Merge pull request #101 from nf-core/dev

New version 1.3.0

.github/.dockstore.yml

@@ -3,3 +3,4 @@ version: 1.2
 workflows:
   - subclass: nfl
     primaryDescriptorPath: /nextflow.config
+    publish: True

.github/CONTRIBUTING.md

@@ -9,9 +9,7 @@ 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 nf-core
-Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
+> 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
 
@@ -20,8 +18,9 @@ If you'd like to write some code for nf-core/hic, the standard workflow is as fo
 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
-4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
+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).
+5. 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/).
 
@@ -32,14 +31,14 @@ Typically, pull-requests are only fully reviewed when these tests are passing, t
 
 There are typically two types of tests that run:
 
-### Lint Tests
+### Lint tests
 
 `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
+### Pipeline tests
 
 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.
@@ -55,8 +54,75 @@ These tests are run both with the latest available version of `Nextflow` and als
 * 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://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)).
 
-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)).
+For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/usage) 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)).
+
+## Pipeline contribution conventions
+
+To make the nf-core/hic code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+
+### Adding a new step
+
+If you wish to contribute a new step, please use the following coding standards:
+
+1. Define the corresponding input channel into your new process from the expected previous process channel
+2. Write the process block (see below).
+3. Define the output channel if needed (see below).
+4. Add any new flags/options to `nextflow.config` with a default (see below).
+5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`).
+6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
+7. Add sanity checks for all relevant parameters.
+8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
+9. Do local tests that the new code works properly and as expected.
+10. Add a new test command in `.github/workflow/ci.yaml`.
+11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
+12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
+13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+
+### Default values
+
+Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+
+Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.
+
+### Default processes resource requirements
+
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+
+### Naming schemes
+
+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>`
+
+### Nextflow version bumping
+
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+
+### Software version reporting
+
+If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
+
+Add to the script block of the process, something like the following:
+
+```bash
+<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
+```
+
+or
+
+```bash
+<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
+```
+
+You then need to edit the script `bin/scrape_software_versions.py` to:
+
+1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
+2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
+
+### Images and figures
+
+For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

.github/ISSUE_TEMPLATE/bug_report.md

+---
+name: Bug report
+about: Report something that is broken or incorrect
+labels: bug
+---
+
 <!--
 # nf-core/hic bug report
 
@@ -7,6 +13,13 @@ Thanks for telling us about a problem with the pipeline.
 Please delete this text and anything that's not relevant from the template below:
 -->
 
+## Check Documentation
+
+I have checked the following places for your error:
+
+- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+- [ ] [nf-core/hic pipeline documentation](https://nf-co.re/hic/usage)
+
 ## Description of the bug
 
 <!-- A clear and concise description of what the bug is. -->
@@ -22,6 +35,13 @@ Steps to reproduce the behaviour:
 
 <!-- A clear and concise description of what you expected to happen. -->
 
+## Log files
+
+Have you provided the following extra information/files:
+
+- [ ] The command used to run the pipeline
+- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the pipeline -->
+
 ## System
 
 - Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
@@ -35,7 +55,7 @@ Steps to reproduce the behaviour:
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/hic:1.0.0] -->
 

.github/ISSUE_TEMPLATE/config.yml

+blank_issues_enabled: false
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #hic channel"
+    url: https://nfcore.slack.com/channels/hic
+    about: Discussion about the nf-core/hic pipeline

.github/ISSUE_TEMPLATE/feature_request.md

+---
+name: Feature request
+about: Suggest an idea for the nf-core/hic pipeline
+labels: enhancement
+---
+
 <!--
 # nf-core/hic feature request
 
@@ -5,7 +11,6 @@ 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:
-
 -->
 
 ## Is your feature request related to a problem? Please describe
@@ -25,4 +30,3 @@ Please delete this text and anything that's not relevant from the template below
 ## Additional context
 
 <!-- Add any other context about the feature request here. -->
-

.github/PULL_REQUEST_TEMPLATE.md

@@ -10,12 +10,18 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
 -->
+<!-- markdownlint-disable ul-indent -->
 
 ## PR checklist
 
-- [ ] This comment contains a description of changes (with reason)
-- [ ] `CHANGELOG.md` is updated
+- [ ] This comment contains a description of changes (with reason).
 - [ ] 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)
-
+    - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
+    - [ ] 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`).
+- [ ] Usage Documentation in `docs/usage.md` is updated.
+- [ ] Output Documentation in `docs/output.md` is updated.
+- [ ] `CHANGELOG.md` is updated.
+- [ ] `README.md` is updated (including new tool citations and authors/contributors).

.github/markdownlint.yml

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

.github/workflows/awsfulltest.yml

 name: nf-core AWS full size tests
-# This workflow is triggered on push to the master branch.
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  workflow_run:
+    workflows: ["nf-core Docker push (release)"]
+    types: [completed]
+  workflow_dispatch:
+
+
+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 }}
+
 
 jobs:
   run-awstest:
@@ -13,7 +26,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7
@@ -23,13 +36,6 @@ jobs:
         # 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 \

.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
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It runs the -profile 'test' on AWS batch.
 
 on:
-  push:
-    branches:
-      - master
+  workflow_dispatch:
+
+
+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 }}
+
 
 jobs:
   run-awstest:
@@ -14,7 +23,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7
@@ -23,17 +32,10 @@ jobs:
       - name: Start AWS batch job
         # 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": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          --container-overrides '{"command": ["nf-core/hic", "-r '"${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/branch.yml

@@ -2,7 +2,7 @@ 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:
+  pull_request_target:
     branches: [master]
 
 jobs:
@@ -23,13 +23,22 @@ jobs:
         uses: mshick/add-pr-comment@v1
         with:
           message: |
+            ## This PR is against the `master` branch :x:
+
+            * Do not close this PR
+            * Click _Edit_ and change the `base` to `dev`
+            * This CI test will remain failed until you push a new commit
+
+            ---
+
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{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 ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{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.
+            Note that even after this, the test will continue to show as failing until you push a new commit.
 
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ci.yml

@@ -8,6 +8,9 @@ on:
   release:
     types: [published]
 
+# Uncomment if we need an edge release of Nextflow again
+# env: NXF_EDGE: 1
+
 jobs:
   test:
     name: Run workflow tests
@@ -20,29 +23,31 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['19.10.0', '']
+        nxf_ver: ['20.04.0', '']
     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
+        uses: technote-space/get-diff-action@v4
         with:
-          PREFIX_FILTER: |
+          FILES: |
             Dockerfile
             environment.yml
 
       - name: Build new docker image
-        if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/hic:1.2.2
+        if: env.MATCHED_FILES
+        run: docker build --no-cache . -t nfcore/hic:1.3.0
 
       - name: Pull docker image
-        if: ${{ !env.GIT_DIFF }}
+        if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/hic:dev
-          docker tag nfcore/hic:dev nfcore/hic:1.2.2
+          docker tag nfcore/hic:dev nfcore/hic:1.3.0
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/

.github/workflows/linting.yml

@@ -19,6 +19,34 @@ jobs:
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
         run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.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: |
+            ## 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 . --config .github/markdownlint.yml --fix`
+                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
+
+            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
+
+
   YAML:
     runs-on: ubuntu-latest
     steps:
@@ -29,13 +57,44 @@ jobs:
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
+
+      # 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 `yaml-lint`
+                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
+            * Fix the markdown errors
+                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
+                * Fix any reported errors in your YAML files
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            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!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
+
       - name: Check out pipeline code
         uses: actions/checkout@v2
+
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
@@ -55,11 +114,19 @@ jobs:
           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 -l lint_log.txt lint ${GITHUB_WORKSPACE}
+        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE} --markdown lint_results.md
+
+      - name: Save PR number
+        if: ${{ always() }}
+        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v2
         with:
-          name: linting-log-file
-          path: lint_log.txt
+          name: linting-logs
+          path: |
+            lint_log.txt
+            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
+
+on:
+  workflow_run:
+    workflows: ["nf-core linting"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download lint results
+        uses: dawidd6/action-download-artifact@v2
+        with:
+          workflow: linting.yml
+
+      - name: Get PR number
+        id: pr_number
+        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+
+      - name: Post PR comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          number: ${{ steps.pr_number.outputs.pr_number }}
+          path: linting-logs/lint_results.md
+

.github/workflows/push_dockerhub_dev.yml

+name: nf-core Docker push (dev)
+# 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
+
+jobs:
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub (dev)
+    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: ${{ secrets.DOCKERHUB_PASS }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache . -t nfcore/hic:dev
+
+      - name: Push Docker image to DockerHub (dev)
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/hic:dev

.github/workflows/push_dockerhub.yml → .github/workflows/push_dockerhub_release.yml

-name: nf-core Docker push
+name: nf-core Docker push (release)
 # 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]
 
 jobs:
   push_dockerhub:
-    name: Push new Docker image to Docker Hub
+    name: Push new Docker image to Docker Hub (release)
     runs-on: ubuntu-latest
     # Only run for the nf-core repo, for releases and merged PRs
     if: ${{ github.repository == 'nf-core/hic' }}
@@ -24,15 +21,7 @@ jobs:
       - 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

.nf-core-lint.yml

+files_unchanged:
+  - .github/ISSUE_TEMPLATE/bug_report.md
+  - .github/PULL_REQUEST_TEMPLATE.md

CHANGELOG.md

@@ -3,6 +3,32 @@
 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).
 
+## v1.3.0 - 2021-22-05
+
+* Change the `/tmp/` folder to `./tmp/` folder so that all tmp files are now in the work directory (#24)
+* Add `--hicpro_maps` options to generate the raw and normalized HiC-Pro maps. The default is now to use cooler
+* Add chromosome compartments calling with cooltools (#53)
+* Add HiCExplorer distance decay quality control (#54)
+* Add HiCExplorer TADs calling (#55)
+* Add insulation score TADs calling (#55)
+* Generate cooler/txt contact maps
+* Normalize Hi-C data with cooler instead of iced
+* New `--digestion` parameter to automatically set the restriction_site and ligation_site motifs
+* New `--keep_multi` and `keep_dup` options. Default: false
+* Template update for nf-core/tools
+* Minor fix to summary log messages in pipeline header
+
+### `Fixed`
+
+* Fix bug in stats report which were not all correcly exported in the results folder
+* Fix recurrent bug in input file extension (#86)
+* Fix bug in `--bin_size` parameter (#85)
+* `--min_mapq` is ignored if `--keep_multi` is used
+
+### `Deprecated`
+
+* `--rm_dup` and `--rm_multi` are replaced by `--keep_dups` and `--keep_multi`
+
 ## v1.2.2 - 2020-09-02
 
 ### `Added`

CODE_OF_CONDUCT.md

-# Contributor Covenant Code of Conduct
+# Code of Conduct at nf-core (v1.0)
 
 ## Our Pledge
 
-In the interest of fostering an open and welcoming environment, we as
-contributors and maintainers pledge to making participation in our project
-and our community a harassment-free experience for everyone, regardless of
-age, body size, disability, ethnicity, gender identity and expression, level
-of experience, nationality, personal appearance, race, religion, or sexual
-identity and orientation.
+In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of:
 
-## Our Standards
+- Age
+- Body size
+- Familial status
+- Gender identity and expression
+- Geographical location
+- Level of experience
+- Nationality and national origins
+- Native language
+- Physical and neurological ability
+- Race or ethnicity
+- Religion
+- Sexual identity and orientation
+- Socioeconomic status
 
-Examples of behavior that contributes to creating a positive environment
-include:
+Please note that the list above is alphabetised and is therefore not ranked in any order of preference or importance.
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+## Preamble
 
-Examples of unacceptable behavior by participants include:
+> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply.
 
-* The use of sexualized language or imagery and unwelcome sexual attention
-or advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic
-address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
-professional setting
+An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva.
+
+nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals.
+
+We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc.
+
+Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities.
+
+We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC.
+
+Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re
 
 ## Our Responsibilities
 
-Project maintainers are responsible for clarifying the standards of acceptable
-behavior and are expected to take appropriate and fair corrective action in
-response to any instances of unacceptable behavior.
+The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
+
+The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC.
+
+## When are where does this Code of Conduct apply?
+
+Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference:
+
+- Communicating with an official project email address.
+- Communicating with community members within the nf-core Slack channel.
+- Participating in hackathons organised by nf-core (both online and in-person events).
+- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence.
+- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc.
+- Representing nf-core on social media. This includes both official and personal accounts.
+
+## nf-core cares 😊
+
+nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order):
+
+- Ask for consent before sharing another community member’s personal information (including photographs) on social media.
+- Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity.
+- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !)
+- Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.)
+- Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can)
+- Focus on what is best for the team and the community. (When in doubt, ask)
+- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn.
+- Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!)
+- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**)
+- Take breaks when you feel like you need them.
+- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.)
+
+## nf-core frowns on 😕
+
+The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces.
+
+- Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom.
+- “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online.
+- Spamming or trolling of individuals on social media.
+- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention.
+- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience.
+
+### Online Trolling
+
+The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately.
+
+All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls.
+
+## Procedures for Reporting CoC violations
 
-Project maintainers have the right and responsibility to remove, edit, or
-reject comments, commits, code, wiki edits, issues, and other contributions
-that are not aligned to this Code of Conduct, or to ban temporarily or
-permanently any contributor for other behaviors that they deem inappropriate,
-threatening, offensive, or harmful.
+If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible.
 
-## Scope
+You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s).
 
-This Code of Conduct applies both within project spaces and in public spaces
-when an individual is representing the project or its community. Examples of
-representing a project or community include using an official project e-mail
-address, posting via an official social media account, or acting as an
-appointed representative at an online or offline event. Representation of a
-project may be further defined and clarified by project maintainers.
+Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course.
 
-## Enforcement
+All reports will be handled with utmost discretion and confidentially.
 
-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.
+## Attribution and Acknowledgements
 
-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.
+- The [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4)
+- The [OpenCon 2017 Code of Conduct](http://www.opencon2017.org/code_of_conduct) (CC BY 4.0 OpenCon organisers, SPARC and Right to Research Coalition)
+- The [eLife innovation sprint 2020 Code of Conduct](https://sprint.elifesciences.org/code-of-conduct/)
+- The [Mozilla Community Participation Guidelines v3.1](https://www.mozilla.org/en-US/about/governance/policies/participation/) (version 3.1, CC BY-SA 3.0 Mozilla)
 
-## Attribution
+## Changelog
 
-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]
+### v1.0 - March 12th, 2021
 
-[homepage]: https://contributor-covenant.org
-[version]: https://www.contributor-covenant.org/version/1/4/code-of-conduct/
+- Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC.

Dockerfile

-FROM nfcore/base:1.10.2
-
+FROM nfcore/base:1.14
 LABEL authors="Nicolas Servant" \
       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
 
+# Install the conda environment
 COPY environment.yml /
 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-1.2.2/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-hic-1.3.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-hic-1.2.2 > nf-core-hic-1.2.2.yml
+RUN conda env export --name nf-core-hic-1.3.0 > nf-core-hic-1.3.0.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

README.md

-# ![nf-core/hic](docs/images/nfcore-hic_logo.png)
+# ![nf-core/hic](docs/images/nf-core-hic_logo.png)
 
 **Analysis of Chromosome Conformation Capture data (Hi-C)**.
 
 [![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/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.04.0-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)
@@ -14,7 +14,7 @@
 
 ## Introduction
 
-This pipeline is based on the
+This pipeline was originally set up from the
 [HiC-Pro workflow](https://github.com/nservant/HiC-Pro).
 It was designed to process Hi-C data from raw FastQ files (paired-end Illumina
 data) to normalized contact maps.
@@ -24,6 +24,10 @@ In practice, this workflow was successfully applied to many data-sets including
 dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or
 HiChip data.
 
+Contact maps are generated in standard formats including HiC-Pro, and cooler for
+downstream analysis and visualization.
+Addition analysis steps such as compartments and TADs calling are also available.
+
 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
@@ -31,28 +35,30 @@ results highly reproducible.
 
 ## Pipeline summary
 
+1. HiC-Pro data processing ([`HiC-Pro`](https://github.com/nservant/HiC-Pro))
    1. Mapping using a two steps strategy to rescue reads spanning the ligation
-sites (bowtie2)
+   sites ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
    2. Detection of valid interaction products
    3. Duplicates removal
-4. Create genome-wide contact maps at various resolution
-5. Contact maps normalization using the ICE algorithm (iced)
-6. Quality controls and report (MultiQC)
-7. Addition export for visualisation and downstream analysis (cooler)
+   4. Generate raw and normalized contact maps ([`iced`](https://github.com/hiclib/iced))
+2. Create genome-wide contact maps at various resolutions ([`cooler`](https://github.com/open2c/cooler))
+3. Contact maps normalization using balancing algorithm ([`cooler`](https://github.com/open2c/cooler))
+4. Export to various contact maps formats ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`cooler`](https://github.com/open2c/cooler))
+5. Quality controls ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`HiCExplorer`](https://github.com/deeptools/HiCExplorer))
+6. Compartments calling ([`cooltools`](https://cooltools.readthedocs.io/en/latest/))
+7. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooltools`](https://cooltools.readthedocs.io/en/latest/))
+8. Quality control report ([`MultiQC`](https://multiqc.info/))
 
 ## Quick Start
 
-i. Install [`nextflow`](https://nf-co.re/usage/installation)
+1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=20.04.0`)
 
-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))
+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))_
 
-iii. Download the pipeline and test it on a minimal dataset with a single command
+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>
+    nextflow run nf-core/hic -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
     > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation)
@@ -61,35 +67,17 @@ 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!
+4. Start running your own analysis!
 
     ```bash
-nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
+    nextflow run nf-core/hic -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
     ```
 
-See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running
-the pipeline.
-
 ## Documentation
 
-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
-    * [Local installation](https://nf-co.re/usage/local_installation)
-    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
-    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
-3. [Running the pipeline](docs/usage.md)
-4. [Output and how to interpret the results](docs/output.md)
-5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
-
-The nf-core/hic pipeline comes with documentation about the pipeline which
-you can read at [https://nf-co.re/hic/usage](https://nf-co.re/hic/usage) or
-find in the [`docs/` directory](docs).
+The nf-core/hic pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/hic/usage) and [output](https://nf-co.re/hic/output).
 
-For further information or help, don't hesitate to get in touch on
-[Slack](https://nfcore.slack.com/channels/hic).
+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
@@ -100,9 +88,7 @@ nf-core/hic was originally written by Nicolas Servant.
 
 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)).
+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
 
@@ -113,8 +99,14 @@ 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.
+> 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)
+
+In addition, references of tools and data used in this pipeline are as follows:
+
+> **HiC-Pro: An optimized and flexible pipeline for Hi-C processing.**
+>
+> Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chongjian Chen, Jean-Philippe Vert, Job Dekker, Edith Heard, Emmanuel Barillot.
+>
+> Genome Biology 2015, 16:259 doi: [10.1186/s13059-015-0831-x](https://dx.doi.org/10.1186/s13059-015-0831-x)