diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..ea27a58
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,27 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                "python.linting.enabled": true,
+                "python.linting.pylintEnabled": true,
+                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+                "python.linting.flake8Path": "/opt/conda/bin/flake8",
+                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}
diff --git a/.editorconfig b/.editorconfig
index b78de6e..b6b3190 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js,cff}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules
diff --git a/.gitattributes b/.gitattributes
index 050bb12..7a2dabc 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 811c655..f03b44e 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -93,3 +93,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/sanger-tol/sequencecomposition/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index b01ea4b..acb4521 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -38,13 +38,14 @@ body:
     id: system
     attributes:
       label: System information
-      description: "* Nextflow version _(eg. 22.04.0)_
+      description: "* Nextflow version _(eg. 22.10.1)_
 
         * Hardware _(eg. HPC, Desktop, Cloud)_
 
         * Executor _(eg. slurm, local, awsbatch)_
 
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
 
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
 
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 31aad91..7335760 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'sanger-tol/sequencecomposition'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == sanger-tol/sequencecomposition ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == sanger-tol/sequencecomposition ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6bf76a5..12a3b37 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,6 +11,10 @@ on:
 env:
   NXF_ANSI_LOG: false
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Run pipeline with test data
@@ -20,11 +24,11 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.04.0"
+          - "22.10.1"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
@@ -35,9 +39,6 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
-      - name: Run the full test profile of the pipeline (requires sanger-tol/insdcdownload)
+      - name: Run the full test profile of the pipeline
         run: |
-          mkdir ${GITHUB_WORKSPACE}/data
-          cd ${GITHUB_WORKSPACE}/data
-          nextflow run sanger-tol/insdcdownload -revision 1.1.0 -profile test_full,docker --outdir ./results_full
           nextflow run ${GITHUB_WORKSPACE} -profile test_full,docker --outdir ./results_full
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
new file mode 100644
index 0000000..694e90e
--- /dev/null
+++ b/.github/workflows/clean-up.yml
@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index a547e1d..64186dd 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -8,23 +8,23 @@ jobs:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
-      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      contains(github.event.comment.body, '@sanger-tolsoft fix linting') &&
       github.repository == 'sanger-tol/sequencecomposition'
     runs-on: ubuntu-latest
     steps:
-      # Use the @nf-core-bot token to check out so we can push later
+      # Use the @sanger-tolsoft token to check out so we can push later
       - uses: actions/checkout@v3
         with:
-          token: ${{ secrets.nf_core_bot_auth_token }}
+          token: ${{ secrets.sangertolsoft_access_token }}
 
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
         run: gh pr checkout ${{ github.event.issue.number }}
         env:
-          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+          GITHUB_TOKEN: ${{ secrets.sangertolsoft_access_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "::set-output name=result::fail"
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'
@@ -46,8 +46,8 @@ jobs:
       - name: Commit & push changes
         if: steps.prettier_status.outputs.result == 'fail'
         run: |
-          git config user.email "core@nf-co.re"
-          git config user.name "nf-core-bot"
+          git config user.email "105875386+sanger-tolsoft@users.noreply.github.com"
+          git config user.name "sanger-tolsoft"
           git config push.default upstream
           git add .
           git status
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 48808e8..7ebc310 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -4,6 +4,8 @@ name: nf-core linting
 # that the code meets the nf-core guidelines.
 on:
   push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -12,22 +14,22 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
 
       - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|cff\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
 
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -38,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -69,20 +71,20 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.8"
           architecture: "x64"
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core==2.5
+          pip install nf-core==2.8
 
       - name: Run nf-core lint
         env:
@@ -97,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 04758f6..0bbcd30 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2
diff --git a/.github/workflows/sanger_test.yml b/.github/workflows/sanger_test.yml
new file mode 100644
index 0000000..e69af1e
--- /dev/null
+++ b/.github/workflows/sanger_test.yml
@@ -0,0 +1,29 @@
+name: sanger-tol LSF tests
+
+on:
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run LSF tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Launch workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
+          workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}",
+            }
+          profiles: test,sanger,singularity,cleanup
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/sanger_test_full.yml b/.github/workflows/sanger_test_full.yml
new file mode 100644
index 0000000..e028c6b
--- /dev/null
+++ b/.github/workflows/sanger_test_full.yml
@@ -0,0 +1,43 @@
+name: sanger-tol LSF full size tests
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run LSF full size tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Sets env vars for push
+        run: |
+          echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV
+        if: github.event_name == 'push'
+
+      - name: Sets env vars for workflow_dispatch
+        run: |
+          echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV
+        if: github.event_name == 'workflow_dispatch'
+
+      - name: Launch workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ env.REVISION }}
+          workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }}
+          parameters: |
+            {
+              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
+            }
+          profiles: test_full,sanger,singularity,cleanup
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.nf-core.yml b/.nf-core.yml
index f8e409c..e88d9ab 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,6 @@
 repository_type: pipeline
 lint:
   files_exist:
-    - CODE_OF_CONDUCT.md
     - assets/multiqc_config.yml
     - assets/nf-core-sequencecomposition_logo_light.png
     - conf/igenomes.config
@@ -20,3 +19,5 @@ lint:
   nextflow_config:
     - manifest.name
     - manifest.homePage
+  multiqc_config:
+    - report_comment
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..0c31cdb
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier
diff --git a/.prettierignore b/.prettierignore
index d0e7ae5..437d763 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,4 +1,6 @@
 email_template.html
+adaptivecard.json
+slackreport.json
 .nextflow*
 work/
 data/
@@ -7,3 +9,4 @@ results/
 testing/
 testing*
 *.pyc
+bin/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8b2ec29..4089287 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,21 +3,56 @@
 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).
 
-## v1.0.0 - [2022-10-08]
+## [[1.1.0](https://github.com/sanger-tol/sequencecomposition/releases/tag/1.1.0)] – Polite Platyfish – [2024-12-05]
+
+### Enhancements & fixes
+
+- Upgrade to the version 2.8 of the nf-core template.
+- nf-core module updates to remove Anaconda references
+- Updated configuration of the GitHub CI to improve testing.
+- Simpler samplesheet format, with just the path to the Fasta file and the output directory.
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| htslib     |             | 1.20        |
+| MultiQC    | 1.13        | 1.20        |
+| Python     | 3.8.3,3.9   | 3.9.1       |
+| samtools   |             | 1.21        |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
+
+## [[1.0.0](https://github.com/sanger-tol/sequencecomposition/releases/tag/1.0.0)] – Apophis – [2022-10-08]
 
 Initial release of sanger-tol/sequencecomposition, created with the [nf-core](https://nf-co.re/) template.
 
-### `Added`
+### Enhancements & fixes
 
 - Run `fasta_windows` on an assembly
 - Convert all outputs to TSV and bedGraph files
 - Index all output files with `tabix`
 
-### `Dependencies`
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Dependency    | Old version | New version |
+| ------------- | ----------- | ----------- |
+| fasta_windows |             | 0.2.4       |
+| MultiQC       |             | 1.13        |
+| Python        |             | 3.8.3,3.9   |
+| tabix         |             | 1.11        |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
 
-All dependencies are automatically fetched by Singularity.
+### Parameters
 
-- fasta_windows
-- bgzip
-- tabix
-- python3
+| Old parameter | New parameter        |
+| ------------- | -------------------- |
+|               | --input              |
+|               | --fasta              |
+|               | --window_size_info   |
+|               | --selected_fw_output |
diff --git a/CITATION.cff b/CITATION.cff
index 51922d2..7b800b4 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -2,25 +2,29 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: sanger-tol/sequencecomposition v1.0.0 - Apophis
+title: sanger-tol/sequencecomposition
 message: >-
-  If you use this software, please cite it using the
-  metadata from this file.
+    If you use this software, please cite it using the
+    metadata from this file.
 type: software
 authors:
-  - given-names: Matthieu
-    family-names: Muffato
-    affiliation: Wellcome Sanger Institute
-    orcid: "https://orcid.org/0000-0002-7860-3560"
-  - given-names: Priyanka
-    family-names: Surana
-    orcid: "https://orcid.org/0000-0002-7167-0875"
-    affiliation: Wellcome Sanger Institute
+    - given-names: Matthieu
+      family-names: Muffato
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0002-7860-3560"
+    - given-names: Priyanka
+      family-names: Surana
+      orcid: "https://orcid.org/0000-0002-7167-0875"
+      affiliation: Wellcome Sanger Institute
+    - given-names: Tyler
+      family-names: Chafin
+      orcid: "https://orcid.org/0000-0001-8687-5905"
+      affiliation: Wellcome Sanger Institute
 identifiers:
-  - type: doi
-    value: 10.5281/zenodo.7155169
+    - type: doi
+      value: 10.5281/zenodo.7155168
 repository-code: "https://github.com/sanger-tol/sequencecomposition"
 license: MIT
 commit: TODO
-version: 1.0.0
+version: 2.0.0
 date-released: "2022-10-08"
diff --git a/CITATIONS.md b/CITATIONS.md
index 69a44d6..1c79132 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -20,9 +20,9 @@
 
 ## Software packaging/containerisation tools
 
-- [Anaconda](https://anaconda.com)
+- [Conda](https://conda.org/)
 
-  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+  > conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. https://github.com/conda/conda
 
 - [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
 
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
new file mode 100644
index 0000000..f4fd052
--- /dev/null
+++ b/CODE_OF_CONDUCT.md
@@ -0,0 +1,111 @@
+# Code of Conduct at nf-core (v1.0)
+
+## Our Pledge
+
+In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of:
+
+- Age
+- Body size
+- Familial status
+- Gender identity and expression
+- Geographical location
+- Level of experience
+- Nationality and national origins
+- Native language
+- Physical and neurological ability
+- Race or ethnicity
+- Religion
+- Sexual identity and orientation
+- Socioeconomic status
+
+Please note that the list above is alphabetised and is therefore not ranked in any order of preference or importance.
+
+## Preamble
+
+> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply.
+
+An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva.
+
+nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals.
+
+We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc.
+
+Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities.
+
+We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC.
+
+Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re
+
+## Our Responsibilities
+
+The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
+
+The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC.
+
+## When are where does this Code of Conduct apply?
+
+Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference:
+
+- Communicating with an official project email address.
+- Communicating with community members within the nf-core Slack channel.
+- Participating in hackathons organised by nf-core (both online and in-person events).
+- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence.
+- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc.
+- Representing nf-core on social media. This includes both official and personal accounts.
+
+## nf-core cares 😊
+
+nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order):
+
+- Ask for consent before sharing another community member’s personal information (including photographs) on social media.
+- Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity.
+- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !)
+- Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.)
+- Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can)
+- Focus on what is best for the team and the community. (When in doubt, ask)
+- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn.
+- Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!)
+- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**)
+- Take breaks when you feel like you need them.
+- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.)
+
+## nf-core frowns on 😕
+
+The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces.
+
+- Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom.
+- “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online.
+- Spamming or trolling of individuals on social media.
+- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention.
+- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience.
+
+### Online Trolling
+
+The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately.
+
+All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls.
+
+## Procedures for Reporting CoC violations
+
+If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible.
+
+You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s).
+
+Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course.
+
+All reports will be handled with utmost discretion and confidentially.
+
+## Attribution and Acknowledgements
+
+- The [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4)
+- The [OpenCon 2017 Code of Conduct](http://www.opencon2017.org/code_of_conduct) (CC BY 4.0 OpenCon organisers, SPARC and Right to Research Coalition)
+- The [eLife innovation sprint 2020 Code of Conduct](https://sprint.elifesciences.org/code-of-conduct/)
+- The [Mozilla Community Participation Guidelines v3.1](https://www.mozilla.org/en-US/about/governance/policies/participation/) (version 3.1, CC BY-SA 3.0 Mozilla)
+
+## Changelog
+
+### v1.0 - March 12th, 2021
+
+- Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC.
diff --git a/LICENSE b/LICENSE
index d878e86..a9bcd4d 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Genome Research Ltd.
+Copyright (c) 2022-2024 Genome Research Ltd.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index 2c6453f..3711b94 100644
--- a/README.md
+++ b/README.md
@@ -3,10 +3,10 @@
 [![GitHub Actions CI Status](https://github.com/sanger-tol/sequencecomposition/workflows/nf-core%20CI/badge.svg)](https://github.com/sanger-tol/sequencecomposition/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/sanger-tol/sequencecomposition/workflows/nf-core%20linting/badge.svg)](https://github.com/sanger-tol/sequencecomposition/actions?query=workflow%3A%22nf-core+linting%22)
 
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7155169-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7155169)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7155168-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7155168)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.04.0-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=conda)](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/)
 
@@ -18,14 +18,6 @@
 
 **sanger-tol/sequencecomposition** is a bioinformatics analysis pipeline that extracts statistics from a genome about its sequence composition.
 
-The 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!
-
-On release, automated continuous integration tests run the pipeline on a full-sized dataset on the GitHub CI infrastructure. This ensures that the pipeline runs in a third-party environment, and has sensible resource allocation defaults set to run on real-world datasets.
-
-## Pipeline summary
-
-## Overview
-
 The pipeline takes an assembly Fasta file (possibly compressed), runs `fasta_windows` on it, and transforms the outputs into files more practical for downstream use.
 
 Steps involved:
@@ -35,39 +27,35 @@ Steps involved:
   files `fasta_windows` outputs.
 - Compress and index all bedGraph and TSV files with `bgzip` and `tabix`.
 
-## Quick Start
-
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.04.0`)
+## Usage
 
-2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
+> **Note**
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
+> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
+> with `-profile test` before running the workflow on actual data.
 
-3. Download the pipeline and test it on a minimal dataset with a single command:
+The easiest is to provide the path of the Fasta file to analyse like this:
 
-   ```bash
-   nextflow run sanger-tol/sequencecomposition -profile test,YOURPROFILE --outdir <OUTDIR>
-   ```
+```console
+nextflow run sanger-tol/sequencecomposition --fasta /path/to/genome.fa
+```
 
-   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
+> **Warning:**
+> 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/usage/configuration#custom-configuration-files).
 
-   > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
-   > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-   > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
-   > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
+The pipeline also supports bulk downloads through a sample-sheet.
+More information about this mode on our [pipeline website](https://pipelines.tol.sanger.ac.uk/sequencecomposition/usage).
 
-4. Start running your own analysis!
-
-   ```console
-   nextflow run sanger-tol/sequencecomposition --fasta /path/to/genome.fa --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
-   ```
-
-## Documentation
+## Credits
 
-The sanger-tol/sequencecomposition pipeline comes with documentation about the pipeline [usage](docs/usage.md) and [output](docs/output.md).
+sanger-tol/sequencecomposition was originally written by [Matthieu Muffato](https://github.com/muffato).
 
-## Credits
+We thank the following people for their assistance in the development of this pipeline:
 
-sanger-tol/sequencecomposition was originally written by @muffato, with
-help from @priyanka-surana.
+- [Priyanka Surana](https://github.com/priyanka-surana) for providing reviews.
+- [Tyler Chafin](https://github.com/tkchafin) for updates.
 
 ## Contributions and Support
 
@@ -77,7 +65,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use sanger-tol/sequencecomposition for your analysis, please cite it using the following doi: [10.5281/zenodo.7155169](https://doi.org/10.5281/zenodo.7155169)
+If you use sanger-tol/sequencecomposition for your analysis, please cite it using the following doi: [10.5281/zenodo.7155168](https://doi.org/10.5281/zenodo.7155168)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
new file mode 100644
index 0000000..fa19b59
--- /dev/null
+++ b/assets/adaptivecard.json
@@ -0,0 +1,67 @@
+{
+    "type": "message",
+    "attachments": [
+        {
+            "contentType": "application/vnd.microsoft.card.adaptive",
+            "contentUrl": null,
+            "content": {
+                "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                "msteams": {
+                    "width": "Full"
+                },
+                "type": "AdaptiveCard",
+                "version": "1.2",
+                "body": [
+                    {
+                        "type": "TextBlock",
+                        "size": "Large",
+                        "weight": "Bolder",
+                        "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
+                        "text": "sanger-tol/sequencecomposition v${version} - ${runName}",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "spacing": "None",
+                        "text": "Completed at ${dateComplete} (duration: ${duration})",
+                        "isSubtle": true,
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "The command used to launch the workflow was as follows:",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "${commandLine}",
+                        "isSubtle": true,
+                        "wrap": true
+                    }
+                ],
+                "actions": [
+                    {
+                        "type": "Action.ShowCard",
+                        "title": "Pipeline Configuration",
+                        "card": {
+                            "type": "AdaptiveCard",
+                            "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                            "body": [
+                                {
+                                    "type": "FactSet",
+                                    "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
+                                    ]
+                                }
+                            ]
+                        }
+                    }
+                ]
+            }
+        }
+    ]
+}
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 9992d6d..8bf07f8 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,7 +1,5 @@
-species_dir,assembly_name
-25g/data/echinoderms/Asterias_rubens,eAstRub1.3
-25g/data/insects/Osmia_bicornis,iOsmBic2.1
-25g/data/insects/Osmia_bicornis,iOsmBic2.1_alternate_haplotype
-darwin/data/fungi/Laetiporus_sulphureus,gfLaeSulp1.1
-darwin/data/insects/Noctua_fimbriata,ilNocFimb1.1
-darwin/data/mammals/Meles_meles,mMelMel3.2_paternal_haplotype
+outdir,fasta
+Asterias_rubens/eAstRub1.3,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/459/465/GCA_902459465.3_eAstRub1.3/GCA_902459465.3_eAstRub1.3_genomic.fna.gz
+Osmia_bicornis/iOsmBic2.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/907/164/935/GCA_907164935.1_iOsmBic2.1/GCA_907164935.1_iOsmBic2.1_genomic.fna.gz
+Osmia_bicornis/iOsmBic2.1_alternate_haplotype,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/907/164/925/GCA_907164925.1_iOsmBic2.1_alternate_haplotype/GCA_907164925.1_iOsmBic2.1_alternate_haplotype_genomic.fna.gz
+Noctua_fimbriata/ilNocFimb1.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/163/415/GCA_905163415.1_ilNocFimb1.1/GCA_905163415.1_ilNocFimb1.1_genomic.fna.gz
diff --git a/assets/schema_input.json b/assets/schema_input.json
index b3be168..ce7704a 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -7,22 +7,17 @@
     "items": {
         "type": "object",
         "properties": {
-            "species_dir": {
+            "outdir": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Species directory must be provided and exist"
             },
-            "assembly_name": {
+            "fasta": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Assembly name must be provided and cannot contain spaces"
-            },
-            "assembly_accession": {
-                "type": "string",
-                "pattern": "^GCA_[0-9]{9}\\.[0-9]+$",
-                "errorMessage": "Assembly accession number must be provided and be of the form GCA_*"
+                "errorMessage": "Assembly path is mandatory"
             }
         },
-        "required": ["species_dir", "assembly_name"]
+        "required": ["outdir", "fasta"]
     }
 }
diff --git a/assets/slackreport.json b/assets/slackreport.json
new file mode 100644
index 0000000..11b3b6c
--- /dev/null
+++ b/assets/slackreport.json
@@ -0,0 +1,34 @@
+{
+    "attachments": [
+        {
+            "fallback": "Plain-text summary of the attachment.",
+            "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
+            "author_name": "sanger-tol/sequencecomposition v${version} - ${runName}",
+            "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
+            "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
+            "fields": [
+                {
+                    "title": "Command used to launch the workflow",
+                    "value": "```${commandLine}```",
+                    "short": false
+                }
+                <%
+                    if (!success) { %>
+                    ,
+                    {
+                        "title": "Full error message",
+                        "value": "```${errorReport}```",
+                        "short": false
+                    },
+                    {
+                        "title": "Pipeline configuration",
+                        "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
+                        "short": false
+                    }
+                    <% }
+                %>
+            ],
+            "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
+        }
+    ]
+}
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 71411bc..324656a 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -28,9 +28,8 @@ class RowChecker:
 
     def __init__(
         self,
-        dir_col="species_dir",
-        name_col="assembly_name",
-        accession_col="assembly_accession",
+        dir_col="outdir",
+        fasta_col="fasta",
         **kwargs,
     ):
         """
@@ -38,20 +37,16 @@ def __init__(
 
         Args:
             dir_col (str): The name of the column that contains the species directory
-                (default "species_dir").
-            name_col (str): The name of the column that contains the assembly name
-                (default "assembly_name").
-            accession_col (str): The name of the column that contains the accession
-                number (default "assembly_accession").
+                (default "outdir").
+            fasta_col (str): The name of the column that contains the path to the
+                Fasta (default "fasta").
 
         """
         super().__init__(**kwargs)
         self._dir_col = dir_col
-        self._name_col = name_col
-        self._accession_col = accession_col
+        self._fasta_col = fasta_col
         self._seen = set()
         self.modified = []
-        self._regex_accession = re.compile(r"^GCA_[0-9]{9}\.[0-9]+$")
 
     def validate_and_transform(self, row):
         """
@@ -63,9 +58,8 @@ def validate_and_transform(self, row):
 
         """
         self._validate_dir(row)
-        self._validate_name(row)
-        self._validate_accession(row)
-        self._seen.add((row[self._name_col], row[self._dir_col]))
+        self._validate_fasta(row)
+        self._seen.add(row[self._fasta_col])
         self.modified.append(row)
 
     def _validate_dir(self, row):
@@ -73,32 +67,17 @@ def _validate_dir(self, row):
         if not row[self._dir_col]:
             raise AssertionError("Species directory is required.")
 
-    def _validate_accession(self, row):
-        """Assert that the accession number exists and matches the expected nomenclature."""
-        if (
-            self._accession_col in row
-            and row[self._accession_col]
-            and not self._regex_accession.match(row[self._accession_col])
-        ):
-            raise AssertionError(
-                "Accession numbers must match %s." % self._regex_accession
-            )
-
-    def _validate_name(self, row):
-        """Assert that the assembly name is non-empty and has no space."""
-        if not row[self._name_col]:
-            raise AssertionError("Assembly name is required.")
-        if " " in row[self._name_col]:
-            raise AssertionError("Accession names must not contain whitespace.")
-
     def validate_unique_assemblies(self):
         """
         Assert that the assembly parameters are unique.
         """
         if len(self._seen) != len(self.modified):
-            raise AssertionError(
-                "The pair of species directories and assembly names must be unique."
-            )
+            raise AssertionError("The pair of species directories and assembly names must be unique.")
+
+    def _validate_fasta(self, row):
+        """Assert that the fasta path is not only white space."""
+        if set(row[self._fasta_col]) == set(" "):
+            raise AssertionError("Paths cannot only be whitespace.")
 
 
 def read_head(handle, num_lines=10):
@@ -129,9 +108,6 @@ def sniff_format(handle):
     peek = read_head(handle)
     handle.seek(0)
     sniffer = csv.Sniffer()
-    # if not sniffer.has_header(peek):
-    #     logger.critical(f"The given sample sheet does not appear to contain a header.")
-    #     sys.exit(1)
     dialect = sniffer.sniff(peek)
     return dialect
 
@@ -151,22 +127,21 @@ def check_samplesheet(file_in, file_out):
     Example:
         This function checks that the samplesheet follows the following structure::
 
-            species_dir,assembly_name
-            darwin/data/fungi/Laetiporus_sulphureus,gfLaeSulp1.1
-            darwin/data/mammals/Meles_meles,mMelMel3.2_paternal_haplotype
+            outdir,fasta
+            Asterias_rubens/eAstRub1.3,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/459/465/GCA_902459465.3_eAstRub1.3/GCA_902459465.3_eAstRub1.3_genomic.fna.gz
+            Osmia_bicornis/iOsmBic2.1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/907/164/935/GCA_907164935.1_iOsmBic2.1/GCA_907164935.1_iOsmBic2.1_genomic.fna.gz
     """
     required_columns = {
-        "species_dir",
-        "assembly_name",
+        "outdir",
+        "fasta",
     }
     # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
     with file_in.open(newline="") as in_handle:
         reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle))
         # Validate the existence of the expected header columns.
         if not required_columns.issubset(reader.fieldnames):
-            logger.critical(
-                f"The sample sheet **must** contain the column headers: {', '.join(required_columns)}."
-            )
+            req_cols = ", ".join(required_columns)
+            logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.")
             sys.exit(1)
         # Validate each row.
         checker = RowChecker()
diff --git a/conf/base.config b/conf/base.config
index bccacdb..042878b 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -6,7 +6,7 @@
 
 process {
 
-    errorStrategy = { task.exitStatus in [130,143,137,104,134,139] ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 2
     maxErrors     = '-1'
 
@@ -16,12 +16,18 @@ process {
     memory = { check_max( 50.MB * task.attempt, 'memory' ) }
     time   = { check_max( 30.min * task.attempt, 'time' ) }
 
+    // tabix needs pointers to the sequences in memory
+    withName: '.*:.*:FASTA_WINDOWS:TABIX_TABIX_.*' {
+        // 50 MB per 25,000 sequences
+        memory = { check_max( 50.MB * task.attempt * Math.ceil(meta.n_sequences / 25000), 'memory' ) }
+    }
+
     // fasta_windows takes more memory on larger genomes
     withName: 'FASTAWINDOWS' {
         // 1 CPU per 1 Gbp
         cpus   = { check_max( Math.ceil(fasta.size() / 1000000000), 'cpus' ) }
-        // 250 MB per 100 Mbp
-        memory = { check_max( 250.MB * task.attempt * Math.ceil(fasta.size() / 100000000), 'memory' ) }
+        // 100 MB per 45 Mbp
+        memory = { check_max( 100.MB * task.attempt * Math.ceil(fasta.size() / 45000000), 'memory' ) }
     }
 
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
diff --git a/conf/modules.config b/conf/modules.config
index c72226c..3fd46c6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -14,7 +14,7 @@ process {
 
     withName: '.*:.*:.*:TABIX_.*' {
         publishDir = [
-            path: { "${meta.analysis_dir}/${meta.analysis_subdir}" },
+            path: { "${meta.outdir}/${meta.analysis_subdir}" },
             mode: 'copy',
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/docs/output.md b/docs/output.md
index 8877fcc..e52d543 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -96,7 +96,7 @@ Additionally, these frequencies are extracted in bedGraph files:
 
 ### Pipeline information
 
-- `pipeline_info/`
+- `pipeline_info/sequencecomposition/`
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
diff --git a/docs/usage.md b/docs/usage.md
index 18b1df7..ada3aac 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1,5 +1,9 @@
 # sanger-tol/sequencecomposition: Usage
 
+## :warning: Please read this documentation on the nf-core website: [https://pipelines.tol.sanger.ac.uk/sequencecomposition/usage](https://pipelines.tol.sanger.ac.uk/sequencecomposition/usage)
+
+> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
+
 ## Introduction
 
 The pipeline takes a Fasta file, and computes all the sequence composition metrics on it.
@@ -31,6 +35,26 @@ work                # Directory containing the nextflow working files
 # Other nextflow hidden files, eg. history of pipeline runs and old logs.
 ```
 
+If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file.
+
+Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
+
+> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+> The above pipeline run specified with a params file in yaml format:
+
+```bash
+nextflow run sanger-tol/sequencecomposition -profile docker -params-file params.yaml
+```
+
+with `params.yaml` containing:
+
+```yaml
+fasta: "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/927/399/515/GCA_927399515.1_gfLaeSulp1.1/GCA_927399515.1_gfLaeSulp1.1_genomic.fna.gz"
+outdir: "./results/"
+```
+
+You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
+
 ## Bulk download
 
 The pipeline can download multiple assemblies at once, by providing them in a `.csv` file through the `--input` parameter.
@@ -40,19 +64,18 @@ It has to be a comma-separated file with 2 columns, and a header row as shown in
 nextflow run sanger-tol/sequencecomposition --input '[path to samplesheet file]' --outdir <OUTDIR>
 ```
 
-The values in the file are used to make up the paths under which the Fasta files can be found,
-and the outputs be written.
+The values in the file are used to make up the `--fasta` and `--outdir` parameters.
 
 ```console
-species_dir,assembly_name
-darwin/data/fungi/Laetiporus_sulphureus,gfLaeSulp1.1
-darwin/data/mammals/Meles_meles,mMelMel3.2_paternal_haplotype
+outdir,fasta
+Laetiporus_sulphureus/gfLaeSulp1.1,/path/to/gfLaeSulp1.1.fasta
+Meles_meles/mMelMel3.2_paternal_haplotype,/path/to/mMelMel3.2_paternal_haplotype.fasta
 ```
 
-| Column          | Description                                                                                   |
-| --------------- | --------------------------------------------------------------------------------------------- |
-| `species_dir`   | Base directory of that species, which is expected to comply with the ToL directory structure. |
-| `assembly_name` | Name of the assembly, as on the NCBI website, e.g. `gfLaeSulp1.1`.                            |
+| Column   | Description                                                                                                                                     |
+| -------- | ----------------------------------------------------------------------------------------------------------------------------------------------- |
+| `outdir` | Output directory for this pipeline (evaluated from `--outdir` if a relative path). Analysis results are in a sub-directory `gene/base_content`. |
+| `fasta`  | Path to the Fasta file of this assembly (can be a remote file).                                                                                 |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
@@ -68,9 +91,13 @@ nextflow pull sanger-tol/sequencecomposition
 
 It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
-First, go to the [sanger-tol/sequencecomposition releases page](https://github.com/sanger-tol/sequencecomposition/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`.
+First, go to the [sanger-tol/sequencecomposition releases page](https://github.com/sanger-tol/sequencecomposition/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
+
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
+To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+
+> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
 
 ## Core Nextflow arguments
 
@@ -80,7 +107,7 @@ This version number will be logged in reports when you run the pipeline, so that
 
 Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
 
-Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. When using Biocontainers, most of these software packaging methods pull Docker containers from quay.io except for Singularity which directly downloads Singularity images via https hosted by the [Galaxy project](https://depot.galaxyproject.org/singularity/) and Conda which downloads and installs software locally from [Bioconda](https://bioconda.github.io/).
+Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
 > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
@@ -89,7 +116,7 @@ The pipeline also dynamically loads configurations from [https://github.com/nf-c
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
-If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended.
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
 
 - `docker`
   - A generic configuration profile to be used with [Docker](https://docker.com/)
@@ -101,8 +128,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
 - `charliecloud`
   - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+- `apptainer`
+  - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `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 or Charliecloud.
+  - 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.
 - `test`
   - A profile with a minimal configuration for automated testing
   - Corresponds to defining the assembly to download as command-line parameters so needs no other parameters
@@ -126,96 +155,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
 
-For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue:
-
-```console
-[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1)
-Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)'
+To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
 
-Caused by:
-    Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137)
+### Custom Containers
 
-Command executed:
-    STAR \
-        --genomeDir star \
-        --readFilesIn WT_REP1_trimmed.fq.gz  \
-        --runThreadN 2 \
-        --outFileNamePrefix WT_REP1. \
-        <TRUNCATED>
+In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
 
-Command exit status:
-    137
+To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
 
-Command output:
-    (empty)
+### Custom Tool Arguments
 
-Command error:
-    .command.sh: line 9:  30 Killed    STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. <TRUNCATED>
-Work dir:
-    /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb
+A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default.
 
-Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-```
-
-To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN).
-We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/software/star/align/main.nf`.
-If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9).
-The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements.
-The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB.
-Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB.
-The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
-
-```nextflow
-process {
-    withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' {
-        memory = 100.GB
-    }
-}
-```
-
-> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden.
->
-> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly.
-
-### Updating containers
-
-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. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`.
-
-1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19)
-2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags)
-3. Create the custom config accordingly:
-
-   - For Docker:
-
-     ```nextflow
-     process {
-         withName: PANGOLIN {
-             container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
-         }
-     }
-     ```
-
-   - For Singularity:
-
-     ```nextflow
-     process {
-         withName: PANGOLIN {
-             container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
-         }
-     }
-     ```
-
-   - For Conda:
-
-     ```nextflow
-     process {
-         withName: PANGOLIN {
-             conda = 'bioconda::pangolin=3.0.5'
-         }
-     }
-     ```
-
-> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch.
+To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website.
 
 ### nf-core/configs
 
@@ -225,6 +177,14 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
+## Azure Resource Requests
+
+To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
+We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
+
+Note that the choice of VM size depends on your quota and the overall workload during the analysis.
+For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
+
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
index b3d092f..9b34804 100755
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -2,6 +2,7 @@
 // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
 //
 
+import nextflow.Nextflow
 import org.everit.json.schema.Schema
 import org.everit.json.schema.loader.SchemaLoader
 import org.everit.json.schema.ValidationException
@@ -46,7 +47,6 @@ class NfcoreSchema {
             'quiet',
             'syslog',
             'v',
-            'version',
 
             // Options for `nextflow run` command
             'ansi',
@@ -84,6 +84,7 @@ class NfcoreSchema {
             'stub-run',
             'test',
             'w',
+            'with-apptainer',
             'with-charliecloud',
             'with-conda',
             'with-dag',
@@ -178,7 +179,7 @@ class NfcoreSchema {
         }
 
         if (has_error) {
-            System.exit(1)
+            Nextflow.error('Exiting!')
         }
     }
 
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 78966e9..85785ef 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -32,6 +32,25 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Generate version string
+    //
+    public static String version(workflow) {
+        String version_string = ""
+
+        if (workflow.manifest.version) {
+            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+            version_string += "${prefix_v}${workflow.manifest.version}"
+        }
+
+        if (workflow.commitId) {
+            def git_shortsha = workflow.commitId.substring(0, 7)
+            version_string += "-g${git_shortsha}"
+        }
+
+        return version_string
+    }
+
     //
     // Construct and send completion email
     //
@@ -61,7 +80,7 @@ class NfcoreTemplate {
         misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
         def email_fields = [:]
-        email_fields['version']      = workflow.manifest.version
+        email_fields['version']      = NfcoreTemplate.version(workflow)
         email_fields['runName']      = workflow.runName
         email_fields['success']      = workflow.success
         email_fields['dateComplete'] = workflow.complete
@@ -113,7 +132,7 @@ class NfcoreTemplate {
         }
 
         // Write summary e-mail HTML to a file
-        def output_d = new File("${params.outdir}/pipeline_info/")
+        def output_d = new File("${params.tracedir}/")
         if (!output_d.exists()) {
             output_d.mkdirs()
         }
@@ -123,6 +142,64 @@ class NfcoreTemplate {
         output_tf.withWriter { w -> w << email_txt }
     }
 
+    //
+    // Construct and send a notification to a web server as JSON
+    // e.g. Microsoft Teams and Slack
+    //
+    public static void IM_notification(workflow, params, summary_params, projectDir, log) {
+        def hook_url = params.hook_url
+
+        def summary = [:]
+        for (group in summary_params.keySet()) {
+            summary << summary_params[group]
+        }
+
+        def misc_fields = [:]
+        misc_fields['start']                                = workflow.start
+        misc_fields['complete']                             = workflow.complete
+        misc_fields['scriptfile']                           = workflow.scriptFile
+        misc_fields['scriptid']                             = workflow.scriptId
+        if (workflow.repository) misc_fields['repository']  = workflow.repository
+        if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
+        if (workflow.revision)   misc_fields['revision']    = workflow.revision
+        misc_fields['nxf_version']                          = workflow.nextflow.version
+        misc_fields['nxf_build']                            = workflow.nextflow.build
+        misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+
+        def msg_fields = [:]
+        msg_fields['version']      = NfcoreTemplate.version(workflow)
+        msg_fields['runName']      = workflow.runName
+        msg_fields['success']      = workflow.success
+        msg_fields['dateComplete'] = workflow.complete
+        msg_fields['duration']     = workflow.duration
+        msg_fields['exitStatus']   = workflow.exitStatus
+        msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+        msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
+        msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
+        msg_fields['projectDir']   = workflow.projectDir
+        msg_fields['summary']      = summary << misc_fields
+
+        // Render the JSON template
+        def engine       = new groovy.text.GStringTemplateEngine()
+        // Different JSON depending on the service provider
+        // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+        def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+        def hf            = new File("$projectDir/assets/${json_path}")
+        def json_template = engine.createTemplate(hf).make(msg_fields)
+        def json_message  = json_template.toString()
+
+        // POST
+        def post = new URL(hook_url).openConnection();
+        post.setRequestMethod("POST")
+        post.setDoOutput(true)
+        post.setRequestProperty("Content-Type", "application/json")
+        post.getOutputStream().write(json_message.getBytes("UTF-8"));
+        def postRC = post.getResponseCode();
+        if (! postRC.equals(200)) {
+            log.warn(post.getErrorStream().getText());
+        }
+    }
+
     //
     // Print pipeline summary on completion
     //
@@ -132,7 +209,7 @@ class NfcoreTemplate {
             if (workflow.stats.ignoredCount == 0) {
                 log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
             } else {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
             }
         } else {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
@@ -220,18 +297,19 @@ class NfcoreTemplate {
     //
     public static String logo(workflow, monochrome_logs) {
         Map colors = logColours(monochrome_logs)
+        String workflow_version = NfcoreTemplate.version(workflow)
         String.format(
             """\n
             ${dashedLine(monochrome_logs)}
-            ${colors.blue}   _____                                ${colors.green} _______   ${colors.red} _${colors.reset}
-            ${colors.blue}  / ____|                               ${colors.green}|__   __|  ${colors.red}| |${colors.reset}
-            ${colors.blue} | (___   __ _ _ __   __ _  ___ _ __ ${colors.reset}______${colors.green}| |${colors.yellow} ___ ${colors.red}| |${colors.reset}
-            ${colors.blue}  \\___ \\ / _` | '_ \\ / _` |/ _ \\ '__|${colors.reset}______${colors.green}| |${colors.yellow}/ _ \\${colors.red}| |${colors.reset}
-            ${colors.blue}  ____) | (_| | | | | (_| |  __/ |         ${colors.green}| |${colors.yellow} (_) ${colors.red}| |____${colors.reset}
-            ${colors.blue} |_____/ \\__,_|_| |_|\\__, |\\___|_|         ${colors.green}|_|${colors.yellow}\\___/${colors.red}}|______|${colors.reset}
+            ${colors.blue}   _____                               ${colors.green} _______   ${colors.red} _${colors.reset}
+            ${colors.blue}  / ____|                              ${colors.green}|__   __|  ${colors.red}| |${colors.reset}
+            ${colors.blue} | (___   __ _ _ __   __ _  ___ _ __ ${colors.reset} ___ ${colors.green}| |${colors.yellow} ___ ${colors.red}| |${colors.reset}
+            ${colors.blue}  \\___ \\ / _` | '_ \\ / _` |/ _ \\ '__|${colors.reset}|___|${colors.green}| |${colors.yellow}/ _ \\${colors.red}| |${colors.reset}
+            ${colors.blue}  ____) | (_| | | | | (_| |  __/ |        ${colors.green}| |${colors.yellow} (_) ${colors.red}| |____${colors.reset}
+            ${colors.blue} |_____/ \\__,_|_| |_|\\__, |\\___|_|        ${colors.green}|_|${colors.yellow}\\___/${colors.red}|______|${colors.reset}
             ${colors.blue}                      __/ |${colors.reset}
             ${colors.blue}                     |___/${colors.reset}
-            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+            ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
             ${dashedLine(monochrome_logs)}
             """.stripIndent()
         )
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
old mode 100755
new mode 100644
index 28567bd..13cb02d
--- a/lib/Utils.groovy
+++ b/lib/Utils.groovy
@@ -21,19 +21,26 @@ class Utils {
         }
 
         // Check that all channels are present
-        def required_channels = ['conda-forge', 'bioconda', 'defaults']
-        def conda_check_failed = !required_channels.every { ch -> ch in channels }
+        // This channel list is ordered by required channel priority.
+        def required_channels_in_order = ['conda-forge', 'bioconda']
+        def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
         // Check that they are in the right order
-        conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
-        conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
+        def channel_priority_violation = false
+        def n = required_channels_in_order.size()
+        for (int i = 0; i < n - 1; i++) {
+            channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+        }
 
-        if (conda_check_failed) {
+        if (channels_missing | channel_priority_violation) {
             log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                 "  There is a problem with your Conda configuration!\n\n" +
                 "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-                "  Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
-                "  NB: The order of the channels matters!\n" +
+                "  Please refer to https://bioconda.github.io/\n" +
+                "  The observed channel order is \n" +
+                "  ${channels}\n" +
+                "  but the following channel order is required:\n" +
+                "  ${required_channels_in_order}\n" +
                 "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         }
     }
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 8a4f10f..e72fa10 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -2,6 +2,8 @@
 // This file holds several functions specific to the main.nf workflow in the sanger-tol/sequencecomposition pipeline
 //
 
+import nextflow.Nextflow
+
 class WorkflowMain {
 
     //
@@ -10,7 +12,7 @@ class WorkflowMain {
     public static String citation(workflow) {
         return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
             "* The pipeline\n" +
-            "  https://doi.org/10.5281/zenodo.7155169\n\n" +
+            "  https://doi.org/10.5281/zenodo.7155168\n\n" +
             "* The nf-core framework\n" +
             "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
             "* Software dependencies\n" +
@@ -18,9 +20,9 @@ class WorkflowMain {
     }
 
     //
-    // Print help to screen if required
+    // Generate help string
     //
-    public static String help(workflow, params, log) {
+    public static String help(workflow, params) {
         def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --fasta reference.fa -profile docker"
         def help_string = ''
         help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
@@ -31,9 +33,9 @@ class WorkflowMain {
     }
 
     //
-    // Print parameter summary log to screen
+    // Generate parameter summary log string
     //
-    public static String paramsSummaryLog(workflow, params, log) {
+    public static String paramsSummaryLog(workflow, params) {
         def summary_log = ''
         summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
         summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
@@ -48,24 +50,30 @@ class WorkflowMain {
     public static void initialise(workflow, params, log) {
         // Print help to screen if required
         if (params.help) {
-            log.info help(workflow, params, log)
+            log.info help(workflow, params)
             System.exit(0)
         }
 
-        // Validate workflow parameters via the JSON schema
-        if (params.validate_params) {
-            NfcoreSchema.validateParameters(workflow, params, log)
+        // Print workflow version and exit on --version
+        if (params.version) {
+            String workflow_version = NfcoreTemplate.version(workflow)
+            log.info "${workflow.manifest.name} ${workflow_version}"
+            System.exit(0)
         }
 
         // Print parameter summary log to screen
+        log.info paramsSummaryLog(workflow, params)
 
-        log.info paramsSummaryLog(workflow, params, log)
+        // Validate workflow parameters via the JSON schema
+        if (params.validate_params) {
+            NfcoreSchema.validateParameters(workflow, params, log)
+        }
 
         // Check that a -profile or Nextflow config has been provided to run the pipeline
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
         // Check that conda channels are set-up correctly
-        if (params.enable_conda) {
+        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
             Utils.checkCondaChannels(log)
         }
 
diff --git a/lib/WorkflowSequencecomposition.groovy b/lib/WorkflowSequencecomposition.groovy
index 83ff215..4197402 100755
--- a/lib/WorkflowSequencecomposition.groovy
+++ b/lib/WorkflowSequencecomposition.groovy
@@ -2,6 +2,8 @@
 // This file holds several functions specific to the workflow/sequencecomposition.nf in the sanger-tol/sequencecomposition pipeline
 //
 
+import nextflow.Nextflow
+
 class WorkflowSequencecomposition {
 
     //
@@ -13,15 +15,16 @@ class WorkflowSequencecomposition {
         if (params.input) {
             def f = new File(params.input);
             if (!f.exists()) {
-                log.error "'${params.input}' doesn't exist"
-                System.exit(1)
+                Nextflow.error "'${params.input}' doesn't exist"
             }
         } else {
-            if (!params.fasta || !params.outdir) {
-                log.error "Either --input, or --fasta and--outdir must be provided"
-                System.exit(1)
+            if (!params.fasta) {
+                Nextflow.error "Either --input or --fasta must be provided"
             }
         }
+        if (!params.outdir) {
+            Nextflow.error "--outdir is mandatory"
+        }
     }
 
 }
diff --git a/modules.json b/modules.json
index bd678fb..17b2131 100644
--- a/modules.json
+++ b/modules.json
@@ -2,29 +2,43 @@
     "name": "sanger-tol/sequencecomposition",
     "homePage": "https://github.com/sanger-tol/sequencecomposition",
     "repos": {
-        "nf-core/modules": {
-            "git_url": "https://github.com/nf-core/modules.git",
+        "https://github.com/nf-core/modules.git": {
             "modules": {
-                "custom/dumpsoftwareversions": {
-                    "branch": "master",
-                    "git_sha": "82501fe6d0d12614db67751d30af98d16e63dc59"
-                },
-                "fastawindows": {
-                    "branch": "master",
-                    "git_sha": "4f78d40b1168d242d4c0db8302e41044b2935964"
-                },
-                "gunzip": {
-                    "branch": "master",
-                    "git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb"
-                },
-                "tabix/bgzip": {
-                    "branch": "master",
-                    "git_sha": "31c0b49f6527ef196e89eca49a36af2de71711f8"
-                },
-                "tabix/tabix": {
-                    "branch": "master",
-                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
+                "nf-core": {
+                    "custom/dumpsoftwareversions": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
+                    "custom/getchromsizes": {
+                        "branch": "master",
+                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
+                        "installed_by": ["modules"]
+                    },
+                    "fastawindows": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
+                    "gunzip": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
+                    "tabix/bgzip": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
+                    "tabix/tabix": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {}
             }
         }
     }
diff --git a/modules/local/extract_column.nf b/modules/local/extract_column.nf
index cfbd983..da2128e 100644
--- a/modules/local/extract_column.nf
+++ b/modules/local/extract_column.nf
@@ -2,10 +2,10 @@ process EXTRACT_COLUMN {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.1" : null)
+    conda "conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'biocontainers/python:3.9--1' }"
 
     input:
     tuple val(meta), path(tsv)
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index c7fd910..50ba637 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda "conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'quay.io/biocontainers/python:3.8.3' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'biocontainers/python:3.9--1' }"
 
     input:
     path samplesheet
diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
new file mode 100644
index 0000000..9d79af9
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::multiqc=1.20
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
similarity index 74%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
rename to modules/nf-core/custom/dumpsoftwareversions/main.nf
index cebb6e0..105f926 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.20--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
new file mode 100644
index 0000000..dc1e412
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
@@ -0,0 +1,43 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: custom_dumpsoftwareversions
+description: Custom module used to dump software versions within the nf-core pipeline
+  template
+keywords:
+  - custom
+  - dump
+  - version
+tools:
+  - custom:
+      description: Custom module used to dump software versions within the nf-core pipeline
+        template
+      homepage: https://github.com/nf-core/tools
+      documentation: https://github.com/nf-core/tools
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - versions:
+        type: file
+        description: YML file containing software versions
+        pattern: "*.yml"
+output:
+  - yml:
+      - software_versions.yml:
+          type: file
+          description: Standard YML file containing software versions
+          pattern: "software_versions.yml"
+  - mqc_yml:
+      - software_versions_mqc.yml:
+          type: file
+          description: MultiQC custom content YML file containing software versions
+          pattern: "software_versions_mqc.yml"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@grst"
+maintainers:
+  - "@drpatelh"
+  - "@grst"
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
new file mode 100755
index 0000000..b83b32c
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+
+
+"""Provide functions to merge multiple versions.yml files."""
+
+import platform
+from textwrap import dedent
+
+import yaml
+
+
+def _make_versions_html(versions):
+    """Generate a tabular HTML output of all versions for MultiQC."""
+    html = [
+        dedent(
+            """\\
+            <style>
+            #nf-core-versions tbody:nth-child(even) {
+                background-color: #f2f2f2;
+            }
+            </style>
+            <table class="table" style="width:100%" id="nf-core-versions">
+                <thead>
+                    <tr>
+                        <th> Process Name </th>
+                        <th> Software </th>
+                        <th> Version  </th>
+                    </tr>
+                </thead>
+            """
+        )
+    ]
+    for process, tmp_versions in sorted(versions.items()):
+        html.append("<tbody>")
+        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
+            html.append(
+                dedent(
+                    f"""\\
+                    <tr>
+                        <td><samp>{process if (i == 0) else ''}</samp></td>
+                        <td><samp>{tool}</samp></td>
+                        <td><samp>{version}</samp></td>
+                    </tr>
+                    """
+                )
+            )
+        html.append("</tbody>")
+    html.append("</table>")
+    return "\\n".join(html)
+
+
+def main():
+    """Load all version files and generate merged output."""
+    versions_this_module = {}
+    versions_this_module["${task.process}"] = {
+        "python": platform.python_version(),
+        "yaml": yaml.__version__,
+    }
+
+    with open("$versions") as f:
+        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+
+    # aggregate versions by the module name (derived from fully-qualified process name)
+    versions_by_module = {}
+    for process, process_versions in versions_by_process.items():
+        module = process.split(":")[-1]
+        try:
+            if versions_by_module[module] != process_versions:
+                raise AssertionError(
+                    "We assume that software versions are the same between all modules. "
+                    "If you see this error-message it means you discovered an edge-case "
+                    "and should open an issue in nf-core/tools. "
+                )
+        except KeyError:
+            versions_by_module[module] = process_versions
+
+    versions_by_module["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
+        "$workflow.manifest.name": "$workflow.manifest.version",
+    }
+
+    versions_mqc = {
+        "id": "software_versions",
+        "section_name": "${workflow.manifest.name} Software Versions",
+        "section_href": "https://github.com/${workflow.manifest.name}",
+        "plot_type": "html",
+        "description": "are collected at run time from the software output.",
+        "data": _make_versions_html(versions_by_module),
+    }
+
+    with open("software_versions.yml", "w") as f:
+        yaml.dump(versions_by_module, f, default_flow_style=False)
+    with open("software_versions_mqc.yml", "w") as f:
+        yaml.dump(versions_mqc, f, default_flow_style=False)
+
+    with open("versions.yml", "w") as f:
+        yaml.dump(versions_this_module, f, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
new file mode 100644
index 0000000..b1e1630
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
@@ -0,0 +1,43 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS"
+    script "../main.nf"
+    process "CUSTOM_DUMPSOFTWAREVERSIONS"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom"
+    tag "dumpsoftwareversions"
+    tag "custom/dumpsoftwareversions"
+
+    test("Should run without failures") {
+        when {
+            process {
+                """
+                def tool1_version = '''
+                TOOL1:
+                    tool1: 0.11.9
+                '''.stripIndent()
+
+                def tool2_version = '''
+                TOOL2:
+                    tool2: 1.9
+                '''.stripIndent()
+
+                input[0] = Channel.of(tool1_version, tool2_version).collectFile()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    file(process.out.mqc_yml[0]).readLines()[0..10],
+                    file(process.out.yml[0]).readLines()[0..7]
+                    ).match()
+                }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
new file mode 100644
index 0000000..5f59a93
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
@@ -0,0 +1,33 @@
+{
+    "Should run without failures": {
+        "content": [
+            [
+                "versions.yml:md5,76d454d92244589d32455833f7c1ba6d"
+            ],
+            [
+                "data: \"<style>\\n#nf-core-versions tbody:nth-child(even) {\\n    background-color: #f2f2f2;\\n\\",
+                "  }\\n</style>\\n<table class=\\\"table\\\" style=\\\"width:100%\\\" id=\\\"nf-core-versions\\\"\\",
+                "  >\\n    <thead>\\n        <tr>\\n            <th> Process Name </th>\\n            <th>\\",
+                "  \\ Software </th>\\n            <th> Version  </th>\\n        </tr>\\n    </thead>\\n\\",
+                "  \\n<tbody>\\n<tr>\\n    <td><samp>CUSTOM_DUMPSOFTWAREVERSIONS</samp></td>\\n    <td><samp>python</samp></td>\\n\\",
+                "  \\    <td><samp>3.11.7</samp></td>\\n</tr>\\n\\n<tr>\\n    <td><samp></samp></td>\\n \\",
+                "  \\   <td><samp>yaml</samp></td>\\n    <td><samp>5.4.1</samp></td>\\n</tr>\\n\\n</tbody>\\n\\",
+                "  <tbody>\\n<tr>\\n    <td><samp>TOOL1</samp></td>\\n    <td><samp>tool1</samp></td>\\n\\",
+                "  \\    <td><samp>0.11.9</samp></td>\\n</tr>\\n\\n</tbody>\\n<tbody>\\n<tr>\\n    <td><samp>TOOL2</samp></td>\\n\\",
+                "  \\    <td><samp>tool2</samp></td>\\n    <td><samp>1.9</samp></td>\\n</tr>\\n\\n</tbody>\\n\\",
+                "  <tbody>\\n<tr>\\n    <td><samp>Workflow</samp></td>\\n    <td><samp>Nextflow</samp></td>\\n\\"
+            ],
+            [
+                "CUSTOM_DUMPSOFTWAREVERSIONS:",
+                "  python: 3.11.7",
+                "  yaml: 5.4.1",
+                "TOOL1:",
+                "  tool1: 0.11.9",
+                "TOOL2:",
+                "  tool2: '1.9'",
+                "Workflow:"
+            ]
+        ],
+        "timestamp": "2024-01-09T23:01:18.710682"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
new file mode 100644
index 0000000..405aa24
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
@@ -0,0 +1,2 @@
+custom/dumpsoftwareversions:
+  - modules/nf-core/custom/dumpsoftwareversions/**
diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml
new file mode 100644
index 0000000..2bcd47e
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/environment.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
new file mode 100644
index 0000000..d8c7405
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/main.nf
@@ -0,0 +1,47 @@
+process CUSTOM_GETCHROMSIZES {
+    tag "$fasta"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path ("*.sizes"), emit: sizes
+    tuple val(meta), path ("*.fai")  , emit: fai
+    tuple val(meta), path ("*.gzi")  , emit: gzi, optional: true
+    path  "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    samtools faidx $fasta
+    cut -f 1,2 ${fasta}.fai > ${fasta}.sizes
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${fasta}.fai
+    touch ${fasta}.sizes
+    if [[ "${fasta.extension}" == "gz" ]]; then
+        touch ${fasta}.gzi
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/custom/getchromsizes/meta.yml b/modules/nf-core/custom/getchromsizes/meta.yml
new file mode 100644
index 0000000..2a0e8da
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/meta.yml
@@ -0,0 +1,69 @@
+name: custom_getchromsizes
+description: Generates a FASTA file of chromosome sizes and a fasta index file
+keywords:
+  - fasta
+  - chromosome
+  - indexing
+tools:
+  - samtools:
+      description: Tools for dealing with SAM, BAM and CRAM files
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/samtools.html
+      tool_dev_url: https://github.com/samtools/samtools
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: FASTA file
+        pattern: "*.{fa,fasta,fna,fas}"
+output:
+  - sizes:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.sizes":
+          type: file
+          description: File containing chromosome lengths
+          pattern: "*.{sizes}"
+  - fai:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.fai":
+          type: file
+          description: FASTA index file
+          pattern: "*.{fai}"
+  - gzi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.gzi":
+          type: file
+          description: Optional gzip index file for compressed inputs
+          pattern: "*.gzi"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@tamara-hodgetts"
+  - "@chris-cheshire"
+  - "@muffato"
+maintainers:
+  - "@tamara-hodgetts"
+  - "@chris-cheshire"
+  - "@muffato"
diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test b/modules/nf-core/custom/getchromsizes/tests/main.nf.test
new file mode 100644
index 0000000..2f741a4
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test
@@ -0,0 +1,99 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_GETCHROMSIZES"
+    script "../main.nf"
+    process "CUSTOM_GETCHROMSIZES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom"
+    tag "custom/getchromsizes"
+
+    test("test_custom_getchromsizes") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_custom_getchromsizes_bgzip") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_custom_getchromsizes - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_custom_getchromsizes_bgzip - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap
new file mode 100644
index 0000000..d2072e2
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap
@@ -0,0 +1,242 @@
+{
+    "test_custom_getchromsizes_bgzip - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-18T10:11:37.459094476"
+    },
+    "test_custom_getchromsizes": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-18T10:11:01.526301351"
+    },
+    "test_custom_getchromsizes_bgzip": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-18T10:11:14.32456385"
+    },
+    "test_custom_getchromsizes - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-18T10:11:26.505487624"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/custom/getchromsizes/tests/tags.yml b/modules/nf-core/custom/getchromsizes/tests/tags.yml
new file mode 100644
index 0000000..d89a805
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/tests/tags.yml
@@ -0,0 +1,2 @@
+custom/getchromsizes:
+  - modules/nf-core/custom/getchromsizes/**
diff --git a/modules/nf-core/fastawindows/environment.yml b/modules/nf-core/fastawindows/environment.yml
new file mode 100644
index 0000000..6775fb2
--- /dev/null
+++ b/modules/nf-core/fastawindows/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fasta_windows=0.2.4
diff --git a/modules/nf-core/modules/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf
similarity index 66%
rename from modules/nf-core/modules/fastawindows/main.nf
rename to modules/nf-core/fastawindows/main.nf
index d25573f..bf5a3b7 100644
--- a/modules/nf-core/modules/fastawindows/main.nf
+++ b/modules/nf-core/fastawindows/main.nf
@@ -2,10 +2,10 @@ process FASTAWINDOWS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fasta_windows:0.2.4--hec16e2b_0':
-        'quay.io/biocontainers/fasta_windows:0.2.4--hec16e2b_0' }"
+        'biocontainers/fasta_windows:0.2.4--hec16e2b_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -32,6 +32,25 @@ process FASTAWINDOWS {
         --fasta $fasta \\
         --output ${prefix}
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fasta_windows: \$(fasta_windows --version | cut -d' ' -f3)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p fw_out
+
+    touch fw_out/${prefix}_freq_windows.tsv
+    touch fw_out/${prefix}_mononuc_windows.tsv
+    touch fw_out/${prefix}_dinuc_windows.tsv
+    touch fw_out/${prefix}_trinuc_windows.tsv
+    touch fw_out/${prefix}_tetranuc_windows.tsv
+
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fasta_windows: \$(fasta_windows --version | cut -d' ' -f3)
diff --git a/modules/nf-core/fastawindows/meta.yml b/modules/nf-core/fastawindows/meta.yml
new file mode 100644
index 0000000..f8ee004
--- /dev/null
+++ b/modules/nf-core/fastawindows/meta.yml
@@ -0,0 +1,85 @@
+name: "fastawindows"
+description: Quickly compute statistics over a fasta file in windows.
+keywords:
+  - genome
+  - fasta
+  - tsv
+  - bed
+tools:
+  - "fastawindows":
+      description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal
+        level genome assemblies. The executable takes a fasta formatted file and calculates
+        some statistics of interest in windows"
+      homepage: "https://github.com/tolkit/fasta_windows"
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: FASTA file
+        pattern: "*.{fa,fasta,fna}"
+output:
+  - freq:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - fw_out/*_freq_windows.tsv:
+          type: file
+          description: TSV file with frequencies and statistics
+          pattern: "*.{tsv}"
+  - mononuc:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - fw_out/*_mononuc_windows.tsv:
+          type: file
+          description: TSV file with mononucleotide counts
+          pattern: "*.{tsv}"
+  - dinuc:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - fw_out/*_dinuc_windows.tsv:
+          type: file
+          description: TSV file with dinucleotide counts
+          pattern: "*.{tsv}"
+  - trinuc:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - fw_out/*_trinuc_windows.tsv:
+          type: file
+          description: TSV file with trinucleotide counts
+          pattern: "*.{tsv}"
+  - tetranuc:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - fw_out/*_tetranuc_windows.tsv:
+          type: file
+          description: TSV file with tetranucleotide counts
+          pattern: "*.{tsv}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@muffato"
+maintainers:
+  - "@muffato"
diff --git a/modules/nf-core/fastawindows/tests/main.nf.test b/modules/nf-core/fastawindows/tests/main.nf.test
new file mode 100644
index 0000000..f4bea49
--- /dev/null
+++ b/modules/nf-core/fastawindows/tests/main.nf.test
@@ -0,0 +1,57 @@
+
+nextflow_process {
+
+    name "Test Process FASTAWINDOWS"
+    script "../main.nf"
+    process "FASTAWINDOWS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fastawindows"
+
+    test("test-fastawindows") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-fastawindows-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/fastawindows/tests/main.nf.test.snap b/modules/nf-core/fastawindows/tests/main.nf.test.snap
new file mode 100644
index 0000000..f3474d3
--- /dev/null
+++ b/modules/nf-core/fastawindows/tests/main.nf.test.snap
@@ -0,0 +1,196 @@
+{
+    "test-fastawindows-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_freq_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_mononuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_dinuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_trinuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_tetranuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,4e46686969aa8883f8092693ebcf7dab"
+                ],
+                "dinuc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_dinuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "freq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_freq_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "mononuc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_mononuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tetranuc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_tetranuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trinuc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_trinuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4e46686969aa8883f8092693ebcf7dab"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-30T09:58:57.148076"
+    },
+    "test-fastawindows": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_freq_windows.tsv:md5,237d50ac5ec2bef3142020d569fa5765"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_mononuc_windows.tsv:md5,a1b4437d0c71d9cfd676de6bda2633f0"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_dinuc_windows.tsv:md5,696a9f2a4b2114dfbd6b414694f56a11"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_trinuc_windows.tsv:md5,dfb05b758f0474e937e2d6ba6fe46dae"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_tetranuc_windows.tsv:md5,e621537175ee8019360f8b6e8f4330b7"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,4e46686969aa8883f8092693ebcf7dab"
+                ],
+                "dinuc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_dinuc_windows.tsv:md5,696a9f2a4b2114dfbd6b414694f56a11"
+                    ]
+                ],
+                "freq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_freq_windows.tsv:md5,237d50ac5ec2bef3142020d569fa5765"
+                    ]
+                ],
+                "mononuc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_mononuc_windows.tsv:md5,a1b4437d0c71d9cfd676de6bda2633f0"
+                    ]
+                ],
+                "tetranuc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_tetranuc_windows.tsv:md5,e621537175ee8019360f8b6e8f4330b7"
+                    ]
+                ],
+                "trinuc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_trinuc_windows.tsv:md5,dfb05b758f0474e937e2d6ba6fe46dae"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4e46686969aa8883f8092693ebcf7dab"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-29T21:22:58.322943"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
new file mode 100644
index 0000000..c779485
--- /dev/null
+++ b/modules/nf-core/gunzip/environment.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::grep=3.11
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
new file mode 100644
index 0000000..5e67e3b
--- /dev/null
+++ b/modules/nf-core/gunzip/main.nf
@@ -0,0 +1,55 @@
+process GUNZIP {
+    tag "$archive"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:22.04' :
+        'nf-core/ubuntu:22.04' }"
+
+    input:
+    tuple val(meta), path(archive)
+
+    output:
+    tuple val(meta), path("$gunzip"), emit: gunzip
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args        = task.ext.args ?: ''
+    def extension   = ( archive.toString() - '.gz' ).tokenize('.')[-1]
+    def name        = archive.toString() - '.gz' - ".$extension"
+    def prefix      = task.ext.prefix ?: name
+    gunzip          = prefix + ".$extension"
+    """
+    # Not calling gunzip itself because it creates files
+    # with the original group ownership rather than the
+    # default one for that user / the work directory
+    gzip \\
+        -cd \\
+        $args \\
+        $archive \\
+        > $gunzip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args        = task.ext.args ?: ''
+    def extension   = ( archive.toString() - '.gz' ).tokenize('.')[-1]
+    def name        = archive.toString() - '.gz' - ".$extension"
+    def prefix      = task.ext.prefix ?: name
+    gunzip          = prefix + ".$extension"
+    """
+    touch $gunzip
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
new file mode 100644
index 0000000..9066c03
--- /dev/null
+++ b/modules/nf-core/gunzip/meta.yml
@@ -0,0 +1,47 @@
+name: gunzip
+description: Compresses and decompresses files.
+keywords:
+  - gunzip
+  - compression
+  - decompression
+tools:
+  - gunzip:
+      description: |
+        gzip is a file format and a software application used for file compression and decompression.
+      documentation: https://www.gnu.org/software/gzip/manual/gzip.html
+      licence: ["GPL-3.0-or-later"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Optional groovy Map containing meta information
+          e.g. [ id:'test', single_end:false ]
+    - archive:
+        type: file
+        description: File to be compressed/uncompressed
+        pattern: "*.*"
+output:
+  - gunzip:
+      - meta:
+          type: file
+          description: Compressed/uncompressed file
+          pattern: "*.*"
+      - $gunzip:
+          type: file
+          description: Compressed/uncompressed file
+          pattern: "*.*"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
+  - "@gallvp"
diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test
new file mode 100644
index 0000000..776211a
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/main.nf.test
@@ -0,0 +1,121 @@
+nextflow_process {
+
+    name "Test Process GUNZIP"
+    script "../main.nf"
+    process "GUNZIP"
+    tag "gunzip"
+    tag "modules_nfcore"
+    tag "modules"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("Should run without failures - prefix") {
+
+        config './nextflow.config'
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [ id: 'test' ],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("Should run without failures - stub") {
+
+        options '-stub'
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("Should run without failures - prefix - stub") {
+
+        options '-stub'
+        config './nextflow.config'
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [ id: 'test' ],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap
new file mode 100644
index 0000000..069967e
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/main.nf.test.snap
@@ -0,0 +1,134 @@
+{
+    "Should run without failures - prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-25T11:35:10.861293"
+    },
+    "Should run without failures - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-25T11:35:05.857145"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-10-17T15:35:37.690477896"
+    },
+    "Should run without failures - prefix": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-25T11:33:32.921739"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config
new file mode 100644
index 0000000..dec7764
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: GUNZIP {
+        ext.prefix = { "${meta.id}.xyz" }
+    }
+}
diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml
new file mode 100644
index 0000000..fd3f691
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/tags.yml
@@ -0,0 +1,2 @@
+gunzip:
+  - modules/nf-core/gunzip/**
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
deleted file mode 100644
index 60b546a..0000000
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: custom_dumpsoftwareversions
-description: Custom module used to dump software versions within the nf-core pipeline template
-keywords:
-  - custom
-  - version
-tools:
-  - custom:
-      description: Custom module used to dump software versions within the nf-core pipeline template
-      homepage: https://github.com/nf-core/tools
-      documentation: https://github.com/nf-core/tools
-      licence: ["MIT"]
-input:
-  - versions:
-      type: file
-      description: YML file containing software versions
-      pattern: "*.yml"
-
-output:
-  - yml:
-      type: file
-      description: Standard YML file containing software versions
-      pattern: "software_versions.yml"
-  - mqc_yml:
-      type: file
-      description: MultiQC custom content YML file containing software versions
-      pattern: "software_versions_mqc.yml"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@drpatelh"
-  - "@grst"
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
deleted file mode 100644
index 7c2abfa..0000000
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ /dev/null
@@ -1,90 +0,0 @@
-#!/usr/bin/env python
-
-import yaml
-import platform
-from textwrap import dedent
-
-
-def _make_versions_html(versions):
-    html = [
-        dedent(
-            """\\
-            <style>
-            #nf-core-versions tbody:nth-child(even) {
-                background-color: #f2f2f2;
-            }
-            </style>
-            <table class="table" style="width:100%" id="nf-core-versions">
-                <thead>
-                    <tr>
-                        <th> Process Name </th>
-                        <th> Software </th>
-                        <th> Version  </th>
-                    </tr>
-                </thead>
-            """
-        )
-    ]
-    for process, tmp_versions in sorted(versions.items()):
-        html.append("<tbody>")
-        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
-            html.append(
-                dedent(
-                    f"""\\
-                    <tr>
-                        <td><samp>{process if (i == 0) else ''}</samp></td>
-                        <td><samp>{tool}</samp></td>
-                        <td><samp>{version}</samp></td>
-                    </tr>
-                    """
-                )
-            )
-        html.append("</tbody>")
-    html.append("</table>")
-    return "\\n".join(html)
-
-
-versions_this_module = {}
-versions_this_module["${task.process}"] = {
-    "python": platform.python_version(),
-    "yaml": yaml.__version__,
-}
-
-with open("$versions") as f:
-    versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-# aggregate versions by the module name (derived from fully-qualified process name)
-versions_by_module = {}
-for process, process_versions in versions_by_process.items():
-    module = process.split(":")[-1]
-    try:
-        if versions_by_module[module] != process_versions:
-            raise AssertionError(
-                "We assume that software versions are the same between all modules. "
-                "If you see this error-message it means you discovered an edge-case "
-                "and should open an issue in nf-core/tools. "
-            )
-    except KeyError:
-        versions_by_module[module] = process_versions
-
-versions_by_module["Workflow"] = {
-    "Nextflow": "$workflow.nextflow.version",
-    "$workflow.manifest.name": "$workflow.manifest.version",
-}
-
-versions_mqc = {
-    "id": "software_versions",
-    "section_name": "${workflow.manifest.name} Software Versions",
-    "section_href": "https://github.com/${workflow.manifest.name}",
-    "plot_type": "html",
-    "description": "are collected at run time from the software output.",
-    "data": _make_versions_html(versions_by_module),
-}
-
-with open("software_versions.yml", "w") as f:
-    yaml.dump(versions_by_module, f, default_flow_style=False)
-with open("software_versions_mqc.yml", "w") as f:
-    yaml.dump(versions_mqc, f, default_flow_style=False)
-
-with open("versions.yml", "w") as f:
-    yaml.dump(versions_this_module, f, default_flow_style=False)
diff --git a/modules/nf-core/modules/fastawindows/meta.yml b/modules/nf-core/modules/fastawindows/meta.yml
deleted file mode 100644
index f074339..0000000
--- a/modules/nf-core/modules/fastawindows/meta.yml
+++ /dev/null
@@ -1,57 +0,0 @@
-name: "fastawindows"
-description: Quickly compute statistics over a fasta file in windows.
-keywords:
-  - genome
-  - fasta
-  - tsv
-  - bed
-tools:
-  - "fastawindows":
-      description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal level genome assemblies. The executable takes a fasta formatted file and calculates some statistics of interest in windows"
-      homepage: "https://github.com/tolkit/fasta_windows"
-      documentation: "None"
-      licence: "['MIT']"
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - fasta:
-      type: file
-      description: FASTA file
-      pattern: "*.{fa,fasta,fna}"
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - freq:
-      type: file
-      description: TSV file with frequencies and statistics
-      pattern: "*.{tsv}"
-  - mononuc:
-      type: file
-      description: TSV file with mononucleotide counts
-      pattern: "*.{tsv}"
-  - dinuc:
-      type: file
-      description: TSV file with dinucleotide counts
-      pattern: "*.{tsv}"
-  - trinuc:
-      type: file
-      description: TSV file with trinucleotide counts
-      pattern: "*.{tsv}"
-  - tetranuc:
-      type: file
-      description: TSV file with tetranucleotide counts
-      pattern: "*.{tsv}"
-authors:
-  - "@muffato"
diff --git a/modules/nf-core/modules/gunzip/main.nf b/modules/nf-core/modules/gunzip/main.nf
deleted file mode 100644
index fa6ba26..0000000
--- a/modules/nf-core/modules/gunzip/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-process GUNZIP {
-    tag "$archive"
-    label 'process_single'
-
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
-
-    input:
-    tuple val(meta), path(archive)
-
-    output:
-    tuple val(meta), path("$gunzip"), emit: gunzip
-    path "versions.yml"             , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    gunzip = archive.toString() - '.gz'
-    """
-    gunzip \\
-        -f \\
-        $args \\
-        $archive
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
-    END_VERSIONS
-    """
-
-    stub:
-    gunzip = archive.toString() - '.gz'
-    """
-    touch $gunzip
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/modules/gunzip/meta.yml b/modules/nf-core/modules/gunzip/meta.yml
deleted file mode 100644
index 4d2ebc8..0000000
--- a/modules/nf-core/modules/gunzip/meta.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: gunzip
-description: Compresses and decompresses files.
-keywords:
-  - gunzip
-  - compression
-tools:
-  - gunzip:
-    description: |
-      gzip is a file format and a software application used for file compression and decompression.
-    documentation: https://www.gnu.org/software/gzip/manual/gzip.html
-    licence: ["GPL-3.0-or-later"]
-input:
-  - meta:
-    type: map
-    description: |
-      Optional groovy Map containing meta information
-      e.g. [ id:'test', single_end:false ]
-  - archive:
-    type: file
-    description: File to be compressed/uncompressed
-    pattern: "*.*"
-output:
-  - gunzip:
-    type: file
-    description: Compressed/uncompressed file
-    pattern: "*.*"
-  - versions:
-    type: file
-    description: File containing software versions
-    pattern: "versions.yml"
-authors:
-  - "@joseespinosa"
-  - "@drpatelh"
-  - "@jfy133"
diff --git a/modules/nf-core/modules/tabix/bgzip/meta.yml b/modules/nf-core/modules/tabix/bgzip/meta.yml
deleted file mode 100644
index 72f0abc..0000000
--- a/modules/nf-core/modules/tabix/bgzip/meta.yml
+++ /dev/null
@@ -1,46 +0,0 @@
-name: tabix_bgzip
-description: Compresses/decompresses files
-keywords:
-  - compress
-  - decompress
-  - bgzip
-  - tabix
-tools:
-  - bgzip:
-      description: |
-        Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
-      homepage: https://www.htslib.org/doc/tabix.html
-      documentation: http://www.htslib.org/doc/bgzip.html
-      doi: 10.1093/bioinformatics/btp352
-      licence: ["MIT"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: file to compress or to decompress
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - output:
-      type: file
-      description: Output compressed/decompressed file
-      pattern: "*."
-  - gzi:
-      type: file
-      description: Optional gzip index file for compressed inputs
-      pattern: "*.gzi"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@joseespinosa"
-  - "@drpatelh"
-  - "@maxulysse"
diff --git a/modules/nf-core/modules/tabix/tabix/meta.yml b/modules/nf-core/modules/tabix/tabix/meta.yml
deleted file mode 100644
index fcc6e52..0000000
--- a/modules/nf-core/modules/tabix/tabix/meta.yml
+++ /dev/null
@@ -1,45 +0,0 @@
-name: tabix_tabix
-description: create tabix index from a sorted bgzip tab-delimited genome file
-keywords:
-  - index
-  - tabix
-  - vcf
-tools:
-  - tabix:
-      description: Generic indexer for TAB-delimited genome position files.
-      homepage: https://www.htslib.org/doc/tabix.html
-      documentation: https://www.htslib.org/doc/tabix.1.html
-      doi: 10.1093/bioinformatics/btq671
-      licence: ["MIT"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - tab:
-      type: file
-      description: TAB-delimited genome position file compressed with bgzip
-      pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - tbi:
-      type: file
-      description: tabix index file
-      pattern: "*.{tbi}"
-  - csi:
-      type: file
-      description: coordinate sorted index file
-      pattern: "*.{csi}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@joseespinosa"
-  - "@drpatelh"
-  - "@maxulysse"
diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml
new file mode 100644
index 0000000..017c259
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/environment.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - bioconda::htslib=1.20
+  - bioconda::tabix=1.11
diff --git a/modules/nf-core/modules/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf
similarity index 59%
rename from modules/nf-core/modules/tabix/bgzip/main.nf
rename to modules/nf-core/tabix/bgzip/main.nf
index aaef785..67991c7 100644
--- a/modules/nf-core/modules/tabix/bgzip/main.nf
+++ b/modules/nf-core/tabix/bgzip/main.nf
@@ -2,10 +2,10 @@ process TABIX_BGZIP {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
-        'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' :
+        'biocontainers/htslib:1.20--h5efdd21_2' }"
 
     input:
     tuple val(meta), path(input)
@@ -22,15 +22,30 @@ process TABIX_BGZIP {
     def args = task.ext.args ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
     in_bgzip = ["gz", "bgz", "bgzf"].contains(input.getExtension())
-    output   = in_bgzip ? input.getBaseName() : "${prefix}.${input.getExtension()}.gz"
-    command1 = in_bgzip ? '-d' : '-c'
-    command2 = in_bgzip ? ''   : " > ${output}"
+    extension = in_bgzip ? input.getBaseName().tokenize(".")[-1] : input.getExtension()
+    output   = in_bgzip ? "${prefix}.${extension}" : "${prefix}.${extension}.gz"
+    command = in_bgzip ? '-d' : ''
     // Name the index according to $prefix, unless a name has been requested
     if ((args.matches("(^| )-i\\b") || args.matches("(^| )--index(\$| )")) && !args.matches("(^| )-I\\b") && !args.matches("(^| )--index-name\\b")) {
         args = args + " -I ${output}.gzi"
     }
     """
-    bgzip $command1 $args -@${task.cpus} $input $command2
+    bgzip $command -c $args -@${task.cpus} $input > ${output}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    in_bgzip = ["gz", "bgz", "bgzf"].contains(input.getExtension())
+    output   = in_bgzip ? input.getBaseName() : "${prefix}.${input.getExtension()}.gz"
+
+    """
+    echo "" | gzip > ${output}
+    touch ${output}.gzi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml
new file mode 100644
index 0000000..131e92c
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/meta.yml
@@ -0,0 +1,61 @@
+name: tabix_bgzip
+description: Compresses/decompresses files
+keywords:
+  - compress
+  - decompress
+  - bgzip
+  - tabix
+tools:
+  - bgzip:
+      description: |
+        Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: http://www.htslib.org/doc/bgzip.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      identifier: biotools:tabix
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: file to compress or to decompress
+output:
+  - output:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${output}:
+          type: file
+          description: Output compressed/decompressed file
+          pattern: "*."
+  - gzi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${output}.gzi:
+          type: file
+          description: Optional gzip index file for compressed inputs
+          pattern: "*.gzi"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@maxulysse"
+  - "@nvnieuwk"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@maxulysse"
+  - "@nvnieuwk"
diff --git a/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config
new file mode 100644
index 0000000..6b6ff55
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_BGZIP {
+        ext.args = ' -i'
+    }
+}
diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test b/modules/nf-core/tabix/bgzip/tests/main.nf.test
new file mode 100644
index 0000000..d784aa0
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test
@@ -0,0 +1,111 @@
+nextflow_process {
+
+    name "Test Process TABIX_BGZIP"
+    script "modules/nf-core/tabix/bgzip/main.nf"
+    process "TABIX_BGZIP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tabix"
+    tag "tabix/bgzip"
+
+    test("sarscov2_vcf_bgzip_compress") {
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'bgzip_test' ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.output[0][1]).name
+                                ).match("bgzip_test")
+                }
+            )
+        }
+    }
+
+    test("homo_genome_bedgz_compress") {
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'bedgz_test' ],
+                            [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed.gz', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.output[0][1]).name
+                                ).match("bedgz_test")
+                }
+            )
+        }
+    }
+
+    test("sarscov2_vcf_bgzip_compress_stub") {
+        options '-stub'
+        config "./bgzip_compress.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:"test_stub" ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.output[0][1]).name
+                                ).match("test_stub")
+                }
+            )
+        }
+    }
+
+    test("sarscov2_vcf_bgzip_compress_gzi") {
+        config "./bgzip_compress.config"
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:"gzi_compress_test" ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.gzi[0][1]).name
+                                ).match("gzi_compress_test")
+                }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap
new file mode 100644
index 0000000..0748143
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap
@@ -0,0 +1,218 @@
+{
+    "gzi_compress_test": {
+        "content": [
+            "gzi_compress_test.vcf.gz.gzi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-02-19T14:52:29.328146"
+    },
+    "homo_genome_bedgz_compress": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "bedgz_test"
+                        },
+                        "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
+                ],
+                "gzi": [
+                    
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "bedgz_test"
+                        },
+                        "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-19T11:28:34.159992362"
+    },
+    "test_stub": {
+        "content": [
+            "test_stub.vcf.gz"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-02-19T14:52:20.811489"
+    },
+    "sarscov2_vcf_bgzip_compress": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "bgzip_test"
+                        },
+                        "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
+                ],
+                "gzi": [
+                    
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "bgzip_test"
+                        },
+                        "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-19T11:28:22.087769106"
+    },
+    "sarscov2_vcf_bgzip_compress_gzi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "gzi_compress_test"
+                        },
+                        "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "gzi_compress_test"
+                        },
+                        "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "gzi_compress_test"
+                        },
+                        "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0"
+                    ]
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "gzi_compress_test"
+                        },
+                        "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-19T11:28:57.15091665"
+    },
+    "bgzip_test": {
+        "content": [
+            "bgzip_test.vcf.gz"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-02-19T14:52:03.768295"
+    },
+    "bedgz_test": {
+        "content": [
+            "bedgz_test.bed"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-02-19T14:52:12.453855"
+    },
+    "sarscov2_vcf_bgzip_compress_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-19T11:28:45.219404786"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/bgzip/tests/tags.yml b/modules/nf-core/tabix/bgzip/tests/tags.yml
new file mode 100644
index 0000000..de0eec8
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/tags.yml
@@ -0,0 +1,2 @@
+tabix/bgzip:
+  - "modules/nf-core/tabix/bgzip/**"
diff --git a/modules/nf-core/tabix/bgzip/tests/vcf_none.config b/modules/nf-core/tabix/bgzip/tests/vcf_none.config
new file mode 100644
index 0000000..f3a3c46
--- /dev/null
+++ b/modules/nf-core/tabix/bgzip/tests/vcf_none.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_BGZIP {
+        ext.args = ''
+    }
+}
diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml
new file mode 100644
index 0000000..017c259
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/environment.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - bioconda::htslib=1.20
+  - bioconda::tabix=1.11
diff --git a/modules/nf-core/modules/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
similarity index 76%
rename from modules/nf-core/modules/tabix/tabix/main.nf
rename to modules/nf-core/tabix/tabix/main.nf
index 21b2e79..13acd67 100644
--- a/modules/nf-core/modules/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -2,10 +2,10 @@ process TABIX_TABIX {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
-        'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' :
+        'biocontainers/htslib:1.20--h5efdd21_2' }"
 
     input:
     tuple val(meta), path(tab)
@@ -21,7 +21,10 @@ process TABIX_TABIX {
     script:
     def args = task.ext.args ?: ''
     """
-    tabix $args $tab
+    tabix \\
+        --threads $task.cpus \\
+        $args \\
+        $tab
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -30,11 +33,11 @@ process TABIX_TABIX {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${tab}.tbi
-    cat <<-END_VERSIONS > versions.yml
+    touch ${tab}.csi
 
+    cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
new file mode 100644
index 0000000..7864832
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -0,0 +1,58 @@
+name: tabix_tabix
+description: create tabix index from a sorted bgzip tab-delimited genome file
+keywords:
+  - index
+  - tabix
+  - vcf
+tools:
+  - tabix:
+      description: Generic indexer for TAB-delimited genome position files.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: https://www.htslib.org/doc/tabix.1.html
+      doi: 10.1093/bioinformatics/btq671
+      licence: ["MIT"]
+      identifier: biotools:tabix
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - tab:
+        type: file
+        description: TAB-delimited genome position file compressed with bgzip
+        pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
+output:
+  - tbi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: tabix index file
+          pattern: "*.{tbi}"
+  - csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: coordinate sorted index file
+          pattern: "*.{csi}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@maxulysse"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@maxulysse"
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
new file mode 100644
index 0000000..102b0d7
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -0,0 +1,136 @@
+nextflow_process {
+
+    name "Test Process TABIX_TABIX"
+    script "modules/nf-core/tabix/tabix/main.nf"
+    process "TABIX_TABIX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tabix"
+    tag "tabix/tabix"
+
+    test("sarscov2_bedgz_tbi") {
+        config "./tabix_bed.config"
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'tbi_bed' ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    file(process.out.tbi[0][1]).name
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2_gff_tbi") {
+        config "./tabix_gff.config"
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'tbi_gff' ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    file(process.out.tbi[0][1]).name).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2_vcf_tbi") {
+        config "./tabix_vcf_tbi.config"
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'tbi_vcf' ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    file(process.out.tbi[0][1]).name
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2_vcf_csi") {
+        config "./tabix_vcf_csi.config"
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'vcf_csi' ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    file(process.out.csi[0][1]).name
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2_vcf_csi_stub") {
+        config "./tabix_vcf_csi.config"
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'vcf_csi_stub' ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    file(process.out.csi[0][1]).name
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
new file mode 100644
index 0000000..c2b9ed0
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -0,0 +1,212 @@
+{
+    "sarscov2_gff_tbi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tbi_gff"
+                        },
+                        "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "tbi_gff"
+                        },
+                        "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ]
+            },
+            "genome.gff3.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-19T12:06:25.653807564"
+    },
+    "sarscov2_bedgz_tbi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tbi_bed"
+                        },
+                        "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "tbi_bed"
+                        },
+                        "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ]
+            },
+            "test.bed.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-19T12:06:09.754082161"
+    },
+    "sarscov2_vcf_tbi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tbi_vcf"
+                        },
+                        "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "tbi_vcf"
+                        },
+                        "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ]
+            },
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-19T12:06:40.042648294"
+    },
+    "sarscov2_vcf_csi_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ]
+            },
+            "test.vcf.gz.csi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-19T12:07:08.700367261"
+    },
+    "sarscov2_vcf_csi": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "vcf_csi"
+                        },
+                        "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "vcf_csi"
+                        },
+                        "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b"
+                    ]
+                ],
+                "tbi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                ]
+            },
+            "test.vcf.gz.csi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-19T12:06:55.362067748"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_bed.config b/modules/nf-core/tabix/tabix/tests/tabix_bed.config
new file mode 100644
index 0000000..7ff0590
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tabix_bed.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_TABIX {
+        ext.args = '-p bed'
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_gff.config b/modules/nf-core/tabix/tabix/tests/tabix_gff.config
new file mode 100644
index 0000000..20c0a1e
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tabix_gff.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_TABIX {
+        ext.args = '-p gff'
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config
new file mode 100644
index 0000000..eb4f2d7
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_TABIX {
+        ext.args = '-p vcf --csi'
+    }
+}
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config
new file mode 100644
index 0000000..2774c8a
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config
@@ -0,0 +1,5 @@
+process {
+    withName: TABIX_TABIX {
+        ext.args = '-p vcf'
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tags.yml b/modules/nf-core/tabix/tabix/tests/tags.yml
new file mode 100644
index 0000000..6eda065
--- /dev/null
+++ b/modules/nf-core/tabix/tabix/tests/tags.yml
@@ -0,0 +1,2 @@
+tabix/tabix:
+  - "modules/nf-core/tabix/tabix/**"
diff --git a/nextflow.config b/nextflow.config
index 47bc0dc..fe7519e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,18 +16,19 @@ params {
     selected_fw_output         = "${projectDir}/assets/fasta_windows.csv"
 
     // Boilerplate options
-    outdir                     = null
-    tracedir                   = "${params.outdir}/pipeline_info"
+    outdir                     = 'results'
+    tracedir                   = "${params.outdir}/pipeline_info/sequencecomposition"
     publish_dir_mode           = 'copy'
     email                      = null
     email_on_fail              = null
     plaintext_email            = false
     monochrome_logs            = false
+    hook_url                   = null
     help                       = false
+    version                    = false
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'
-    enable_conda               = false
 
 
     // Config options
@@ -66,62 +67,92 @@ try {
 // }
 
 
-
 profiles {
-    debug { process.beforeScript = 'echo $HOSTNAME' }
+    cleanup { cleanup = true }
+    debug {
+        dumpHashes             = true
+        process.beforeScript   = 'echo $HOSTNAME'
+        cleanup                = false
+    }
     conda {
-        params.enable_conda    = true
+        conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        apptainer.enabled      = false
     }
     mamba {
-        params.enable_conda    = true
+        conda.enabled          = true
         conda.useMamba         = true
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        apptainer.enabled      = false
     }
     docker {
         docker.enabled         = true
+        docker.registry        = 'quay.io'
         docker.userEmulation   = true
+        conda.enabled          = false
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        apptainer.enabled      = false
+    }
+    arm {
+        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
         singularity.enabled    = true
         singularity.autoMounts = true
+        conda.enabled          = false
         docker.enabled         = false
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        apptainer.enabled      = false
     }
     podman {
         podman.enabled         = true
+        podman.registry        = 'quay.io'
+        conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        apptainer.enabled      = false
     }
     shifter {
         shifter.enabled        = true
+        conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false
         charliecloud.enabled   = false
+        apptainer.enabled      = false
     }
     charliecloud {
         charliecloud.enabled   = true
+        conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
+        apptainer.enabled      = false
+    }
+    apptainer {
+        apptainer.enabled      = true
+        conda.enabled          = false
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
     }
     gitpod {
         executor.name          = 'local'
@@ -168,12 +199,13 @@ dag {
 
 manifest {
     name            = 'sanger-tol/sequencecomposition'
-    author          = '@muffato'
+    author          = """@muffato"""
     homePage        = 'https://github.com/sanger-tol/sequencecomposition'
-    description     = 'Pipeline that extracts statistics from a genome about its sequence composition'
+    description     = """Pipeline that extracts statistics from a genome about its sequence composition"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=22.04.0'
-    version         = '1.0.0'
+    nextflowVersion = '!>=22.10.1'
+    version         = '1.1.0'
+    doi             = '10.5281/zenodo.7155168'
 }
 
 // Load modules.config for DSL2 module specific options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c6fef00..7ce6c53 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -22,7 +22,8 @@
                 "outdir": {
                     "type": "string",
                     "format": "directory-path",
-                    "description": "The output directory where the results will be saved. Not considered when running the pipeline with a .csv file as input.",
+                    "description": "The output directory where the results will be saved. Not considered for sample-sheet entries that have an absolute path.",
+                    "default": "results",
                     "fa_icon": "fas fa-folder-open"
                 },
                 "selected_fw_output": {
@@ -46,7 +47,7 @@
                     "pattern": "^\\S+\\.csv$",
                     "schema": "assets/schema_input.json",
                     "description": "Path to comma-separated file containing information about the genomes to analyse. Used for bulk analysis of many genomes.",
-                    "help_text": "The file has to be a comma-separated file with two columns, and a header row. The columns names must be `species_dir` and `assembly_name`. An additional `assembly_accession` column can be provided too.",
+                    "help_text": "The file has to be a comma-separated file with two columns, and a header row. The columns names must be `outdir` and `fasta`.",
                     "fa_icon": "fas fa-file-csv"
                 },
                 "email": {
@@ -155,6 +156,12 @@
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
                 },
+                "version": {
+                    "type": "boolean",
+                    "description": "Display version and exit.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",
@@ -184,10 +191,17 @@
                     "fa_icon": "fas fa-palette",
                     "hidden": true
                 },
+                "hook_url": {
+                    "type": "string",
+                    "description": "Incoming hook URL for messaging service",
+                    "fa_icon": "fas fa-people-group",
+                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
+                    "hidden": true
+                },
                 "tracedir": {
                     "type": "string",
                     "description": "Directory to keep pipeline Nextflow logs and reports.",
-                    "default": "${params.outdir}/pipeline_info",
+                    "default": "${params.outdir}/pipeline_info/sequencecomposition",
                     "fa_icon": "fas fa-cogs",
                     "hidden": true
                 },
@@ -204,12 +218,6 @@
                     "description": "Show all params when using `--help`",
                     "hidden": true,
                     "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "enable_conda": {
-                    "type": "boolean",
-                    "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-bacon"
                 }
             }
         }
diff --git a/pipeline_template.yml b/pipeline_template.yml
new file mode 100644
index 0000000..0aa7398
--- /dev/null
+++ b/pipeline_template.yml
@@ -0,0 +1,3 @@
+prefix: sanger-tol
+skip:
+  - igenomes
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..0d62beb
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,10 @@
+# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
+[tool.black]
+line-length = 120
+target_version = ["py37", "py38", "py39", "py310"]
+
+[tool.isort]
+profile = "black"
+known_first_party = ["nf_core"]
+multi_line_output = 3
diff --git a/subworkflows/local/fasta_windows.nf b/subworkflows/local/fasta_windows.nf
index 2a654ad..5a43b28 100644
--- a/subworkflows/local/fasta_windows.nf
+++ b/subworkflows/local/fasta_windows.nf
@@ -3,15 +3,15 @@
 //
 
 include { EXTRACT_COLUMN          } from '../../modules/local/extract_column'
-include { FASTAWINDOWS            } from '../../modules/nf-core/modules/fastawindows/main'
-include { TABIX_BGZIP             } from '../../modules/nf-core/modules/tabix/bgzip/main'
-include { TABIX_TABIX as TABIX_TABIX_CSI   } from '../../modules/nf-core/modules/tabix/tabix/main'
-include { TABIX_TABIX as TABIX_TABIX_TBI   } from '../../modules/nf-core/modules/tabix/tabix/main'
+include { FASTAWINDOWS            } from '../../modules/nf-core/fastawindows/main'
+include { TABIX_BGZIP             } from '../../modules/nf-core/tabix/bgzip/main'
+include { TABIX_TABIX as TABIX_TABIX_CSI   } from '../../modules/nf-core/tabix/tabix/main'
+include { TABIX_TABIX as TABIX_TABIX_TBI   } from '../../modules/nf-core/tabix/tabix/main'
 
 workflow FASTA_WINDOWS {
 
     take:
-    fasta               // file: /path/to/genome.fa
+    fasta_fai           // [file: /path/to/genome.fa, file: /path/to/genome.fai]
     output_selection    // file: /path/to/fasta_windows.csv
     window_size_info    // value, used to build meta.id and name files
 
@@ -20,7 +20,7 @@ workflow FASTA_WINDOWS {
     ch_versions = Channel.empty()
 
     // Run fasta_windows
-    FASTAWINDOWS ( fasta )
+    FASTAWINDOWS ( fasta_fai.map { meta, fasta, fai -> [meta, fasta] } )
     ch_versions       = ch_versions.mix(FASTAWINDOWS.out.versions.first())
 
     // List of:
@@ -53,6 +53,7 @@ workflow FASTA_WINDOWS {
         // column number
         ch_freq_bed_input.map { it[2] }
     ).bedgraph
+
     ch_versions       = ch_versions.mix(EXTRACT_COLUMN.out.versions.first())
 
     // Add meta information to the tsv files
@@ -67,10 +68,17 @@ workflow FASTA_WINDOWS {
     ch_compressed_bed = TABIX_BGZIP ( ch_freq_bed.mix(ch_tsv) ).output
     ch_versions       = ch_versions.mix(TABIX_BGZIP.out.versions.first())
 
-    // Index the BED file in two formats for maximum compatibility
-    ch_indexed_bed_csi= TABIX_TABIX_CSI ( ch_compressed_bed ).csi
+    // Try indexing the BED file in two formats for maximum compatibility
+    // but each has its own limitations
+    tabix_selector      = ch_compressed_bed.branch { meta, bed ->
+        tbi_and_csi: meta.max_length < 2**29
+        only_csi:    meta.max_length < 2**32
+    }
+
+    // Do the indexing on the compatible bedGraph files
+    ch_indexed_bed_csi= TABIX_TABIX_CSI ( tabix_selector.tbi_and_csi.mix(tabix_selector.only_csi) ).csi
     ch_versions       = ch_versions.mix(TABIX_TABIX_CSI.out.versions.first())
-    ch_indexed_bed_tbi= TABIX_TABIX_TBI ( ch_compressed_bed ).tbi
+    ch_indexed_bed_tbi= TABIX_TABIX_TBI ( tabix_selector.tbi_and_csi ).tbi
     ch_versions       = ch_versions.mix(TABIX_TABIX_TBI.out.versions.first())
 
 
@@ -78,3 +86,4 @@ workflow FASTA_WINDOWS {
     bedgraph = ch_compressed_bed
     versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
 }
+
diff --git a/subworkflows/local/params_check.nf b/subworkflows/local/params_check.nf
index 5a91b9c..93dfe3b 100644
--- a/subworkflows/local/params_check.nf
+++ b/subworkflows/local/params_check.nf
@@ -2,84 +2,113 @@
 // Check and parse the input parameters
 //
 
-include { GUNZIP            } from '../../modules/nf-core/modules/gunzip/main'
-include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
+include { CUSTOM_GETCHROMSIZES } from '../../modules/nf-core/custom/getchromsizes/main'
+include { GUNZIP               } from '../../modules/nf-core/gunzip/main'
+include { SAMPLESHEET_CHECK    } from '../../modules/local/samplesheet_check'
 
 workflow PARAMS_CHECK {
 
     take:
-    inputs          // tuple, see below
+    samplesheet  // file
+    cli_params   // tuple, see below
+    outdir       // file output directory
 
 
     main:
-
-    def (samplesheet, fasta, outdir) = inputs
-
     ch_versions = Channel.empty()
 
     ch_inputs = Channel.empty()
     if (samplesheet) {
-
         SAMPLESHEET_CHECK ( file(samplesheet, checkIfExists: true) )
             .csv
-            // Provides species_dir and assembly_name
+            // Provides outdir and fasta
             .splitCsv ( header:true, sep:',' )
-            // Add assembly_path, following the Tree of Life directory structure
-            .map {
-                it + [
-                    assembly_path: "${it["species_dir"]}/assembly/release/${it["assembly_name"]}/insdc",
-                    ]
-            }
-            .map {
-                // If assembly_accession is missing, load the accession number from file, following the Tree of Life directory structure
-                it["assembly_accession"] ? it : it + [
-                    assembly_accession: file("${it["assembly_path"]}/ACCESSION", checkIfExists: true).text.trim(),
-                ]
-            }
-            // Convert to tuple(meta,file) as required by GUNZIP and FASTAWINDOWS
             .map { [
-                [
-                    id: it["assembly_accession"],
-                    analysis_dir: "${it["species_dir"]}/analysis/${it["assembly_name"]}",
-                ],
-                file("${it["assembly_path"]}/${it["assembly_accession"]}.fa.gz", checkIfExists: true),
+                (it["outdir"].startsWith("/") ? "" : outdir + "/") + it["outdir"],
+                it["fasta"],
             ] }
             .set { ch_inputs }
 
         ch_versions = ch_versions.mix(SAMPLESHEET_CHECK.out.versions)
 
     } else {
+        // Add the other input channel in, as it's expected to have all the parameters in the right order
+        ch_inputs = ch_inputs.mix(cli_params.map { [outdir] + it } )
+    }
 
+    ch_input_files = ch_inputs.map { outdir, fasta ->
         file_fasta = file(fasta, checkIfExists: true)
-        ch_inputs = Channel.of(
+        // Trick to strip the Fasta extension for gzipped files too, without having to list all possible extensions
+        id = file(fasta.replace(".gz", "")).baseName
+        return [
             [
-                [
-                    id: file_fasta.baseName,
-                    analysis_dir: outdir,
-                ],
-                file_fasta,
-            ]
-        )
-
+                id: id,
+                outdir: outdir,
+            ],
+            file_fasta,
+            file(fasta + ".fai"),
+        ]
     }
 
-    // Only flow to gunzip when required
-    ch_parsed_fasta_name = ch_inputs.branch {
-        meta, filename ->
-            compressed : filename.getExtension().equals('gz')
-            uncompressed : true
+    // Identify the Fasta files that are compressed
+    ch_parsed_fasta_name = ch_input_files.branch {
+        meta, fasta, fai ->
+            compressed : fasta.getExtension().equals('gz')      // (meta, fasta_gz, fai)
+            uncompressed : true                                 // (meta, fasta, fai)
     }
 
-    // gunzip .fa.gz files
-    ch_unzipped_fasta   = GUNZIP ( ch_parsed_fasta_name.compressed ).gunzip
+    // uncompress them, with some channel manipulations to maintain the triplet (meta, fasta, fai)
+    gunzip_input        = ch_parsed_fasta_name.compressed.map { meta, fasta_gz, fai -> [meta, fasta_gz] }
+    ch_unzipped_fasta   = GUNZIP(gunzip_input).gunzip                   // (meta, fasta)
+                            .join(ch_parsed_fasta_name.compressed)      // joined with (meta, fasta_gz, fai) makes (meta, fasta, fasta_gz, fai)
+                            .map { meta, fasta, fasta_gz, fai -> [meta, fasta, fai] }
     ch_versions         = ch_versions.mix(GUNZIP.out.versions.first())
 
-    // Combine with preexisting .fa files
-    ch_plain_fasta      = ch_parsed_fasta_name.uncompressed.mix(ch_unzipped_fasta)
-
+    // Check if the faidx index is present
+    ch_parsed_fasta_name.uncompressed.mix(ch_unzipped_fasta).branch {
+        meta, fasta, fai ->
+            indexed : fai.exists()
+            notindexed : true
+                return [meta, fasta]    // remove fai from the channel because it will be added by CUSTOM_GETCHROMSIZES below
+    } . set { ch_inputs_checked }
+
+    // Generate Samtools index and chromosome sizes file, again with some channel manipulations
+    ch_samtools_faidx   = ch_inputs_checked.notindexed                                          // (meta, fasta)
+                            .join( CUSTOM_GETCHROMSIZES (ch_inputs_checked.notindexed).fai )    // joined with (meta, fai) makes (meta, fasta, fai)
+    ch_versions         = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)
+
+    // Read the .fai file, extract sequence statistics, and make an extended meta map
+    ch_fasta_fai = ch_inputs_checked.indexed.mix(ch_samtools_faidx).map {
+        meta, fasta, fai -> [meta + get_sequence_map(fai), fasta, fai]
+    }
 
     emit:
-    plain_fasta = ch_plain_fasta       // channel: [ val(meta), path/to/fasta ]
-    versions    = ch_versions          // channel: versions.yml
+    fasta_fai = ch_fasta_fai       // channel: [ val(meta), path/to/fasta, path/to/fai ]
+    versions  = ch_versions        // channel: versions.yml
 }
 
+// Read the .fai file to extract the number of sequences, the maximum and total sequence length
+// Inspired from https://github.com/nf-core/rnaseq/blob/3.10.1/lib/WorkflowRnaseq.groovy
+def get_sequence_map(fai_file) {
+    def n_sequences = 0
+    def max_length = 0
+    def total_length = 0
+    fai_file.eachLine { line ->
+        def lspl   = line.split('\t')
+        def chrom  = lspl[0]
+        def length = lspl[1].toInteger()
+        n_sequences ++
+        total_length += length
+        if (length > max_length) {
+            max_length = length
+        }
+    }
+
+    def sequence_map = [:]
+    sequence_map.n_sequences = n_sequences
+    sequence_map.total_length = total_length
+    if (n_sequences) {
+        sequence_map.max_length = max_length
+    }
+    return sequence_map
+}
diff --git a/tower.yml b/tower.yml
new file mode 100644
index 0000000..787aedf
--- /dev/null
+++ b/tower.yml
@@ -0,0 +1,5 @@
+reports:
+  multiqc_report.html:
+    display: "MultiQC HTML report"
+  samplesheet.csv:
+    display: "Auto-created samplesheet with collated metadata and FASTQ paths"
diff --git a/workflows/sequencecomposition.nf b/workflows/sequencecomposition.nf
index 83e177f..be6d7e9 100644
--- a/workflows/sequencecomposition.nf
+++ b/workflows/sequencecomposition.nf
@@ -30,7 +30,7 @@ include { FASTA_WINDOWS } from '../subworkflows/local/fasta_windows'
 //
 // MODULE: Installed directly from nf-core/modules
 //
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -43,17 +43,19 @@ workflow SEQUENCECOMPOSITION {
     ch_versions = Channel.empty()
 
     PARAMS_CHECK (
-        [
-            params.input,
-            params.fasta,
-            params.outdir,
-        ]
+        params.input,
+        Channel.of(
+            [
+                params.fasta,
+            ]
+        ),
+        params.outdir,
     )
     ch_versions         = ch_versions.mix(PARAMS_CHECK.out.versions)
 
     // Statistics extraction
     FASTA_WINDOWS (
-        PARAMS_CHECK.out.plain_fasta,
+        PARAMS_CHECK.out.fasta_fai,
         file(params.selected_fw_output, checkExists: true),
         params.window_size_info,
     )
@@ -75,6 +77,9 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
+    if (params.hook_url) {
+        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
+    }
 }
 
 /*