Template update for nf-core/tools version 1.10.1

.github/.dockstore.yml

+# Dockstore config version, not pipeline version
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /nextflow.config

.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 ;)
+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 go is the Gitter chatroom where you can ask us questions directly: https://gitter.im/nf-core/Lobby
+> 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 [Gitter](https://gitter.im/nf-core/Lobby)
+
+For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/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:
+-->
+
+## Description of the bug
 
-#### Describe the bug
-A clear and concise description of what the bug is.
+<!-- 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
-A clear and concise description of what you expected to happen.
+1. Command line: <!-- [e.g. `nextflow run ...`] -->
+2. See error: <!-- [Please provide your error message] -->
+
+## 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...] -->
+
+## Nextflow Installation
+
+- Version: <!-- [e.g. 19.10.0] -->
 
-#### 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...]
+## 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.
+<!-- 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
+
+<!-- A clear and concise description of what the problem is. -->
+
+<!-- e.g. [I'm always frustrated when ...] -->
+
+## Describe the solution you'd like
+
+<!-- A clear and concise description of what you want to happen. -->
 
-#### 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 alternatives you've considered
 
-#### Describe the solution you'd like
-A clear and concise description of what you want to happen.
+<!-- A clear and concise description of any alternative solutions or features 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.
+<!-- 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).
+
+Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
+-->
 
 ## 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)
+- [ ] `CHANGELOG.md` is updated
+- [ ] If you've fixed a bug or added code that should be tested, add tests!
+- [ ] Documentation in `docs` is updated
+- [ ] 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)

.github/markdownlint.yml

+# Markdownlint configuration file
+default: true,
+line-length: false
+no-duplicate-header:
+    siblings_only: true

.github/workflows/awsfulltest.yml

+name: nf-core AWS full size tests
+# This workflow is triggered on push to the master branch.
+# It runs the -profile 'test_full' on AWS batch
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  run-awstest:
+    name: Run AWS full tests
+    if: github.repository == 'nf-core/hic'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Miniconda
+        uses: goanpeca/setup-miniconda@v1.0.2
+        with:
+          auto-update-conda: true
+          python-version: 3.7
+      - name: Install awscli
+        run: conda install -c conda-forge awscli
+      - name: Start AWS batch job
+        # 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
+        # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
+        env:
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+        run: |
+          aws batch submit-job \
+            --region eu-west-1 \
+            --job-name nf-core-hic \
+            --job-queue $AWS_JOB_QUEUE \
+            --job-definition $AWS_JOB_DEFINITION \
+            --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/awstest.yml

+name: nf-core AWS test
+# This workflow is triggered on push to the master branch.
+# It runs the -profile 'test' on AWS batch
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  run-awstest:
+    name: Run AWS tests
+    if: github.repository == 'nf-core/hic'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Miniconda
+        uses: goanpeca/setup-miniconda@v1.0.2
+        with:
+          auto-update-conda: true
+          python-version: 3.7
+      - name: Install awscli
+        run: conda install -c conda-forge awscli
+      - name: Start AWS batch job
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        # For example: adding multiple test runs with different parameters
+        # Remember that you can parallelise this by using strategy.matrix
+        env:
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+        run: |
+          aws batch submit-job \
+          --region eu-west-1 \
+          --job-name nf-core-hic \
+          --job-queue $AWS_JOB_QUEUE \
+          --job-definition $AWS_JOB_DEFINITION \
+          --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.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-latest
+    steps:
+      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      - 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" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Hi @${{ github.event.pull_request.user.login }},
+
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            The `master` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+
+            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+

.github/workflows/ci.yml

+name: nf-core CI
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  test:
+    name: Run workflow tests
+    # 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') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ['19.10.0', '']
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v1
+        with:
+          PREFIX_FILTER: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.GIT_DIFF
+        run: docker build --no-cache . -t nfcore/hic:dev
+
+      - name: Pull docker image
+        if: ${{ !env.GIT_DIFF }}
+        run: |
+          docker pull nfcore/hic:dev
+          docker tag nfcore/hic:dev nfcore/hic:dev
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with test data
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        # For example: adding multiple test runs with different parameters
+        # Remember that you can parallelise this by using strategy.matrix
+        run: |
+          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:
+
+      - name: Check out pipeline code
+        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
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core lint ${GITHUB_WORKSPACE}
+

.github/workflows/push_dockerhub.yml

+name: nf-core Docker push
+# This builds the docker image and pushes it to DockerHub
+# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
+on:
+  push:
+    branches:
+      - dev
+  release:
+    types: [published]
+
+push_dockerhub:
+  name: Push new Docker image to Docker Hub
+  runs-on: ubuntu-latest
+  # Only run for the nf-core repo, for releases and merged PRs
+  if: ${{ github.repository == 'nf-core/hic' }}
+  env:
+    DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+    DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+  steps:
+    - name: Check out pipeline code
+      uses: actions/checkout@v2
+
+    - name: Build new docker image
+      run: docker build --no-cache . -t nfcore/hic:latest
+
+    - name: Push Docker image to DockerHub (dev)
+      if: ${{ github.event_name == 'push' }}
+      run: |
+        echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+        docker tag nfcore/hic:latest nfcore/hic:dev
+        docker push nfcore/hic:dev
+
+    - name: Push Docker image to DockerHub (release)
+      if: ${{ github.event_name == 'release' }}
+      run: |
+        echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+        docker push nfcore/hic:latest
+        docker tag nfcore/hic:latest nfcore/hic:${{ github.event.release.tag_name }}
+        docker push nfcore/hic:${{ github.event.release.tag_name }}

.gitignore

@@ -3,4 +3,7 @@ work/
 data/
 results/
 .DS_Store
-tests/test_data
+tests/
+testing/
+testing*
+*.pyc

.travis.yml

-sudo: required
-language: python
-jdk: openjdk8
-services: docker
-python: '3.6'
-cache: pip
-matrix:
-  fast_finish: true
-
-before_install:
-  # PRs to master are only ok if coming from dev branch
-  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
-  # 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
-  - docker tag nfcore/hic:dev nfcore/hic:latest
-
-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
-
-env:
-  - NXF_VER='0.32.0' # 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}
-  # Run the pipeline with the test profile
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker

CHANGELOG.md

 # nf-core/hic: Changelog
 
-## v1.0dev - <date>
-Initial release of nf-core/hic, created with the [nf-core](http://nf-co.re/) template.
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## v1.2.1 - [date]
+
+Initial release of nf-core/hic, created with the [nf-core](https://nf-co.re/) template.
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`

CODE_OF_CONDUCT.md

@@ -34,13 +34,13 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on the [Gitter channel](https://gitter.im/nf-core/Lobby). 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 of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [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 of specific enforcement policies may be posted separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct/][version]
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+[homepage]: https://contributor-covenant.org
+[version]: https://www.contributor-covenant.org/version/1/4/code-of-conduct/

Dockerfile

-FROM nfcore/base
+FROM nfcore/base:1.10.1
 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 the conda environment
 COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-hic-1.0dev/bin:$PATH
+RUN conda env create --quiet -f /environment.yml && conda clean -a
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
+ENV PATH /opt/conda/envs/nf-core-hic-1.2.1/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
+RUN conda env export --name nf-core-hic-1.2.1 > nf-core-hic-1.2.1.yml
+
+# Instruct R processes to use these empty files instead of clashing with a local version
+RUN touch .Rprofile
+RUN touch .Renviron

README.md

-# nf-core/hic
-**Analysis of Chromosome Conformation Capture data (Hi-C)**
+# ![nf-core/hic](docs/images/nf-core-hic_logo.png)
 
-[![Build Status](https://travis-ci.org/nf-core/hic.svg?branch=master)](https://travis-ci.org/nf-core/hic)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
+**Analysis of Chromosome Conformation Capture data (Hi-C)**.
 
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.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)](https://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)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hic-4A154B?logo=slack)](https://nfcore.slack.com/channels/hic)
+
+## Introduction
+
+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 comes with docker containers making installation trivial and results highly reproducible.
+
+## Quick Start
+
+1. Install [`nextflow`](https://nf-co.re/usage/installation)
+
+2. 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))_
+
+3. Download the pipeline and test it on a minimal dataset with a single command:
+
+    ```bash
+    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.
+
+4. Start running your own analysis!
 
-### Introduction
-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 comes with docker / singularity containers making installation trivial and results highly reproducible.
+    <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
+    ```bash
+    nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
+    ```
 
-### Documentation
-The nf-core/hic pipeline comes with documentation about the pipeline, found in the `docs/` directory:
+See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
 
-1. [Installation](docs/installation.md)
-2. Pipeline configuration
-    * [Local installation](docs/configuration/local.md)
-    * [Adding your own system](docs/configuration/adding_your_own.md)
-    * [Reference genomes](docs/configuration/reference_genomes.md)  
-3. [Running the pipeline](docs/usage.md)
-4. [Output and how to interpret the results](docs/output.md)
-5. [Troubleshooting](docs/troubleshooting.md)
+## Documentation
+
+The nf-core/hic pipeline comes with documentation about the pipeline which you can read at [https://nf-core/hic/docs](https://nf-core/hic/docs) or find in the [`docs/` directory](docs).
 
 <!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works -->
 
-### Credits
+## 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 the [Slack `#hic` channel](https://nfcore.slack.com/channels/hic) (you can join with [this invite](https://nf-co.re/join/slack)).
+
+## Citation
+
+<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. -->
+<!-- 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) -->
+
+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)

Singularity

-From:nfcore/base
-Bootstrap:docker
-
-%labels
-    MAINTAINER Nicolas Servant
-    DESCRIPTION Singularity image containing all requirements for the nf-core/hic pipeline
-    VERSION 1.0dev
-
-%environment
-    PATH=/opt/conda/envs/nf-core-hic-1.0dev/bin:$PATH
-    export PATH
-
-%files
-    environment.yml /
-
-%post
-    /opt/conda/bin/conda env create -f /environment.yml
-    /opt/conda/bin/conda clean -a

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>