377"
+        "timestamp": "2025-05-22T11:50:41.182332996"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:30:34.743726958"
+        "timestamp": "2025-05-22T11:51:22.448739369"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:30:21.44383553"
+        "timestamp": "2025-05-22T11:51:06.198928424"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 7b6d24fa..927e915e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -46,7 +46,9 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+
+    // Config options
     config_profile_name        = null
     config_profile_description = null
 
@@ -168,6 +170,11 @@ profiles {
             ]
         }
     }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions    = '--nv'
+        singularity.runOptions  = '--nv'
+    }
     test_full { includeConfig 'conf/test_full.config' }
     test      {
         includeConfig 'conf/test.config'
@@ -179,10 +186,15 @@ profiles {
     }
 }
 
-// Load nf-core custom profiles from different Institutions
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+// Load nf-core custom profiles from different institutions
+
+// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
+// Load nf-core/hgtseq custom profiles from different institutions.
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+
 
 // Load nf-core/hgtseq custom profiles from different institutions.
+// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/hgtseq.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -239,7 +251,6 @@ dag {
 
 manifest {
     name            = 'nf-core/hgtseq'
-    author          = """Simone Carpanzano, Francesco Lescai""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
     contributors    = [
         // nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
@@ -270,7 +281,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
@@ -296,7 +307,7 @@ validation {
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/nf-core/hgtseq/blob/master/CITATIONS.md
+    https://github.com/nf-core/hgtseq/blob/main/CITATIONS.md
 """
     }
     summary {
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 1483f1fe..9750995f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/hgtseq/master/nextflow_schema.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/hgtseq/main/nextflow_schema.json",
     "title": "nf-core/hgtseq pipeline parameters",
     "description": "A pipeline to investigate horizontal gene transfer from NGS data",
     "type": "object",
diff --git a/nf-test.config b/nf-test.config
index 2ceca0fb..3a1fff59 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -15,12 +15,10 @@ config {
     profile "test"
 
     // list of filenames or patterns that should be trigger a full test run
-    triggers 'assets/schema_input.json', 'conf/test.config', 'nextflow.config', 'nextflow_schema.json', 'nf-test.config', 'tests/.nftignore', 'tests/nextflow.config'
+    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
 
     // load the necessary plugins
     plugins {
-        load "nft-bam@0.4.0"
-        load "nft-utils@0.0.5"
-        load "nft-vcf@1.0.7"
+        load "nft-utils@0.0.3"
     }
 }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 6c9f2054..3b691923 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -21,9 +21,9 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "Stable",
-            "datePublished": "2025-03-04T14:12:36+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-hgtseq_logo_dark.png\">\n    <img alt=\"nf-core/hgtseq\" src=\"docs/images/nf-core-hgtseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/hgtseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/hgtseq/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/hgtseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/hgtseq/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/hgtseq/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7244734-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7244734)\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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/hgtseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hgtseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/hgtseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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/hgtseq** is a bioinformatics best-practice analysis pipeline built to investigate horizontal gene transfer from NGS data.\n\nThe pipeline uses metagenomic classification of paired-read alignments against a reference genome to identify the presence of non-host microbial sequences within read pairs, and to infer potential integration sites into the host genome.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/hgtseq/results).\n\n## Functionality Overview\n\nA graphical view of the pipeline can be seen below.\n\n<p align=\"center\">\n<img src=\"docs/images/hgtseq_pipeline_metromap.png\" alt=\"nf-core/circdna metromap\" width=\"70%\">\n</p>\n\n## Pipeline summary\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n3. Adapter and quality trimming ([`Trim Galore`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))\n4. Mapping reads using BWA ([`BWA`](http://bio-bwa.sourceforge.net))\n5. Sort and index alignments, extraction reads by sam flag and conversion to fastq format([`SAMtools`](https://www.htslib.org))\n6. Taxonomic classification ([`Kraken2`](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown))\n7. Plotting Kraken2 results ([`Krona`](https://hpc.nih.gov/apps/kronatools.html))\n8. Html analysis report ([`RMarkDown`](https://rmarkdown.rstudio.com))\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/usage/installation) on how\n> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)\n> with `-profile test` before running the workflow on actual data.\n\n```console\nnextflow run nf-core/hgtseq \\\n--input <YOURINPUT>.csv \\\n--outdir <OUTDIR> \\\n--genome GRCh38 \\\n--taxonomy_id \"TAXID\" \\\n-profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \\\n--krakendb /path/to/kraken_db \\\n--kronadb /path/to/krona_db/taxonomy.tab\n```\n\n```bash\nnextflow run nf-core/hgtseq \\\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\n> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;\n> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\nFor more details, please refer to the [usage documentation](https://nf-co.re/hgtseq/usage) and the [parameter documentation](https://nf-co.re/hgtseq/parameters).\n\n## Pipeline output\n\nTo see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/hgtseq/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/hgtseq/output).\n\n## Credits\n\nnf-core/hgtseq was originally written by Simone Carpanzano, Francesco Lescai.\n\nWe thank nf-core community, and in particular the authors of the modules used in the pipeline: Paolo Cozzi, Jose Espinosa-Carrasco, Phil Ewels, Gisela Gabernet, Maxime Garcia, Jeremy Guntoro, Friederike Hanssen, Matthias Hortenhuber, Patrick H\u00fcther, Suzanne Jin, Felix Krueger, Harshil Patel, Alex Peltzer, Abhinav Sharma, Gregor Sturm, James Fellows Yates.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#hgtseq` channel](https://nfcore.slack.com/channels/hgtseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n\nIf you use nf-core/hgtseq for your analysis, please cite it using the following doi: [10.5281/zenodo.7244734](https://doi.org/10.5281/zenodo.7244734)\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",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2025-11-11T09:27:23+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-hgtseq_logo_dark.png\">\n    <img alt=\"nf-core/hgtseq\" src=\"docs/images/nf-core-hgtseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/hgtseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/hgtseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/hgtseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/hgtseq/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/hgtseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7244734-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7244734)\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%A524.04.2-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\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/hgtseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hgtseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/hgtseq)[![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/hgtseq** is a bioinformatics best-practice analysis pipeline built to investigate horizontal gene transfer from NGS data.\n\nThe pipeline uses metagenomic classification of paired-read alignments against a reference genome to identify the presence of non-host microbial sequences within read pairs, and to infer potential integration sites into the host genome.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/hgtseq/results).\n\n## Functionality Overview\n\nA graphical view of the pipeline can be seen below.\n\n<p align=\"center\">\n<img src=\"docs/images/hgtseq_pipeline_metromap.png\" alt=\"nf-core/circdna metromap\" width=\"70%\">\n</p>\n\n## Pipeline summary\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n3. Adapter and quality trimming ([`Trim Galore`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))\n4. Mapping reads using BWA ([`BWA`](http://bio-bwa.sourceforge.net))\n5. Sort and index alignments, extraction reads by sam flag and conversion to fastq format([`SAMtools`](https://www.htslib.org))\n6. Taxonomic classification ([`Kraken2`](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown))\n7. Plotting Kraken2 results ([`Krona`](https://hpc.nih.gov/apps/kronatools.html))\n8. Html analysis report ([`RMarkDown`](https://rmarkdown.rstudio.com))\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/usage/installation) on how\n> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)\n> with `-profile test` before running the workflow on actual data.\n\n```console\nnextflow run nf-core/hgtseq \\\n--input <YOURINPUT>.csv \\\n--outdir <OUTDIR> \\\n--genome GRCh38 \\\n--taxonomy_id \"TAXID\" \\\n-profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \\\n--krakendb /path/to/kraken_db \\\n--kronadb /path/to/krona_db/taxonomy.tab\n```\n\n```bash\nnextflow run nf-core/hgtseq \\\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\n> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;\n> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\nFor more details, please refer to the [usage documentation](https://nf-co.re/hgtseq/usage) and the [parameter documentation](https://nf-co.re/hgtseq/parameters).\n\n## Pipeline output\n\nTo see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/hgtseq/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/hgtseq/output).\n\n## Credits\n\nnf-core/hgtseq was originally written by Simone Carpanzano, Francesco Lescai.\n\nWe thank nf-core community, and in particular the authors of the modules used in the pipeline: Paolo Cozzi, Jose Espinosa-Carrasco, Phil Ewels, Gisela Gabernet, Maxime Garcia, Jeremy Guntoro, Friederike Hanssen, Matthias Hortenhuber, Patrick H\u00fcther, Suzanne Jin, Felix Krueger, Harshil Patel, Alex Peltzer, Abhinav Sharma, Gregor Sturm, James Fellows Yates.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#hgtseq` channel](https://nfcore.slack.com/channels/hgtseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n\nIf you use nf-core/hgtseq for your analysis, please cite it using the following doi: [10.5281/zenodo.7244734](https://doi.org/10.5281/zenodo.7244734)\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": "#dba67cc4-68b8-4fd8-96b1-41c626035d24"
+                    "@id": "#3fee52d7-8428-43da-a1e0-ca1b7fde181e"
                 }
             ],
             "name": "nf-core/hgtseq"
@@ -132,7 +132,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-03-04T15:12:36Z",
+            "dateModified": "2025-11-11T09:27:23Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -165,10 +165,10 @@
             },
             "url": [
                 "https://github.com/nf-core/hgtseq",
-                "https://nf-co.re/hgtseq/1.1.0/"
+                "https://nf-co.re/hgtseq/dev/"
             ],
             "version": [
-                "1.1.0"
+                "1.2.0dev"
             ]
         },
         {
@@ -181,14 +181,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=24.04.2"
+            "version": "!>=24.10.5"
         },
         {
-            "@id": "#dba67cc4-68b8-4fd8-96b1-41c626035d24",
+            "@id": "#3fee52d7-8428-43da-a1e0-ca1b7fde181e",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#e4a29729-9b13-4e21-93bc-3b74e92a9a0c"
+                    "@id": "#31dab6d0-c358-4d19-9e9f-b96a805996af"
                 }
             ],
             "mainEntity": {
@@ -197,10 +197,10 @@
             "name": "Test suite for nf-core/hgtseq"
         },
         {
-            "@id": "#e4a29729-9b13-4e21-93bc-3b74e92a9a0c",
+            "@id": "#31dab6d0-c358-4d19-9e9f-b96a805996af",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/hgtseq",
-            "resource": "repos/nf-core/hgtseq/actions/workflows/ci.yml",
+            "resource": "repos/nf-core/hgtseq/actions/workflows/nf-test.yml",
             "runsOn": {
                 "@id": "https://w3id.org/ro/terms/test#GithubService"
             },
diff --git a/subworkflows/local/reads_qc/main.nf b/subworkflows/local/reads_qc/main.nf
index 34b7a2cf..493f6681 100644
--- a/subworkflows/local/reads_qc/main.nf
+++ b/subworkflows/local/reads_qc/main.nf
@@ -33,4 +33,3 @@ workflow READS_QC {
 
 
 }
-
diff --git a/subworkflows/local/sortbam/main.nf b/subworkflows/local/sortbam/main.nf
index af7ad529..bff9701c 100644
--- a/subworkflows/local/sortbam/main.nf
+++ b/subworkflows/local/sortbam/main.nf
@@ -27,8 +27,11 @@ workflow SORTBAM {
     // which is the reason for creating an additional channel that joins
     // both of them:
 
+    // NOTE: avoid using `remainder: true` here because it triggers a NullPointerException
+    // in Nextflow 25.x when the upstream channel closes before the join completes.
+    // avoid using join at all, and use combine instead to make this more robust
     SAMTOOLS_SORT.out.bam
-        .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true)
+        .combine(SAMTOOLS_INDEX.out.bai, by: 0)
         .set { bam_bai }
 
     emit:
diff --git a/subworkflows/local/utils_nfcore_hgtseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_hgtseq_pipeline/main.nf
index 49eca646..46b1bc1d 100644
--- a/subworkflows/local/utils_nfcore_hgtseq_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_hgtseq_pipeline/main.nf
@@ -260,4 +260,3 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
-
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 0907ac58..09ef842a 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id "nf-schema@2.1.0"
+    id "nf-schema@2.4.2"
 }
 
 validation {
diff --git a/tests/.nftignore b/tests/.nftignore
new file mode 100644
index 00000000..158c83c5
--- /dev/null
+++ b/tests/.nftignore
@@ -0,0 +1,11 @@
+.DS_Store
+multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/multiqc_data/BETA-multiqc.parquet
+multiqc/multiqc_data/multiqc.log
+multiqc/multiqc_data/multiqc_data.json
+multiqc/multiqc_data/multiqc_sources.txt
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/multiqc_report.html
+fastqc/*_fastqc.{html,zip}
+pipeline_info/*.{html,json,txt,yml}
diff --git a/tests/default.nf.test b/tests/default.nf.test
index cc8f1d57..420d5323 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -1,10 +1,10 @@
 nextflow_pipeline {
 
-    name "Test pipeline with default settings"
+    name "Test pipeline"
     script "../main.nf"
     tag "pipeline"
 
-    test("Params: default") {
+    test("-profile test") {
 
         when {
             params {
@@ -22,39 +22,8 @@ nextflow_pipeline {
                 { assert snapshot(
                     // Number of successful tasks
                     workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_hgtseq_software_mqc_versions.yml", "Workflow"),
-                    // All stable path name, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path
-                ).match() }
-            )
-        }
-    }
-
-    test("Params: default - stub") {
-
-        options "-stub"
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
-            assertAll(
-                { assert workflow.success},
-                { assert snapshot(
-                    // Number of successful tasks
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_hgtseq_software_mqc_versions.yml", "Workflow"),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_hgtseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 22e78dd7..98be574c 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1,23 +1,15 @@
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
-----------------------------------------------------------------------------------------
+========================================================================================
+    Nextflow config file for running nf-test tests
+========================================================================================
 */
 
 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/modules/data/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/hgtseq'
 }
 
-// Should resolve issue with accessing s3 from the runners
-aws.client.anonymous = true
-
+aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
 
 process {