Template update for nf-core/tools version 2.3.1

.editorconfig

@@ -8,12 +8,9 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{yml,yaml}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-[*.json]
-insert_final_newline = unset
-
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset

.github/CONTRIBUTING.md

@@ -15,8 +15,7 @@ Contributions to the code are even more welcome ;)
 
 If you'd like to write some code for nf-core/hic, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/hic issues](https://github.com/nf-core/hic/issues) to avoid duplicating work
-    * If there isn't one already, please create one so that others know you're working on this
+1. Check that there isn't already an issue about your idea in the [nf-core/hic issues](https://github.com/nf-core/hic/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/hic repository](https://github.com/nf-core/hic) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
@@ -49,9 +48,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-* On your own fork, make a new branch `patch` based on `upstream/master`.
-* Fix the bug, and bump version (X.Y.Z+1).
-* A PR should be made on `master` from patch to directly this particular bug.
+- On your own fork, make a new branch `patch` based on `upstream/master`.
+- Fix the bug, and bump version (X.Y.Z+1).
+- A PR should be made on `master` from patch to directly this particular bug.
 
 ## Getting help
 
@@ -73,7 +72,7 @@ If you wish to contribute a new step, please use the following coding standards:
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
-9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
@@ -92,8 +91,8 @@ The process resources can be passed on to the tool dynamically within the proces
 
 Please use the following naming schemes, to make it easy to understand what is going where.
 
-* initial process channel: `ch_output_from_<process>`
-* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+- initial process channel: `ch_output_from_<process>`
+- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
 
 ### Nextflow version bumping
 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,7 +2,6 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-
   - type: markdown
     attributes:
       value: |

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,10 +16,10 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
-    - [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
+  - [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/awsfulltest.yml

@@ -18,7 +18,6 @@ jobs:
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
-        
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/awstest.yml

@@ -10,9 +10,9 @@ jobs:
     if: github.repository == 'nf-core/hic'
     runs-on: ubuntu-latest
     steps:
+      # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
-        
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/branch.yml

@@ -13,8 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/hic'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
-
+          "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $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
@@ -43,4 +42,4 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-
+#

.github/workflows/ci.yml

@@ -16,18 +16,18 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hic') }}
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hic') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         # Nextflow versions
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: '21.10.3'
-            NXF_EDGE: ''
+          - NXF_VER: "21.10.3"
+            NXF_EDGE: ""
           # Test latest edge release of Nextflow
-          - NXF_VER: ''
-            NXF_EDGE: '1'
+          - NXF_VER: ""
+            NXF_EDGE: "1"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -48,3 +48,5 @@ jobs:
         # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+
+#

.github/workflows/linting.yml

 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+# It runs the `nf-core lint` and markdown lint tests to ensure
+# that the code meets the nf-core guidelines.
 on:
   push:
   pull_request:
@@ -8,42 +9,6 @@ on:
     types: [published]
 
 jobs:
-  Markdown:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
-      - name: Install markdownlint
-        run: npm install -g markdownlint-cli
-      - name: Run Markdownlint
-        run: markdownlint .
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## Markdown linting is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install `markdownlint-cli`
-                * On Mac: `brew install markdownlint-cli`
-                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
-            * Fix the markdown errors
-                * Automatically: `markdownlint . --fix`
-                * Manually resolve anything left from `markdownlint .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
@@ -55,49 +20,24 @@ jobs:
         run: npm install -g editorconfig-checker
 
       - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+        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')
 
-  YAML:
+  Prettier:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@master
-      - name: 'Yamllint'
-        uses: karancode/yamllint-github-action@master
-        with:
-          yamllint_file_or_dir: '.'
-          yamllint_config_filepath: '.yamllint.yml'
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## YAML linting is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install `yamllint`
-                * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint)
-                instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint)
-            * Fix the markdown errors
-                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml`
-                * Fix any reported errors in your YAML files
+      - uses: actions/checkout@v2
 
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+      - uses: actions/setup-node@v2
 
-            We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install Prettier
+        run: npm install -g prettier
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run Prettier --check
+        run: prettier --check ${GITHUB_WORKSPACE}
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
-
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
@@ -110,8 +50,8 @@ jobs:
 
       - uses: actions/setup-python@v1
         with:
-          python-version: '3.6'
-          architecture: 'x64'
+          python-version: "3.6"
+          architecture: "x64"
 
       - name: Install dependencies
         run: |
@@ -139,3 +79,4 @@ jobs:
             lint_results.md
             PR_number.txt
 
+#

.github/workflows/linting_comment.yml

-
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
@@ -27,4 +26,4 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-
+#

.gitpod.yml

@@ -2,13 +2,13 @@ image: nfcore/gitpod:latest
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - codezombiech.gitignore                 # Language support for .gitignore files
+    - codezombiech.gitignore # Language support for .gitignore files
     # - cssho.vscode-svgviewer                 # SVG viewer
-    - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
-    - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
-    - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
+    - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
     # - nextflow.nextflow                      # Nextflow syntax highlighting
-    - oderwat.indent-rainbow                 # Highlight indentation level
-    - streetsidesoftware.code-spell-checker  # Spelling checker for source code
+    - oderwat.indent-rainbow # Highlight indentation level
+    - streetsidesoftware.code-spell-checker # Spelling checker for source code

.markdownlint.yml

-# Markdownlint configuration file
-default: true
-line-length: false
-ul-indent:
-    indent: 4
-no-duplicate-header:
-    siblings_only: true
-no-inline-html:
-    allowed_elements:
-        - img
-        - p
-        - kbd
-        - details
-        - summary

.prettierrc.yml

+printWidth: 120

.yamllint.yml

-extends: default
-
-rules:
-    document-start: disable
-    line-length: disable
-    truthy: disable

CHANGELOG.md

@@ -11,6 +11,8 @@ Initial release of nf-core/hic, created with the [nf-core](https://nf-co.re/) te
 
 ### `Fixed`
 
+- Clarified conda usage and added an installation tutorial for Singularity since the one on Syllabs' website uses an outdate version of GO Compiler
+
 ### `Dependencies`
 
 ### `Deprecated`

CITATIONS.md

@@ -10,23 +10,26 @@
 
 ## Pipeline tools
 
-* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
-    > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools
 
-* [Anaconda](https://anaconda.com)
-    > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+- [Anaconda](https://anaconda.com)
 
-* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
-    > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
 
-* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
-    > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
 
-* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
 
-* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
-    > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
+- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+
+  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+
+- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+
+- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

README.md

-# ![nf-core/hic](docs/images/nf-core-hic_logo_light.png#gh-light-mode-only) ![nf-core/hic](docs/images/nf-core-hic_logo_dark.png#gh-dark-mode-only)
+# ![nf-core/hic](docs/images/nf-core/hic_logo_light.png#gh-light-mode-only) ![nf-core/hic](docs/images/nf-core/hic_logo_dark.png#gh-dark-mode-only)
 
 [![GitHub Actions CI Status](https://github.com/nf-core/hic/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/hic/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+linting%22)
@@ -17,11 +17,13 @@
 ## Introduction
 
 <!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
+
 **nf-core/hic** is a bioinformatics best-practice analysis pipeline for Analysis of Chromosome Conformation Capture data (Hi-C).
 
 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!
 
 <!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
+
 On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/hic/results).
 
 ## Pipeline summary
@@ -35,28 +37,28 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
 
-2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`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 _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
+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))_.
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-    ```console
-    nextflow run nf-core/hic -profile test,YOURPROFILE --outdir <OUTDIR>
-    ```
+   ```console
+   nextflow run nf-core/hic -profile test,YOURPROFILE --outdir <OUTDIR>
+   ```
 
-    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.
+   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.
 
-    > * 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 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.
 
 4. Start running your own analysis!
 
-    <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
+   <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
-    ```console
-    nextflow run nf-core/hic --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
-    ```
+   ```console
+   nextflow run nf-core/hic --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+   ```
 
 ## Documentation
 
@@ -82,6 +84,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- If you use  nf-core/hic for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
 <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:

assets/email_template.html

 <html>
-<head>
-  <meta charset="utf-8">
-  <meta http-equiv="X-UA-Compatible" content="IE=edge">
-  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <head>
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
 
-  <meta name="description" content="nf-core/hic: Analysis of Chromosome Conformation Capture data (Hi-C)">
-  <title>nf-core/hic Pipeline Report</title>
-</head>
-<body>
-<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
+    <!-- prettier-ignore -->
+    <meta name="description" content="nf-core/hic: Analysis of Chromosome Conformation Capture data (Hi-C)" />
+    <title>nf-core/hic Pipeline Report</title>
+  </head>
+  <body>
+    <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto">
+      <img src="cid:nfcorepipelinelogo" />
 
-<img src="cid:nfcorepipelinelogo">
+      <h1>nf-core/hic v${version}</h1>
+      <h2>Run Name: $runName</h2>
 
-<h1>nf-core/hic v${version}</h1>
-<h2>Run Name: $runName</h2>
-
-<% if (!success){
-    out << """
-    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nf-core/hic execution completed unsuccessfully!</h4>
+      <% if (!success){ out << """
+      <div
+        style="
+          color: #a94442;
+          background-color: #f2dede;
+          border-color: #ebccd1;
+          padding: 15px;
+          margin-bottom: 20px;
+          border: 1px solid transparent;
+          border-radius: 4px;
+        "
+      >
+        <h4 style="margin-top: 0; color: inherit">nf-core/hic execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
-        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
-    </div>
-    """
-} else {
-    out << """
-    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
+      </div>
+      """ } else { out << """
+      <div
+        style="
+          color: #3c763d;
+          background-color: #dff0d8;
+          border-color: #d6e9c6;
+          padding: 15px;
+          margin-bottom: 20px;
+          border: 1px solid transparent;
+          border-radius: 4px;
+        "
+      >
         nf-core/hic execution completed successfully!
-    </div>
-    """
-}
-%>
+      </div>
+      """ } %>
 
-<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
-<p>The command used to launch the workflow was as follows:</p>
-<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
+      <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
+      <p>The command used to launch the workflow was as follows:</p>
+      <pre
+        style="
+          white-space: pre-wrap;
+          overflow: visible;
+          background-color: #ededed;
+          padding: 15px;
+          border-radius: 4px;
+          margin-bottom: 30px;
+        "
+      >
+$commandLine</pre
+      >
 
-<h3>Pipeline Configuration:</h3>
-<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
-    <tbody style="border-bottom: 1px solid #ddd;">
-        <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %>
-    </tbody>
-</table>
+      <h3>Pipeline Configuration:</h3>
+      <table
+        style="
+          width: 100%;
+          max-width: 100%;
+          border-spacing: 0;
+          border-collapse: collapse;
+          border: 0;
+          margin-bottom: 30px;
+        "
+      >
+        <tbody style="border-bottom: 1px solid #ddd">
+          <% out << summary.collect{ k,v -> "
+          <tr>
+            <th
+              style="
+                text-align: left;
+                padding: 8px 0;
+                line-height: 1.42857143;
+                vertical-align: top;
+                border-top: 1px solid #ddd;
+              "
+            >
+              $k
+            </th>
+            <td
+              style="
+                text-align: left;
+                padding: 8px;
+                line-height: 1.42857143;
+                vertical-align: top;
+                border-top: 1px solid #ddd;
+              "
+            >
+              <pre style="white-space: pre-wrap; overflow: visible">$v</pre>
+            </td>
+          </tr>
+          " }.join("\n") %>
+        </tbody>
+      </table>
 
-<p>nf-core/hic</p>
-<p><a href="https://github.com/nf-core/hic">https://github.com/nf-core/hic</a></p>
-
-</div>
-
-</body>
+      <p>nf-core/hic</p>
+      <p><a href="https://github.com/nf-core/hic">https://github.com/nf-core/hic</a></p>
+    </div>
+  </body>
 </html>

assets/multiqc_config.yaml

-report_comment: >
-    This report has been generated by the <a href="https://github.com/nf-core/hic" target="_blank">nf-core/hic</a>
-    analysis pipeline. For information about how to interpret these results, please see the
-    <a href="https://nf-co.re/hic" target="_blank">documentation</a>.
-report_section_order:
-    software_versions:
-        order: -1000
-    nf-core-hic-summary:
-        order: -1001
-
-export_plots: true

assets/multiqc_config.yml

+report_comment: >
+  This report has been generated by the <a href="https://github.com/nf-core/hic" target="_blank">nf-core/hic</a>
+  analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/hic" target="_blank">documentation</a>.
+report_section_order:
+  software_versions:
+    order: -1000
+  "nf-core-hic-summary":
+    order: -1001
+
+export_plots: true