Merge pull request #51 from nservant/dev

nf-core template + python3

.github/CONTRIBUTING.md

 # nf-core/hic: Contributing Guidelines
 
-Hi there! Many thanks for taking an interest in improving nf-core/hic.
+Hi there!
+Many thanks for taking an interest in improving nf-core/hic.
 
-We try to manage the required tasks for nf-core/hic using GitHub issues, you probably came to this page when creating one. Please use the pre-filled template to save time.
+We try to manage the required tasks for nf-core/hic using GitHub issues, you probably came to this page when creating one.
+Please use the pre-filled template to save time.
 
-However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)
-
-> If you need help using or modifying nf-core/hic then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+However, don't be put off by this template - other more general issues and suggestions are welcome!
+Contributions to the code are even more welcome ;)
 
+> If you need help using or modifying nf-core/hic then the best place to ask is on the nf-core
+Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 
 ## Contribution workflow
-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 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
-2. Fork the [nf-core/hic repository](https://github.com/nf-core/hic) to your GitHub account
+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
-4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged.
-
-If you're not used to this workflow with git, you can start with some [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/) or even their [excellent interactive tutorial](https://try.github.io/).
+4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
+If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
 
 ## Tests
-When you create a pull request with changes, [Travis CI](https://travis-ci.org/) will run automatic tests.
+
+When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
 There are typically two types of tests that run:
 
 ### Lint Tests
-The nf-core has a [set of guidelines](http://nf-co.re/guidelines) which all pipelines must adhere to.
+
+`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
 To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
 ### Pipeline Tests
-Each nf-core pipeline should be set up with a minimal set of test-data.
-Travis CI then runs the pipeline on this data to ensure that it exists successfully.
+
+Each `nf-core` pipeline should be set up with a minimal set of test-data.
+`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
 If there are any failures then the automated tests fail.
-These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.
+These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
+
+## Patch
+
+: 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.
 
 ## Getting help
-For further information/help, please consult the [nf-core/hic documentation](https://github.com/nf-core/hic#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/nf-core/hic/docs) and
+don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel
+([join our Slack here](https://nf-co.re/join/slack)).
+

.github/ISSUE_TEMPLATE/bug_report.md

+# nf-core/hic bug report
+
 Hi there!
 
-Thanks for telling us about a problem with the pipeline. Please delete this text and anything that's not relevant from the template below:
+Thanks for telling us about a problem with the pipeline.
+Please delete this text and anything that's not relevant from the template below:
+
+## Describe the bug
 
-#### Describe the bug
 A clear and concise description of what the bug is.
 
-#### Steps to reproduce
+## Steps to reproduce
+
 Steps to reproduce the behaviour:
+
 1. Command line: `nextflow run ...`
 2. See error: _Please provide your error message_
 
-#### Expected behaviour
+## Expected behaviour
+
 A clear and concise description of what you expected to happen.
 
-#### System:
- - Hardware: [e.g. HPC, Desktop, Cloud...]
- - Executor: [e.g. slurm, local, awsbatch...]
- - OS: [e.g. CentOS Linux, macOS, Linux Mint...]
- - Version [e.g. 7, 10.13.6, 18.3...]
+## System
+
+- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
+- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
+- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
+- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
+
+## Nextflow Installation
+
+- Version: <!-- [e.g. 19.10.0] -->
+
+## Container engine
 
-#### Nextflow Installation:
- - Version: [e.g. 0.31.0]
+- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- version: <!-- [e.g. 1.0.0] -->
+- Image tag: <!-- [e.g. nfcore/hic:1.0.0] -->
 
-#### Container engine:
- - Engine: [e.g. Conda, Docker or Singularity]
- - version: [e.g. 1.0.0]
- - Image tag: [e.g. nfcore/hic:1.0.0]
+## Additional context
 
-#### Additional context
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

+# nf-core/hic feature request
+
 Hi there!
 
-Thanks for suggesting a new feature for the pipeline! Please delete this text and anything that's not relevant from the template below:
+Thanks for suggesting a new feature for the pipeline!
+Please delete this text and anything that's not relevant from the template below:
+
+## Is your feature request related to a problem? Please describe
 
-#### Is your feature request related to a problem? Please describe.
 A clear and concise description of what the problem is.
+
 Ex. I'm always frustrated when [...]
 
-#### Describe the solution you'd like
+## Describe the solution you'd like
+
 A clear and concise description of what you want to happen.
 
-#### Describe alternatives you've considered
+## Describe alternatives you've considered
+
 A clear and concise description of any alternative solutions or features you've considered.
 
-#### Additional context
+## Additional context
+
 Add any other context about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

-Many thanks to contributing to nf-core/hic!
+# nf-core/hic pull request
 
-Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
+Many thanks for contributing to nf-core/hic!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
 
 ## PR checklist
- - [ ] 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 necessary, also make a PR on the [nf-core/hic branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/hic)
- - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
- - [ ] Make sure your code lints (`nf-core lint .`).
- - [ ] Documentation in `docs` is updated
- - [ ] `CHANGELOG.md` is updated
- - [ ] `README.md` is updated
-
-**Learn more about contributing:** https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md
+
+- [ ] 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 necessary, also make a PR on the [nf-core/hic branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/hic)
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Make sure your code lints (`nf-core lint .`).
+- [ ] Documentation in `docs` is updated
+- [ ] `CHANGELOG.md` is updated
+- [ ] `README.md` is updated
+
+**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
\ No newline at end of file

.github/markdownlint.yml

 # Markdownlint configuration file
 default: true,
 line-length: false
-no-multiple-blanks: 0
-blanks-around-headers: false
-blanks-around-lists: false
-header-increment: false
 no-duplicate-header:
     siblings_only: true

.github/workflows/branch.yml

+name: nf-core branch protection
+# This workflow is triggered on PRs to master branch on the repository
+# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+on:
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  test:
+    runs-on: ubuntu-18.04
+    steps:
+      # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
+      - name: Check PRs
+        run: |
+          { [[ $(git remote get-url origin) == *nf-core/hic ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]

.github/workflows/ci.yml

+name: nf-core CI
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on: [push, pull_request]
+
+jobs:
+  test:
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ['19.10.0', '']
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Pull docker image
+        run: |
+          docker pull nfcore/hic:dev
+          docker tag nfcore/hic:dev nfcore/hic:dev
+      - name: Run pipeline with test data
+        run: |
+          # nf-core: You can customise CI pipeline run tests as required
+          # (eg. adding multiple test runs with different parameters)
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker

.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
+on:
+  push:
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  Markdown:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+      - name: Install markdownlint
+        run: npm install -g markdownlint-cli
+      - name: Run Markdownlint
+        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+  YAML:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+      - name: Install yaml-lint
+        run: npm install -g yaml-lint
+      - name: Run yaml-lint
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
+  nf-core:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - uses: actions/setup-python@v1
+        with:
+          python-version: '3.6'
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core
+      - name: Run nf-core lint
+        run: nf-core lint ${GITHUB_WORKSPACE}

.gitignore

@@ -3,5 +3,6 @@ work/
 data/
 results/
 .DS_Store
-tests/test_data
+tests/
+testing/
 *.pyc

.travis.yml

-sudo: required
-language: python
-jdk: openjdk8
-services: docker
-python: '3.6'
-cache: pip
-matrix:
-  fast_finish: true
-
-before_install:
-  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))'
-  # Pull the docker image first so the test doesn't wait for this
-  - docker pull nfcore/hic:dev
-  # Fake the tag locally so that the pipeline runs properly
-  # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
-  - docker tag nfcore/hic:dev nfcore/hic:dev
-
-install:
-  # Install Nextflow
-  - mkdir /tmp/nextflow && cd /tmp/nextflow
-  - wget -qO- get.nextflow.io | bash
-  - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
-  # Install nf-core/tools
-  - pip install --upgrade pip
-  - pip install nf-core
-  # Reset
-  - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
-  # Install markdownlint-cli
-  - sudo apt-get install npm && npm install -g markdownlint-cli
-
-env:
-  - NXF_VER='19.04.0' # Specify a minimum NF version that should be tested and work
-  - NXF_VER='' # Plus: get the latest NF version and check that it works
-
-script:
-  # Lint the pipeline code
-  - nf-core lint ${TRAVIS_BUILD_DIR}
-  # Lint the documentation
-  - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
-  # Run the pipeline with the test profile
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker

CHANGELOG.md

 # nf-core/hic: Changelog
 
-## v1.1.1
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## v1.2.0dev - 2020-05-12
+
+### `Added`
+
+* Bump v1.2.0dev
+* Merge template nf-core 1.9
+* Move some options to camel_case
+* Update python scripts for python3
+* Update conda environment file
+  * python base `2.7.15` > `3.7.6`
+  * pip `19.1` > `20.0.1`
+  * scipy `1.2.1` > `1.4.1`
+  * numpy `1.16.3` > `1.18.1`
+  * bx-python `0.8.2` > `0.8.8`
+  * pysam `0.15.2` > `0.15.4`
+  * cooler `0.8.5` > `0.8.6`
+  * multiqc `1.7` > `1.8`
+  * iced `0.5.1` > `0.5.6`
+  * *_New_* pymdown-extensions `7.1`
+  * *_New_* hicexplorer `3.4.3`
+  * *_New_* bioconductor-hitc `1.32.0`
+  * *_New_* r-optparse `1.6.6`
+  * *_New_* ucsc-bedgraphtobigwig `377`
+  * *_New_* cooltools `0.3.2`
+  * *_New_* fanc `0.8.30`
+  * *_Removed_* r-markdown
+
+### `Fixed`
+
+* Sort output of `get_valid_interaction` process as the input files of `remove_duplicates`
+are expected to be sorted (sort -m)
+
+### `Deprecated`
+
+* Command line options converted to `camel_case`:
+  * `--skipMaps` > `--skip_maps`
+  * `--skipIce` > `--skip_ice`
+  * `--skipCool` > `--skip_cool`
+  * `--skipMultiQC` > `--skip_multiqc`
+  * `--saveReference` > `--save_reference`
+  * `--saveAlignedIntermediates` > `--save_aligned_intermediates`
+  * `--saveInteractionBAM` > `--save_interaction_bam`
+
+## v1.1.1 - 2020-04-02
+
+### `Fixed`
 
 * Fix bug in tag. Remove '['
 
 ## v1.1.0 - 2019-10-15
 
+### `Added`
+
 * Update hicpro2higlass with `-p` parameter
 * Support 'N' base motif in restriction/ligation sites
 * Support multiple restriction enzymes/ligattion sites (comma separated) ([#31](https://github.com/nf-core/hic/issues/31))
 * Add --saveInteractionBAM option
 * Add DOI ([#29](https://github.com/nf-core/hic/issues/29))
-* Fix bug for reads extension _1/_2 ([#30](https://github.com/nf-core/hic/issues/30))
 * Update manual ([#28](https://github.com/nf-core/hic/issues/28))
 
-## v1.0 - 2019-05-06
+### `Fixed`
+
+* Fix bug for reads extension `_1`/`_2` ([#30](https://github.com/nf-core/hic/issues/30))
+
+## v1.0 - [2019-05-06]
+
+Initial release of nf-core/hic, created with the [nf-core](http://nf-co.re/) template.
+
+### `Added`
 
 First version of nf-core Hi-C pipeline which is a Nextflow implementation of
 the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/).

CODE_OF_CONDUCT.md

@@ -56,7 +56,7 @@ project may be further defined and clarified by project maintainers.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported by contacting the project team on
-[Slack](https://nf-core-invite.herokuapp.com/). The project team will review
+[Slack](https://nf-co.re/join/slack). The project team will review
 and investigate all complaints, and will respond in a way that it deems
 appropriate to the circumstances. The project team is obligated to maintain
 confidentiality with regard to the reporter of an incident. Further details

Dockerfile

-FROM nfcore/base:1.7
+FROM nfcore/base:1.9
 LABEL authors="Nicolas Servant" \
-      description="Docker image containing all requirements for nf-core/hic pipeline"
+      description="Docker image containing all software requirements for the nf-core/hic pipeline"
 
 ## Install gcc for pip iced install
 RUN apt-get update && apt-get install -y gcc g++ && apt-get clean -y
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-hic-1.1.1dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-hic-1.2.0dev/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
+RUN conda env export --name nf-core-hic-1.2.0dev > nf-core-hic-1.2.0dev.yml
+

README.md

@@ -2,12 +2,12 @@
 
 **Analysis of Chromosome Conformation Capture data (Hi-C)**.
 
-[![Build Status](https://travis-ci.com/nf-core/hic.svg?branch=master)](https://travis-ci.com/nf-core/hic)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.04.0-brightgreen.svg)](https://www.nextflow.io/)
+[![GitHub Actions CI Status](https://github.com/nf-core/hic/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/hic/actions)
+[![GitHub Actions Linting Status](https://github.com/nf-core/hic/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/hic/actions)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/hic.svg)](https://hub.docker.com/r/nfcore/hic)
-![Singularity Container available](https://img.shields.io/badge/singularity-available-7E4C74.svg)
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2669513.svg)](https://doi.org/10.5281/zenodo.2669513)
 
@@ -43,9 +43,10 @@ sites (bowtie2)
 
 i. Install [`nextflow`](https://nf-co.re/usage/installation)
 
-ii. Install one of [`docker`](https://docs.docker.com/engine/installation/),
-[`singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or
-[`conda`](https://conda.io/miniconda.html)
+ii. Install either [`Docker`](https://docs.docker.com/engine/installation/)
+or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/)
+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))
 
 iii. Download the pipeline and test it on a minimal dataset with a single command
 
@@ -53,6 +54,12 @@ iii. Download the pipeline and test it on a minimal dataset with a single comman
 nextflow run nf-core/hic -profile test,<docker/singularity/conda/institute>
 ```
 
+> 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.
+
 iv. Start running your own analysis!
 
 ```bash
@@ -63,8 +70,8 @@ See [usage docs](docs/usage.md) for all of the available options when running th
 
 ## Documentation
 
-The nf-core/hic pipeline comes with documentation about the pipeline, found in
-the `docs/` directory:
+The nf-core/hic pipeline comes with documentation about the pipeline,
+found in the `docs/` directory:
 
 1. [Installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration
@@ -75,27 +82,34 @@ the `docs/` directory:
 4. [Output and how to interpret the results](docs/output.md)
 5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
-## Contributions and Support
-
-If you would like to contribute to this pipeline, please see the
-[contributing guidelines](.github/CONTRIBUTING.md).
-
 For further information or help, don't hesitate to get in touch on
 [Slack](https://nfcore.slack.com/channels/hic).
 You can join with [this invite](https://nf-co.re/join/slack).
 
-
 ## Credits
 
 nf-core/hic was originally written by Nicolas Servant.
 
+## Contributions and Support
+
+If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+
+For further information or help, don't hesitate to get in touch on
+[Slack](https://nfcore.slack.com/channels/hic) (you can join with
+[this invite](https://nf-co.re/join/slack)).
+
 ## Citation
 
 If you use nf-core/hic for your analysis, please cite it using the following
 doi: [10.5281/zenodo.2669513](https://doi.org/10.5281/zenodo.2669513)
 
-You can cite the `nf-core` pre-print as follows:
-Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di
-Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**.
-*bioRxiv*. 2019. p. 610741.
-[doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).
+You can cite the `nf-core` publication as follows:
+
+> **The nf-core framework for community-curated bioinformatics pipelines.**
+>
+> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg,
+Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+>
+> _Nat Biotechnol._ 2020 Feb 13.
+doi:[10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).  
+> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)

assets/email_template.html

@@ -11,6 +11,8 @@
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
+<img src="cid:nfcorepipelinelogo">
+
 <h1>nf-core/hic v${version}</h1>
 <h2>Run Name: $runName</h2>
 

assets/email_template.txt

-========================================
- nf-core/hic v${version}
-========================================
+----------------------------------------------------
+                                        ,--./,-.
+        ___     __   __   __   ___     /,-._.--~\\
+  |\\ | |__  __ /  ` /  \\ |__) |__         }  {
+  | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
+                                        `._,._,'
+  nf-core/hic v${version}
+----------------------------------------------------
+
 Run Name: $runName
 
 <% if (success){

assets/multiqc_config.yaml

@@ -3,7 +3,9 @@ report_comment: >
     analysis pipeline. For information about how to interpret these results, please see the
     <a href="https://github.com/nf-core/hic" target="_blank">documentation</a>.
 report_section_order:
-    nf-core/hic-software-versions:
+    software_versions:
         order: -1000
+    nf-core-hic-summary:
+        order: -1001
 
 export_plots: true

assets/sendmail_template.txt

@@ -8,6 +8,23 @@ Content-Type: text/html; charset=utf-8
 
 $email_html
 
+--nfcoremimeboundary
+Content-Type: image/png;name="nf-core-hic_logo.png"
+Content-Transfer-Encoding: base64
+Content-ID: <nfcorepipelinelogo>
+Content-Disposition: inline; filename="nf-core-hic_logo.png"
+
+<% out << new File("$baseDir/assets/nf-core-hic_logo.png").
+  bytes.
+  encodeBase64().
+  toString().
+  tokenize( '\n' )*.
+  toList()*.
+  collate( 76 )*.
+  collect { it.join() }.
+  flatten().
+  join( '\n' ) %>
+
 <%
 if (mqcFile){
 def mqcFileObj = new File("$mqcFile")