From e013105dc4015a9cb2434fcde6089598f5ad3f40 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Mon, 11 May 2020 17:04:05 +0200
Subject: [PATCH] Template update for nf-core/tools version 1.9

---
 .github/CONTRIBUTING.md                       |  50 +-
 .github/ISSUE_TEMPLATE/bug_report.md          |  43 +-
 .github/ISSUE_TEMPLATE/feature_request.md     |  18 +-
 .github/PULL_REQUEST_TEMPLATE.md              |  28 +-
 .github/markdownlint.yml                      |   5 +
 .github/workflows/branch.yml                  |  16 +
 .github/workflows/ci.yml                      |  30 ++
 .github/workflows/linting.yml                 |  50 ++
 .gitignore                                    |   4 +-
 .travis.yml                                   |  37 --
 CHANGELOG.md                                  |  14 +-
 CODE_OF_CONDUCT.md                            |   2 +-
 Dockerfile                                    |  12 +-
 README.md                                     |  76 ++-
 Singularity                                   |  18 -
 assets/email_template.html                    |   2 +
 assets/email_template.txt                     |  29 +-
 {conf => assets}/multiqc_config.yaml          |   6 +-
 assets/nf-core-hic_logo.png                   | Bin 0 -> 10282 bytes
 assets/sendmail_template.txt                  |  48 +-
 .../scrape_software_versions.cpython-36.pyc   | Bin 1324 -> 0 bytes
 bin/markdown_to_html.py                       | 100 ++++
 bin/markdown_to_html.r                        |  51 --
 bin/scrape_software_versions.py               |  27 +-
 conf/awsbatch.config                          |  13 -
 conf/base.config                              |  46 +-
 conf/igenomes.config                          | 451 ++++++++++++++----
 conf/test.config                              |   9 +-
 docs/README.md                                |  10 +-
 docs/configuration/adding_your_own.md         |  86 ----
 docs/configuration/local.md                   |  46 --
 docs/configuration/reference_genomes.md       |  49 --
 docs/images/nf-core-hic_logo.png              | Bin 0 -> 17777 bytes
 docs/installation.md                          | 110 -----
 docs/output.md                                |   6 +-
 docs/troubleshooting.md                       |  30 --
 docs/usage.md                                 | 193 +++++---
 environment.yml                               |  12 +-
 main.nf                                       | 378 +++++++++------
 nextflow.config                               |  81 ++--
 40 files changed, 1282 insertions(+), 904 deletions(-)
 create mode 100644 .github/markdownlint.yml
 create mode 100644 .github/workflows/branch.yml
 create mode 100644 .github/workflows/ci.yml
 create mode 100644 .github/workflows/linting.yml
 delete mode 100644 .travis.yml
 delete mode 100644 Singularity
 rename {conf => assets}/multiqc_config.yaml (79%)
 create mode 100644 assets/nf-core-hic_logo.png
 delete mode 100644 bin/__pycache__/scrape_software_versions.cpython-36.pyc
 create mode 100755 bin/markdown_to_html.py
 delete mode 100755 bin/markdown_to_html.r
 delete mode 100644 conf/awsbatch.config
 delete mode 100644 docs/configuration/adding_your_own.md
 delete mode 100644 docs/configuration/local.md
 delete mode 100644 docs/configuration/reference_genomes.md
 create mode 100644 docs/images/nf-core-hic_logo.png
 delete mode 100644 docs/installation.md
 delete mode 100644 docs/troubleshooting.md

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index fda99de..276f0e6 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,45 +1,57 @@
 # 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/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)).
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index 8112c95..2b92033 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -1,31 +1,42 @@
+# 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.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
index 1f025b7..57fa7f7 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -1,16 +1,24 @@
+# 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.
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 473c41d..50d7959 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,15 +1,19 @@
-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
diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml
new file mode 100644
index 0000000..96b12a7
--- /dev/null
+++ b/.github/markdownlint.yml
@@ -0,0 +1,5 @@
+# Markdownlint configuration file
+default: true,
+line-length: false
+no-duplicate-header:
+    siblings_only: true
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
new file mode 100644
index 0000000..e95804c
--- /dev/null
+++ b/.github/workflows/branch.yml
@@ -0,0 +1,16 @@
+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" ]]
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..2fe7083
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,30 @@
+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: |
+          # TODO 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
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
new file mode 100644
index 0000000..1e0827a
--- /dev/null
+++ b/.github/workflows/linting.yml
@@ -0,0 +1,50 @@
+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}
diff --git a/.gitignore b/.gitignore
index 46f69e4..6354f37 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,6 @@ work/
 data/
 results/
 .DS_Store
-tests/test_data
+tests/
+testing/
+*.pyc
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 381c4cf..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-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
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0b88e32..7566331 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,16 @@
 # nf-core/hic: Changelog
 
-## v1.0dev - <date>
+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).
+
+## v1.1.1dev - [date]
+
 Initial release of nf-core/hic, created with the [nf-core](http://nf-co.re/) template.
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
index 2109619..cf930c8 100644
--- a/CODE_OF_CONDUCT.md
+++ b/CODE_OF_CONDUCT.md
@@ -34,7 +34,7 @@ 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.
 
diff --git a/Dockerfile b/Dockerfile
index 4d28385..2c53847 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,13 @@
-FROM nfcore/base
+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 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:$PATH
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
+ENV PATH /opt/conda/envs/nf-core-hic-1.1.1dev/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
+RUN conda env export --name nf-core-hic-1.1.1dev > nf-core-hic-1.1.1dev.yml
diff --git a/README.md b/README.md
index 192fa0d..51bef77 100644
--- a/README.md
+++ b/README.md
@@ -1,31 +1,77 @@
-# 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)**.
+
+[![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)
 
-### 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.
+## 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
+
+i. Install [`nextflow`](https://nf-co.re/usage/installation)
+
+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
+
+```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.
+
+iv. Start running your own analysis!
+
+<!-- TODO nf-core: Update the default command above used to run the pipeline -->
 
+```bash
+nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
+```
+
+See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
+
+## Documentation
 
-### Documentation
 The nf-core/hic pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
-1. [Installation](docs/installation.md)
+1. [Installation](https://nf-co.re/usage/installation)
 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)  
+    * [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](docs/troubleshooting.md)
+5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
 <!-- 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 [Slack](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)
diff --git a/Singularity b/Singularity
deleted file mode 100644
index 927866f..0000000
--- a/Singularity
+++ /dev/null
@@ -1,18 +0,0 @@
-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
diff --git a/assets/email_template.html b/assets/email_template.html
index bf19807..177bccd 100644
--- a/assets/email_template.html
+++ b/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>
 
diff --git a/assets/email_template.txt b/assets/email_template.txt
index 59d7b54..a951c5e 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -1,6 +1,12 @@
-========================================
- nf-core/hic v${version}
-========================================
+----------------------------------------------------
+                                        ,--./,-.
+        ___     __   __   __   ___     /,-._.--~\\
+  |\\ | |__  __ /  ` /  \\ |__) |__         }  {
+  | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
+                                        `._,._,'
+  nf-core/hic v${version}
+----------------------------------------------------
+
 Run Name: $runName
 
 <% if (success){
@@ -17,23 +23,6 @@ ${errorReport}
 } %>
 
 
-<% if (!success){
-    out << """####################################################
-## nf-core/hic execution completed unsuccessfully! ##
-####################################################
-The exit status of the task that caused the workflow execution to fail was: $exitStatus.
-The full error message was:
-
-${errorReport}
-"""
-} else {
-    out << "## nf-core/hic execution completed successfully! ##"
-}
-%>
-
-
-
-
 The workflow was completed at $dateComplete (duration: $duration)
 
 The command used to launch the workflow was as follows:
diff --git a/conf/multiqc_config.yaml b/assets/multiqc_config.yaml
similarity index 79%
rename from conf/multiqc_config.yaml
rename to assets/multiqc_config.yaml
index f2a738c..41468ca 100644
--- a/conf/multiqc_config.yaml
+++ b/assets/multiqc_config.yaml
@@ -3,5 +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
diff --git a/assets/nf-core-hic_logo.png b/assets/nf-core-hic_logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..6b364161664e70224fac3a83fb9f02ed0acbd9f8
GIT binary patch
literal 10282
zcmeAS@N?(olHy`uVBq!ia0y~yV4T3fz_6Bsje&t-o{lCr0|NtRfk$L90|Va?5N4dJ
z%_q&kpuphi;uumf=k49<nmM6!e|$V|dH#&b%w>vgQAyjU-D(TsQVI*Gf5H9B`MRsf
z&J(WT@5BTJ^nYCX`YBoSwf9BwT^(KF4i2o0qA8IfDN8q1M3%5F6lvMgGD|F~iZgfC
zlF2iR>+0vsOqq1%sg3dHGd`Ez&%Qpv?xgW^OXHJs-WR`9Xc2JYP^1=dbfsIm1BYVT
zCQ)|TmW$hh7xHm3+3sJubglB#TgEf|mYXyBOD1pAk-C?h_v&?aNtp9w2Bj7O({JDA
z$+ZbP@+|e=SYY?TO(FC1xszi1G9MT|*d)GoSNYppTT9Ppo0cp#R%j70KG`LzEs@tL
zpEUJfb8ED&O!7ug@46owZvO9xjNsd|JN5cHx73|U8zBzq3jW?M9)IUg7`HvERf8kz
ze#WcZDvg`(T<7ey&z=%A-S*S>{pJeCuTBKJ<I|%z&3xOZSvQtF(0lMGEZgknw_1;-
zmp7zaq&_?x!R^J%c>l;P?J%2<PaeE#d$z~u5<AHC1z$ET^_=o6K0&j9d&TDZ-$!nh
z{Ik^Ni@TK-C?7ImL&53C=kwp)-&b3mY!t&R<j^9p$m@O8+w4kB(@&b*;aV?3S6p9L
zm-IGa@n=!f%tJy>CbzCPwz}4RvwqP1^|V)N+%4ldE-U*r91e<BJAYu{RB-AzW+k(u
z<B_t{{@~+#LVPq!=d|V}bZ`8#=Hkzl;+zVJcj~md&+ZdglBBh4S4hnHt&+D>*Iw1S
z;4HDbv*)H!*6rZ8GoM#J+F~s=H(7DkT~!f&xxEMUU(cA{6=PFvmi>T*TVqGQg{jq*
z7dBVBSp?+G=Q#U^UuX<ccm7qerq1?8-fT0e?l1<)WQGe>*)jaKHbNzH_}-Y-dpLzG
zkhWNR<ox=hzFV@h{Pz^a@kB6+wf?%h?BPSV^p$xk4O1=_KR>0?xJxA2u5DxN&4=YX
z);AoLm0o>!<6Q1vYaN(46`ZCN$z6zgl5X8N`}K_Jr&cD&-Kad(>lwAX@bNLX=PUA5
z8bmfeY7G7I{#AV2Q$C}#$Zb_!p;?!%pS(YPVXjj}2CJUV$IsG@nTGqWCQYA|+qU_J
zFYh_OSWgDcMfKN@rKY@LUgx$j;ASdE$hZHh{Zm^66i-=5&WL}KuK6Ik^o)1tl%&Ru
zVy#T4;|zakxnDb^wcz==sh&MMdEdk^OqpBZv@==JMN{f}W!#zC1Hq-IysxfF&C8pq
z-F<6y-l^}a#9u$Y5dYWMS-D2wu;PPTi*=s-<D6nI<}~HYuQ!WlWWSy|F)F~IdX28r
z#jQ{7@qd4RbLZS69_(fJ17&-9gx*N1-o4bssk8Z(_1Sd?1xwOe?gj6^|KLuzJJSgj
zXXmw?CewSaYZm=KWg0ZqK1|4~MPuoe3wKQq{4G7xJwJ5yvHyEZSiW@Y%uAh7{axAf
z_wkTPTUd2w&fCWQ^}x4<6`N8Q=6au1PTp<wae?yW4%H138=7~wm+xI*TFY`UzWQC<
z&jqqiAC~r?_xIm%%tTT3u8M8>{CW||&kbk)Ha>TYed=RXRx2kl#VawFsoQO(V0Z1&
zUBc_-SLDBI&8XsT*dJK)<tpoe^4HVn9(wlofzPDPLY_&#0un55G;h!;s$EpFFhnRj
z`s;~|O<(hGmwtM<cB9LGy-V!sm(ucVwpBl@<I%6E+*X>D_0w?SgU~GDS+g6n%Xxdg
z<lDV&FRfX6b)wV>k#D+s6)Dz7rz+LU{@<9)?X_ArqttR*^+uirq3SDyH-5Y9vAsi}
zHOArNgN>p)miAT7%($v0CVNZ%GUM?iOKFR?o|i1EkKdLonqU82_Oej=i>t+wRbOL5
zZcVtc@A8)1JJaTE{nt9<ltkJ7EPIWBIv<bovnsU~+qFJgbo2L?x^;i;!|F=!e!On_
z_mB7lsS_;gcYnRR=gPND|BuXid}`jBD+(*jzbuQ3^8VNJdAa_>hUMRNOc&4GSE?Rs
zFO*o;IwLQtF}+ZjgZrn^ht6NA>35o{^%N4%2By5Z8nJs$);k8>Bjr4^zNMRO{5;`r
zX<C?fhr0HKS8_`$?;9VF-@f^i&y{wT2{zsNmh4k`u0<w`KizM*(^4V%IM<YG=EseG
zy;<&;SCJdt@$!+*gJnwg-i+*wuU}7>eI9CW8P8t$Te4@bOm=dx-TSF>(%Fx8x1D`q
zcal@r_UXKSrY-+?C4cwbn>_osT1eZ+XPKGa84IE{pWf2l+^>23-IxCpA1Jn%^VTdm
za{m1?#)FR!Sf5krxV_roTd~8M2haCjdhGBz<oOy2#rgbPJ+^HQv0uC7V*}oAR}tY<
zsQh-rN61^qe8Hk0%&lBgN+xhWe6Mlm-u+gIJCoj(e%<xHroqSiw57!Fi<{>E<dR=C
z>$!CG#Wgo)Du=I$5`6hPpm*5|m;3+cZRT9#I=iBW$CJsH{f*3;w=S<)7>+Fo$g;kn
zE3rE?)y>`Q`S#iS%&+AgS{1Zq(Xn60yEd2QXaCMVx;46-dG3z=(#$-MtnA_stc?{(
zJsvL<F{QSIId;d_V<+Ou)6L{-cUa$S%#nMo%Xa2qui2|(xw%rzZUxzkbD7K@OnbS)
z^<PwBb*9e2vv1xp+-kV^=IgJ*)wk?ildq@k-f`soKc+wX;v`R2uDpHb@Qu}Lb1z9}
zc85*Vo>zOe@juII>5toE!tOGkxKwR-(pWzyIZ@nDbj4DQQVYr7QEO~jUN{<yCr2F@
z)AC8bZ|?d{T4IXSmW?j?IiFuR+m^5Y<3Bm^>$2wb<!;kr-p=i3t}8rfV^nr1MJ+p*
zJ@fHKq0U25eHIVq@r(R((DG4BeHUAQ>5GJCU<2DdjyVmxi(|U9XLQwG2s$7ZqxjX}
z1H(Fp726I(wM4J|`u0HLO`9JQC!am7dtesBD0-DWfVrJ1pSADU-PH3-zocuoau<Dn
zq;|G7cULB>AB*47zjeDb?$6pFT*2`}@PqN4>Ja_zhVp4YD({Bhef#s|ONRMJZ~0w4
z<IOKw?PFtby5Mv2EWg-$J5}wg^cQbVd+l)B`QSd$(-$MERW3YTm0hWQr|;>R&o{P8
z=Q$Mjp8fE)R6X{2Xol>EZf?JA$}g>TZa%$HTy*`zPP@ml3BvpQ?pG>!-r-s~{lUA8
z)rJgrm}~ee44xEEXP*9$Yi`t?CpJ7Wo!RN@T@_BU-uTY+{?Ju3EmM{~oE29d-wC_(
z%v+xQS!m%|y9Zo%vbKNSvH7pihm%V7)r=87bF<yM>-QD)ZTc43lgqB9U%$vMjBCp;
zr>yyr^Y3nWG>a=fw`9@k#yfRdpU>z_I{72<*ezq`*_JbTxbL{^_I&>A9fR6^&L48o
zyBm1o1G_#~*X{eXH}>Ro`(GdI<093Xwch`CT^IQ7SLONne@dmQ)C+ju<!uzRYBX+0
zZut9g_u-tQqF>|}ZL6QXp8egCwHv?G#ccLdowQ@3i#YS?6~6LGLf_-27E63!elS5Q
zrdaVq?Ss1qX6{IkpUQW~*VFL+QbylwuhqhmTi-6Ud*5rdZIAB1OWRIo_)O06oVfL`
z?1gJPO>Rn6H}w3B@7XDG+R35+yVlbyA8u?C$(FxixaVu{UHd;f-1XGI^jtTvzwE`d
zL+Xd+R&KeeGnoHy{m{60_r@OHAM#%74~Ka0M0Cz}{Hq(I7<azxvvA}6pxF;5zMs3}
z*|DV0Mp+N%7w*69<d$(@+E(uRzlJAn2p^k$R9UM(t9*}7s?ff(+e<}nwjVh3Fk*Mo
zA1SkF*VEBW23^VC%T1s4-ITTN{(JFRpy0Fgs0`M32Sji6zVXO8&bndotAe$a2lO@U
zlvYeQUEo`IbeeqsrNRSie|-PnQY!HwIL3FyHIt>*=j+>~LjuANo|_(ZP%iT1^V@zJ
z#vFhDboJ?aK00`4ReS}@B3+ZBztTS)x9S})+qd=Gr|^4anLl~l3je-zd_2qL-qja9
z53(HGuYIhF-ErXN)5?9v&w8j#d)VZ@ajAXQQ;!G5f=hNcJ=(ggjpr_FfZ^Tdv;W>X
z*X+~XU~}`-(ch&r&;L1m`fT;HH_28^yvg2W?cV2qOB^uUQo3M8hI``5JO6Y3?vJYW
z^FHkz{-AB<v=hl9*XN7ban8B)!sh|k%%I#Sfsrk*@7V5Vy#8(Cfv>?=R=<4YyhEC6
z{<)g?rD}Zt41ce%pURtc@2T*a?&Ck|KR=)K^lk2~sMS-0BC;*tKh=Ny>7VX1e(Uy4
zXFor^Y<%sKAa}%sj@e;rzXTkc!Mk$Hy{RV!L^S)SB<0!Oo3&w){ITqX72(Ab*C*#r
z-no9&q>@{lUkaz(3E#P>#P;+3E7Km%N}YA^IcL1E+@Z6%H(GX2p3D5@LHyzqmh9#Q
z3nbe;=DF|KH|y;I{l?>khg-fg@*U?*`mpk#O2O6%j}NDAUZJ|<+4dwU^Cc%XUHDzR
zeu1snpMSI2&-{P+XIjOrsOl|-doD)_d1+cDF^0drzt(<pqA~xwJF$Cg0u7?sW$v5K
zPPR^;eRM77+NqZ!x`Vu=k3LA=?S3t0XXfi`&)vSQIdEZK^}bT$%ZLBvUUyx>m~yB(
zvWclViP_7R!^TM<C&9$HBg}Bit7A8mH+*x^xtl1}F=eZ}e9do5bNj+uy{ty*zZ<00
zo~~!MSbN8GlmE`?kKS(2<XI^Yxpw<`!F^|~TX!eda8w9|Z}xutOaB@3`eR=cbq?Aq
z?3q{K8!laN*#CXftGb(>F}cr*{&3%uc&E2BZ0iKZJ6W5g3*VntcxP+0<Gaelv+3d+
z^z(ka4_ek2;LS9jukfyPLAQX|E$2P#+y6~D|GOr}%zo<)-VaV))AgkboL9Ym_aOTI
zak-;)VUZiSmU=9{(eV00e9GI34WSH;yAmyu^?cr(Sn{pXx$UffU)@?=%ikMHj@?Pr
zwPi3|8ev+m_k7*!<@x7dOvz?Du=4l2!@r;J>$%zJrfK@^XFyag@0Nd)w%(~=*tk~S
z`oq(jFCTrm1HN(f*dBKBVf?NBXqWk;@5_WPUUR7V#eB!&dAUaF`}tSrdD&N;xx#h0
zv3zc^^Q;HLUaS4JlkHR2e$`oUMbT=m#*fMA^MdOazFzwI_@@M2+mC&!8KqLoeD+Oc
zI(l_)b=)rd|38zB3@fTu#*4kqmwfok_R@jvjq4vg<Dasqknu^%oevj^iaqa%E6LZh
z-D{k^A>xF9-irJEyLbOxkiKg<gM9O>H>r2~XFCg*?RffR|8s+4?|r?mSLl_Ujl1*v
zoAsUd`(o_QvDm$?e4AudczAC2Prk2nPgtnk6=FXe)9NL>Lb`GF$s5bpa0OTy`)ii6
z9-GJ95Eg$r;`hgU!t2d{)}J`GrmE!n{pkA>{bt)sCR;Py+VUv=`T5kRyLxBjL@sFf
zsaqJfx5%E)Z(EP)s)+E{4%uH7KJ1g-@_m2S#r98|cP9R~zF(hb6JV~Hy#Dy66_(3S
zx!-GfdUIOx8Tt8^FWVM<X8Bk4sF$JnbA9>6^yux&wiwl%TD|_3QGIaLjt}Sc{(QUg
z{_f1|uJ32QzqJ2ooj>Vl`9AxFIUl7CyjYj$Hc$HfuE329b2|i&Fo!6$c^$c+YgnSx
z*2VfxCENG??)(pt|9<BDsejLW!1F-X`Om!X-hJghAYN!XDY$#i>c(W-%Xeq`E|2(d
zVtP`I(i20u=jD&G^uAX-Q{|e>{r`KF-FklUKc`sNFg}QH`2WG<vrEk9G}B_fa|<ep
zA1M^Xie`qZ3Z_Veef+xM-j?e5*V^aXS2@|&{m-s1Jo&r4m(QN>h|uB1@p09^e1k7t
zs1p4)Gt{4-MK|8GtNyHOTl4KG%ZI6(cV-{gW9ZAse|(Ddx1o1>_y0X&d26rc_ZS{O
z|MF+fK}&=4b4zRwyqdQ=T(0ryGT+6EeQz!jtW20~^I+`-28;N=`M=bz-8jE6#xY1^
zFK4FKt>moo6RSo1^SypeT_(L^YR1;J7Y<8p&b>Z=-ra50XOHFXzMgZ(?8}wUx83I5
z-IaU(nC$JK+icsHmiOjtuD*2Jplo&*>+LDm-U;^GzAVh_)mErkQrP<K6<7SSlXl;e
zxcrsowEy2T`L#y;?~~JynKJ$qYs%-GSa#)BA>-NOSAX0;dA~i|N-JIS>e)5@fmJWw
z^?%$g*m30XaecRbw&|rd=bt=aJfNKa-^%*i%RgD+zqd6VRCbr$z_s-1_AN?Fb=Lit
ziP#x0uIp78lWrZZU&H#=s^DoGYwFZ$4O50Wu{sq`Ue{hPy}kD75|LNyyyA<eyfWb8
z-X!b#`2PGFnM1qou9tZ=^KSk8pl>~kUiQkru8qI5*1Ub+>{YRK-75UoUTpN+l=I7M
zZsKuf|B1IIt@X%g^*eHLZDG?ji(RUI7asMMdfUvNc5+?Cg4#Sbu?M$~)ZX#gQXMSc
zb^reSgKO`LT$^7w_i=mG9O<&8#3|Drn}5>ko$dZmoAnQydBK7ycZ_sv6)&AD*U{q;
zy|iKB?&L38^Yn^OZCkwmj9LGZZ#V0ov^MUW_S@*#zRO4XPw(5<p#S!MZeK?JWvPN%
z-JR)AX07{jy^MAC-f-uL@<*ka8nfTFtvGBW5U}&2Uu)mtB3sY%BEI_ncQ~njj$WN9
zH~EtJ;>k_zhgkbknil9b=6MUK2)|hJdwUoA%^J-q^?P3w{Hc5X^~ZwWWkR{jHw6Z<
z{b#sw_{XVzz0a%<8k%$I_Sjd>`+jS}%V*l5zbgbP)^u%|-4(R@g4bW0?aSM%4@lp-
zT{6L1?RM%c+iPCDT1U5Xi~Z35bL))KJLZjYPjgRL{|;UK;Q4#`Pu@E>MLF->qU~G$
z$n?{{`G#*I{)#M)F6%4bpqivtpc4ClW0LM;$0e#}s`KYnYF+P~wYl*{`?h!QEAL$n
z_}H<{-RAu3BX_?}pJyB*&t5t2dgE+$p|<xvzr5TVbdKtZ2m5?p%NC)U9JyBH*o;o*
z>NivTZsi=WT2O!KV8-EDAF|f^`9`Gn9X5`88NRygr|ztMvZg$LuCel;xVQ31^Tz`d
z!+&#3(tUC5M}^s;{rAEv=WTC$G5z|txp&`Q&Wrb%|GbhjW_i9b%Y@c>&(ALY;<3Ey
zN#Z7Njkv>amu_ShRa(eX%e9p?r~Kxlb5}j;7Kodj7FqM^>T*tRQTuhPeDtQ*wR%0>
zo_3IPLuUBr8=EWDBVNCYV)DH(O(7%u<m%cT3X5((dVD)RZT9**Y;W)B-zdMhM_jAg
zb>WY58`h;Qy<xz(aBtV^D?y8=`JTM)`(yTL%N-ZPk6x)g-(Mxc#dcZanp51z3EQta
z|JxXpbH3+Ofbu8FsU6u0k9oC^hHI@e=~%Hrdwuwvvac_FQ!ls4-kjBbD$XI(^@3RW
zUzw9J0-2KhN;?&I>vd24psSK?sJ=+%{@1yyB==by`Ju9}Xi;4Lsc_>pyJj8PE1&p}
z@7$t_d+ZJJVY64JO)+G2xIe|wjJ0oS5I^6xyu4EncTDXvY4|avaO$+vXZJ^Wa9+D-
zbZP(Je`gL9B;}ZhIw&b*<SWj&>UH5>(>&8SX3krWCU4(2%jM^tyFbfB%)Jx2zTReD
zDETbwY1(S@sHTEcXQmwsj-1b5XgP~L``y&;bqNn{>gO5C`3gs^v_CuL+~+wbrW;A-
z|2=v3TnKCb;pMSbw%b1xJxyG8?dRF+ugkP@j^wrO^X0IUmI*!m-EYmTglk>(2^lBO
zykMHOaHhNPx*UsXk5=<7$^3HR?h4JRn_R8!KJ8oaOr|Tk_r!FgnO0(nkIL7qT4a{U
zy(GNZuj`MXNb9BiSGH5UKi~bCn>c0WiBB_4`LCM3Y>7O$Mec0bQ;9$Kr<+`S`$T-(
zweK5+?0>6njf`Gh89CeG;EkX+KaU>1vC-&bMZinH8NS-L)O41r-P!3cS2pYRyrqk_
z6dp`3s``0cH2COe>$5-4Nk?>Lv-cOR4!p0{+Zq~kxO`c4*CB2}v!?d~=j$FMEXscL
zdF@15x0k&K(n{VQz7@*z<>IP@JtmtcPdi@h=(7CsGReH4EUiaU9_tj!9}8|u7F3f9
z4?fqg`#sv?Z`bbUx<@~In}#lHi+)}ir=Dl_DPQT#>Ee0Mbq|`lhF&^S((=5rH!Dad
zW$*LK&xHp|b4wyW78xF$&3Rqu?frnmytx^Q+ZQCwtSd3zrEa{~>Vo2{zQcDO1@2t9
z+{@Q?o!UpImrv!x=ah8*@w@+k@nIU{^j9KlS?{Oy>S^8PwsCvunfr6q%rz0&^<QoD
z+2%;6y4jpL__i|cOpna2+2`NfYYvM0ec^?R_XQqil`O4Kl?vDT>bJ7?t@hgI^Xuxf
z-5I|wUw{Aczr%c<J(h>|*u0u4?z<!PesNLt<R29~n!YUlRQ+f6QoTd<xtlfCEcvm|
zD0=2X=km|Fa-0m$qP+gI&rrDVRboz1_(V2=*}1<qCi{A|_G$a?EvWi={OZ%)5x*|q
z5c|V@S|U&IaMrh^cSmyPMz2^|BD{0z*;Cg21=>fRm0kb*^|iorw_M$S#xEux$Zfgb
zS!mSzUn<6O?GE3?T{{K;GcsNdd#;ldA*LxYUn2H__5ycz<Ihr4&Yp0Qa<~#99MI|B
zdTf`yl85!ClG%rS70<;s-0pZ`^5^$ylXvTWcs-E3^US67-#MN<W(|4S9W}pwTCUv8
z{{60Ghv@bb@tZxEx3^o=TYg}8$lP#DxBXM%9i{I53Ne)dS(jIf<Xv7dQ=em3qvg(N
zok{VG0UivT$9I)}Q2ZV0Yq@TU_UYxzrq{=W-g5mE?YqnOk=UWNk8btuK3&VQeeN5>
z9Zkzc%a_kTz&qWR>j%$==m(q+f~Uk!Q$Az#R=eT<q26DbX?6wL1(_Ws`HHtLrcM1J
z_mGWOhU*XG_v$M3b<e_IY`)u7{a^3s-s!IkxMlS8i|P!ew!aHC{Qf9@_nd2wK0XLY
z&gD7wUbpz}`k%+w{k*NWtt|BJXNjdR)P+`kT))#Q_Fv)B%YW}ktX}!j*JjxwzwV%)
za~Vx1IL0V&RJT`f2wQJ<-_$R$PIKv`*%S9aaC`aVjSNTL{l5RHHTmE6KYn-PIaB_L
zWx{EX61$$oD3;mg&Hvo(WTW1=T611ob?oed>{&|-_Aj>F!4O@denwzg@UFJ&J?}Hm
zM(*yKK5uh=!<{Lug*%J#4{c2KjKBY7Kl54fw>A^rR8Q?bFj=`MuOaxT&878En08t^
zvR*zt*I@5mhB<xp2V*_7w?=+?QWW!6)kpZ|#2@B?Q$O+kX+L}I_R}4Am9;a!c|2(Q
zp|>Wn?o(~cBXgemWjklFC>LLkE%=iChO1z5|MBkDlf`%LY}}glGUm3=YL-y_M}8%y
z-%jv0&#j5sdFZ9D#X6<?M?XdXymEZmq+@S;@9`KX%O7IhQWf2;y=3;)usZ>-s@AeT
z%a+S)i8H)@siv~;$ZUSkEzIlBuZ@{#|7O_*LxcJgHzZAkv~T%+xpO!zTe<92;nU39
zO(2s^-U|JkEBNs6OZL9ymT3v~GUd;s^rH(+H>Ay%tl|H_Icv3po@q%r_d_-YpX`r2
z>`qDCezj3RpW#}RY=8EB-@D6Nt$bB<KCVzJlxz)M>)yCM;OD>VTa7s8IDFZy(4_sO
zZ~f)1Sr6|w)-SYFdone;^t;upd<Q3$wz3+z?6>w$-!-Y9@6{`rv-QlIxTmGPhvn?{
zPmAnxIU>w?_l)&yd+z*Cg-<)D`|p30GyTMSllh(z2Nv((doka{LVk9`;?A<`yY@5W
zA1XcMuO82KulK)IWT0j5qgo^71KVHCnBI14=h2MpirHJWqIFj6ao?D{VH$J$cJ|cE
z@io^gHy#w<k#X_u@@o&ThUopW6}Ymb-rsJW+1sF(;o7gh%sws_Gx^-@LSf$Qiz!J3
zXM>(UuK&JAHeA?p`m1f5=H_U>)BE?|ptgPbJ>ETR<<sL|FMaOb@LTh5wZ3`D_jD8Y
z`BAZ3R33Hfl%0$?s}yZE#roJS)!gQ#%pT|GYFkgeWPfx<cFCH>w>%e3?8*_D7L;{>
zt%}!2w|KeC?Fm<lmu?eYu~DsK(aUVpO~wI=T+UOSUYlkGv7eeUV<Cg}<5jQNwtx9n
zyQ5X){IRo|FOL0pJN$s_Uv)vTjTWaHn|b%ovOBWxci#Nd66>zf8~yvW+MP*KSHFC<
z>5rcru7B}c_?`yt6Y+;kRrj)+n`{?~E@YPYC;a`l*7n|y6AwIetxKEHw)&mkzR!Cs
zt>m)vWpCd4{zKFLbKSjJ+4@e|rCw^ya<_jeu2<gsWn<Jf-Nt1H?w_nPpYQ0Nep~U{
zjN1k}%mIaaWyJ5y4odlc+1B1lIPTiZ&<_!7BFpcX@3|aTa-99b=BQK4Z8x>wo4o(^
z-^RGI-z(pE?ul9L@>5GKp{jp&+5DLsgmx^wJDr*RA=m12Z@%-sJ6Ec`?&nL-7~w$u
zt@-QUA7h<({o%Fkua2F~K9MUiHM;L_>zl9g2iIzDZM-G=!mj@G*LQFH9;gZKldLe!
zyYVjO*z>1L3TlO-3*Y<7zx)10;-UD2J)+_pxPB_H%iJ*2>i6kaJAeOKZ15~>OV#}s
zYi_)He(zK6`sZ&ezID&Nc0;{q<L4sP7aU~@$%dP!ypoFM*mEF!siEV7_`5ql1Pg}+
z#+5wZ8O45(-Qb%R&)a0xVxRa++tR<A%h^Ajc5BZIso67mjhs57q8R@4KKfjDkNeM#
zx|=I|=l!?%FXDDqR^w8}SKleSYz#l~GiUophkmiFfB#ozbIF^k<TsUG6XT5cq@R|(
zUG^%T|II58Hmk3#taqK=RidAZzSazFxc2Ja#lYf2b?kL!dtY2%ec`b5^n^28Bkox}
z<&65f+i<abeElU~)5^13#opE_ICac?z|_Uw&%5Ja|I6bM*Y_vn@*Hjt{I(_}`#-O(
zeSGC?(`SKmZ%po*Z5H&B#aZp>9GBH~cFE@}>M}BpI$M{2UoR(-bJuXz%=FFPW^awm
zel9GPw(fhC^ZtLq_kC54O4o9EZ=Gc<`2I@F;F#QW50?AYx7X|KO8Xn||ENUuwA)t$
zd}WqAZYwNZ_y6_kSO4!-Okz-K(O4>L{(bR`_ZMucSGG)@u_0yM(#bu0MXtC{4Pq|a
zQd;Y^QFN}Cy6DM;XFfE2xA}R8Dc7?{cd1L>QSRw&On>h)H-G;Bd+EU|j3=-09xpp*
zb~=6Qt9KCs!Co)-_b<66f8Tb}pS$Z8ZvNF4oSwLL-maQ_zt8<Yrhx2yYSQ&y*S<ws
z)GRjDeY5Yr&kYy5xEUDOFM!qpxTj~U$F2*I|G$$hfXj5}GJ}sl6LKESJovEn{F}1r
z0Z~gCl6}i`Cr>(mKHB=^t;TSfO`XrPzcgk0GIa<nlIXp?Y1<6>%RhE%iUvpJ8tu&c
z-?Uo(+5?N*RjIwcJ%3{=?e0JQn7?__R+)=&(V)rbqh}8D#_O52{M0Tz<9+t#mdN!}
zn2Z-bnYXFa{cvCGJ-Iiw|E4dD3%B)T5Ofl`+&`P&MEPdVyHLZ;cb%@cu&z1wJwM~c
z#-LZ{&E{2Vec@ic_(l36ZbcX2EJNnZDMj1APoA!o^<g7Z^P{fP<F)puwlBy6Sz5hx
z>+-vdQFoVw%($wxX!#VTwRxVI!cTV<m?|>5aBRGONwe5K%J$BSnkO1d6#~95-cfM)
zWA6<$b(xu+dM!6rf4#H!Q-IMoezWc8J^y8_w35?qbzJ>grzYht=k=>q2hVtT@Vanp
z48MKJ{<&e&uNYR%)X&@gZM^BeGT9;X>T;9SQ-l5rZ{zz^Sywiz^U^CrrqUW6(~^fJ
zoN@{v+o#{IyeQt;|8C!0hxvVJ46J76y~@$I#I4*CIj-!NJleQ7_v8O;BOSE>^#wma
z-ze^~xv$&h%60ZH%d3#d8{N;$xBY)_x!>NUD}N=Qny99u*uo%I_g^OI_c8ILw^Jpm
zyILbQK6Mc}CGg_(mveXHD}MEKYCqN6m!0a9S!#5xjwyNi<lTYcOB}y0{HeU+|DjvI
zFDX|A-+y_(_t#QaH>M5&rzgKpE&U?1VKe*bnGw}8c_;s{w8gxA$hzfMNmBXm-t7Co
zuO7<0Q^u83$7;*nCblAC1IwEUlBWJk*^O?`_dfct>HXFBUtK&vCW#olp5<>`f3d+Y
zJ?QPJON*nDW6Ml7Uru|IoE6afWuE2S>5Rfo9EwsJucS^$H)h+OuQks*Zlc&CaM|HX
zc4Fy+ZO&f<a}Lj{`YBfT+xz*qrD9GUduQn^v&du3`~SY^n)@7n#g-XjDRLbGP90qy
z41!J^fr6Y0P8^C_N{lWXiY~4y4IGLsD>_&N6k7yDCnoNBd`@+{yhG;Yw3VrfEgh3s
zCKT4^l(4l3Bw2w2Qa}{EOk<JK*;_438(nuib-l-+!}#pswQF6B&IiO6i2o2Skl(;I
zBW!miBj=r{#C*26=IXO|9jxD#E^C;(<N7W3KfDzpKaBHy^%Pq&W~>N*Tr2%S`+PA!
z(>A8(4Czem0_)noXcUNkNY>(3d4DQy^PI0YvqO?43k(a4^b%U8vRz~P&anMa({cf)
zGaC8IyG1t~e;k$&-toEH_8)h6H0Nvfc`yI(YT8o#>~UQBvCmO<{X7M(qLo5U9bG2D
z@+Ybbe9f;~vHf7a5Zt^a>m|<v&O5KyJpH|H<r*>N7J<;rWeh>y+zs;|nXgyQlKLT3
zAiR#>okKCLWu}w^10SoMl;f_%`<quc_=kP4QEbV`GTs~TTcY>w%L3JcOy>3aEdmo~
zzGO_{Tc^BVu&QCTbV;saOGk|HIcCEhmi*Zg^Isc?Usu_>qUp;&!5zEREV-X+X-SJ1
zbVx6{&Cc`SUcX<0V&0GSUlwyHe&b4P`?!zekM_HBdjrmTJXX8&*T2I=_k;EMJ-_%K
z*B($_dziyM<oosmom2R%*6#TJK>NVv%JYBwo@a|Vb!000FhstanI>d@{jmAn-XEq{
zuNpPfXuJF?d#vW)mh0EUn18g_?040P=Uj>|m$`)<rnPvKD;m6+`7ZB|)un7v2cZLL
z=eM{uCfj}r^HXN$;!yk+boNT8T-wixc6WY-+eNK>|2n4c_2!QsO&?4*-LdRVpi;|<
z-DzA3iGR00ubg%3{2#riz4Ko7Jg~aeDv%VFwTwZijPZ!?#3zfY)_=5l|NTVQE~k#n
z94qz-X}Q}z#x{GGIfyv<WS<prNaMQS$~(W;MBIr(aAO*m!sS%s6-DnOr>9#rUrlr2
zP?Yjy@_4H%HJ4GbWd%E@La(y-Bo4)8Thq7{jE_!uUb(&pp>ru)&^z1PuV(h0|M%L7
z<Kh;ThAVONpI7F){qk-RxEx{3I$>tg+UJ$U4UZR{=@4*o0h#<$PoBR(^6XCaZULt$
zS9KVV7}U<%aB6S*>W}X|;`wU!t-7;=;mK~1eF9Ebd^WR8n3=+`!~Dq4`A6P97cBdJ
zsO*8wgTe=w73XWW2!v)&V=#)%lHa#Z@lN(Hfe$JlB=2n7derK=b>UyN`v-Mfi)=S+
z`IN(@=<;;d%D=U0tP|S{e%G|TRGHtOeeRdd23hl2+1eA1y**@M|9isO#VrE93uiK&
zD0vv2{hOme<l*dP2i7isx_j9)0Vfj|W7EX5OQbj)^a~0X8!NU51ZGZSFbclQQ?u~m
zOaZ434G)ISd#MNZ8-C7;aO&6_vzcYW%PTFS-)xN!JU#Go$GJkqmKlPxR2$y#)-lQO
z#IP^Pn(?mc!8NI6>Ma6sDh*ezb07G5fN{sZiC;yR8MEABox>u-@n?<NPGP4Gfsi9F
zkAIlIU7)P{deri}UH3PnHUAG%eR`xon7yAVj{OV6=YrY3FW+osEBx&Et6=jvdA2(K
zH){grS_GWVC`gINENRoA)~Yw`3+OJY{IkznRnfe#_K73|0|SGntDnm{r-UW|fA2Yg

literal 0
HcmV?d00001

diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
index fd1cd73..9afc480 100644
--- a/assets/sendmail_template.txt
+++ b/assets/sendmail_template.txt
@@ -1,11 +1,53 @@
 To: $email
 Subject: $subject
 Mime-Version: 1.0
-Content-Type: multipart/related;boundary="nfmimeboundary"
+Content-Type: multipart/related;boundary="nfcoremimeboundary"
 
---nfmimeboundary
+--nfcoremimeboundary
 Content-Type: text/html; charset=utf-8
 
 $email_html
 
---nfmimeboundary--
+--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")
+if (mqcFileObj.length() < mqcMaxSize){
+out << """
+--nfcoremimeboundary
+Content-Type: text/html; name=\"multiqc_report\"
+Content-Transfer-Encoding: base64
+Content-ID: <mqcreport>
+Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
+
+${mqcFileObj.
+  bytes.
+  encodeBase64().
+  toString().
+  tokenize( '\n' )*.
+  toList()*.
+  collate( 76 )*.
+  collect { it.join() }.
+  flatten().
+  join( '\n' )}
+"""
+}}
+%>
+
+--nfcoremimeboundary--
diff --git a/bin/__pycache__/scrape_software_versions.cpython-36.pyc b/bin/__pycache__/scrape_software_versions.cpython-36.pyc
deleted file mode 100644
index 07062ad2b5afae9e2bc03e055e9776da9b619a1c..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 1324
zcmXr!<>l(o6^yB6Wng&BfCRW17#JKF7#NEGFfcHrFr+Z%Fyt~uF*1VKOgT)s%u&o>
zHggV36iW(A3Trx33LBVYPvJ;sO5sf5N@q&pp2HHwn#$bF5XF|llggIDYr_Dh`JgmE
zloqgIsEA2r&0=q6aAAlIh+&H2h~iA;O65#pkYs3P>^F<zPUX(xX=aGxO=ZdAOXW-v
zlw?TdZDxw%PvtM#k|LBPkjkGWm?GHB*vy#9mdatn5YCXo9LNyF5W!HG7tW9>lp@^B
z$jDHklFA0PMFMJzP>M*FKq^NnXEPH>Md1~&YEck7g*li(Q|u)uSTq@L@f8$h=9R>!
zmF6XvWaj5-GT!3$FG@)*N=<ReOfK=O;wy_U$Sg?B$;?aDE2$`{V%3NV*46|G=cQJZ
zq~+w7gN1p@;?oj~OA3?0JYKiN;*vmTg))d@-m>`I(wve^sH_;2qoYukT2!2wpQiv;
zrpZzzUR|w_oS&banVMW$Qj%JvmzS8Es!&^di^C6U*)2AR(YM%rK_&(|SE<_+7bNB>
z6qi)yq}nPa=jY@XSt(nBfwhvIpT47wK1hKbPQ!~>7#J9eSV06E0|UcLMg|6kD(154
z+C&>h1_rLo6e|UFZ0^#_$uCbW($Lf^N-fAqOitBMS5VhcP}f!0RH&`hEzVCXDNig)
z)rI=8Se>gl6&%FzAWz{iQ=zt2AsDJtAq)~aNIEl$Qq!yy)H6y-3W}}t_0uy;GD?&5
zlJj%*u{ltowpN|1ASb^hzNE4s6|65eN1ZDrwK%ybvj7y^RtoBgMX3tO`8heM$t9^N
z3W+5OMWuNPC7HRY3TZ|8xe6s2sR}T!DCC!x6qJ_esdJ?ymLys!)Nm;%C@9#Z<R~QP
zBo-IjDy8J;X5<%TR^{iFB<3jDaaGBI6o9ZzN{L-{t&M(4iJeVK3WS+rSH%gI(@)8<
z(-e;4ijPk#Eh#NZjgK#4Vqjpn#SL{=W`16A5i>}HsVFsyy(l$3wIa0`#3(M!DJj0i
znpu*XTYQT#`xax_EtdR()Vy1a6}MQ5QWI06IAFnli>){{u_!s?7He)|Npi+5wzT}B
z+{BVwtm#Ghr3JTG!P#IXLy;&b9e{{m%k+~n^E30(^7V7_lM{3FlS(slQuLiu^GfoI
z^;7f8isO^>^HLJ^^U`#a^NUjB4fRa)b25|k3o1)8^7D-K%=C*hOHy?U5|gtN(^HG}
z^U~r$>hxjRNw*|5w;(66Bvrq<8Y9ui=j9jYBo=4X*6Jr^=IIwF7bO;?#=~MF9_A~(
zg34PQHo5sJr8%i~pg=3uVPIh3VdP=tU}0kfK^`VHMh*yM7GmUM<X{wFWMNcdX5wID
J6k-%%1OWVvlqCQF

diff --git a/bin/markdown_to_html.py b/bin/markdown_to_html.py
new file mode 100755
index 0000000..57cc426
--- /dev/null
+++ b/bin/markdown_to_html.py
@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+from __future__ import print_function
+import argparse
+import markdown
+import os
+import sys
+
+def convert_markdown(in_fn):
+    input_md = open(in_fn, mode="r", encoding="utf-8").read()
+    html = markdown.markdown(
+        "[TOC]\n" + input_md,
+        extensions = [
+            'pymdownx.extra',
+            'pymdownx.b64',
+            'pymdownx.highlight',
+            'pymdownx.emoji',
+            'pymdownx.tilde',
+            'toc'
+        ],
+        extension_configs = {
+            'pymdownx.b64': {
+                'base_path': os.path.dirname(in_fn)
+            },
+            'pymdownx.highlight': {
+                'noclasses': True
+            },
+            'toc': {
+                'title': 'Table of Contents'
+            }
+        }
+    )
+    return html
+
+def wrap_html(contents):
+    header = """<!DOCTYPE html><html>
+    <head>
+        <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
+        <style>
+            body {
+              font-family: -apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,"Noto Sans",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";
+              padding: 3em;
+              margin-right: 350px;
+              max-width: 100%;
+            }
+            .toc {
+              position: fixed;
+              right: 20px;
+              width: 300px;
+              padding-top: 20px;
+              overflow: scroll;
+              height: calc(100% - 3em - 20px);
+            }
+            .toctitle {
+              font-size: 1.8em;
+              font-weight: bold;
+            }
+            .toc > ul {
+              padding: 0;
+              margin: 1rem 0;
+              list-style-type: none;
+            }
+            .toc > ul ul { padding-left: 20px; }
+            .toc > ul > li > a { display: none; }
+            img { max-width: 800px; }
+            pre {
+              padding: 0.6em 1em;
+            }
+            h2 {
+
+            }
+        </style>
+    </head>
+    <body>
+    <div class="container">
+    """
+    footer = """
+    </div>
+    </body>
+    </html>
+    """
+    return header + contents + footer
+
+
+def parse_args(args=None):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('mdfile', type=argparse.FileType('r'), nargs='?',
+                        help='File to convert. Defaults to stdin.')
+    parser.add_argument('-o', '--out', type=argparse.FileType('w'),
+                        default=sys.stdout,
+                        help='Output file name. Defaults to stdout.')
+    return parser.parse_args(args)
+
+def main(args=None):
+    args = parse_args(args)
+    converted_md = convert_markdown(args.mdfile.name)
+    html = wrap_html(converted_md)
+    args.out.write(html)
+
+if __name__ == '__main__':
+    sys.exit(main())
diff --git a/bin/markdown_to_html.r b/bin/markdown_to_html.r
deleted file mode 100755
index abe1335..0000000
--- a/bin/markdown_to_html.r
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/usr/bin/env Rscript
-
-# Command line argument processing
-args = commandArgs(trailingOnly=TRUE)
-if (length(args) < 2) {
-  stop("Usage: markdown_to_html.r <input.md> <output.html>", call.=FALSE)
-}
-markdown_fn <- args[1]
-output_fn <- args[2]
-
-# Load / install packages
-if (!require("markdown")) {
-  install.packages("markdown", dependencies=TRUE, repos='http://cloud.r-project.org/')
-  library("markdown")
-}
-
-base_css_fn <- getOption("markdown.HTML.stylesheet")
-base_css <- readChar(base_css_fn, file.info(base_css_fn)$size)
-custom_css <-  paste(base_css, "
-body {
-  padding: 3em;
-  margin-right: 350px;
-  max-width: 100%;
-}
-#toc {
-  position: fixed;
-  right: 20px;
-  width: 300px;
-  padding-top: 20px;
-  overflow: scroll;
-  height: calc(100% - 3em - 20px);
-}
-#toc_header {
-  font-size: 1.8em;
-  font-weight: bold;
-}
-#toc > ul {
-  padding-left: 0;
-  list-style-type: none;
-}
-#toc > ul ul { padding-left: 20px; }
-#toc > ul > li > a { display: none; }
-img { max-width: 800px; }
-")
-
-markdownToHTML(
-  file = markdown_fn,
-  output = output_fn,
-  stylesheet = custom_css,
-  options = c('toc', 'base64_images', 'highlight_code')
-)
diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
index 0e98e07..0cdb86e 100755
--- a/bin/scrape_software_versions.py
+++ b/bin/scrape_software_versions.py
@@ -18,15 +18,23 @@ results['MultiQC'] = '<span style="color:#999999;\">N/A</span>'
 
 # Search each file using its regex
 for k, v in regexes.items():
-    with open(v[0]) as x:
-        versions = x.read()
-        match = re.search(v[1], versions)
-        if match:
-            results[k] = "v{}".format(match.group(1))
+    try:
+        with open(v[0]) as x:
+            versions = x.read()
+            match = re.search(v[1], versions)
+            if match:
+                results[k] = "v{}".format(match.group(1))
+    except IOError:
+        results[k] = False
+
+# Remove software set to false in results
+for k in list(results):
+    if not results[k]:
+        del(results[k])
 
 # Dump to YAML
 print ('''
-id: 'nf-core/hic-software-versions'
+id: 'software_versions'
 section_name: 'nf-core/hic Software Versions'
 section_href: 'https://github.com/nf-core/hic'
 plot_type: 'html'
@@ -35,5 +43,10 @@ data: |
     <dl class="dl-horizontal">
 ''')
 for k,v in results.items():
-    print("        <dt>{}</dt><dd>{}</dd>".format(k,v))
+    print("        <dt>{}</dt><dd><samp>{}</samp></dd>".format(k,v))
 print ("    </dl>")
+
+# Write out regexes as csv file:
+with open('software_versions.csv', 'w') as f:
+    for k,v in results.items():
+        f.write("{}\t{}\n".format(k,v))
diff --git a/conf/awsbatch.config b/conf/awsbatch.config
deleted file mode 100644
index 79078c7..0000000
--- a/conf/awsbatch.config
+++ /dev/null
@@ -1,13 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for AWS Batch
- * -------------------------------------------------
- * Imported under the 'awsbatch' Nextflow profile in nextflow.config
- * Uses docker for software depedencies automagically, so not specified here.
- */
-
-aws.region = params.awsregion
-process.executor = 'awsbatch'
-process.queue = params.awsqueue
-executor.awscli = '/home/ec2-user/miniconda/bin/aws'
-params.tracedir = './'
diff --git a/conf/base.config b/conf/base.config
index 23c9e4a..0b2ea22 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -11,31 +11,41 @@
 
 process {
 
-  container = params.container
-
   // TODO nf-core: Check the defaults for all processes
   cpus = { check_max( 1 * task.attempt, 'cpus' ) }
-  memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-  time = { check_max( 2.h * task.attempt, 'time' ) }
+  memory = { check_max( 7.GB * task.attempt, 'memory' ) }
+  time = { check_max( 4.h * task.attempt, 'time' ) }
 
-  errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'finish' }
+  errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
   maxRetries = 1
   maxErrors = '-1'
 
   // Process-specific resource requirements
-  // TODO nf-core: Customise requirements for specific processes
-  withName: fastqc {
-    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
+  // NOTE - Only one of the labels below are used in the fastqc process in the main script.
+  //        If possible, it would be nice to keep the same label naming convention when
+  //        adding in your processes.
+  // TODO nf-core: Customise requirements for specific processes.
+  // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+  withLabel:process_low {
+    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
+    memory = { check_max( 14.GB * task.attempt, 'memory' ) }
+    time = { check_max( 6.h * task.attempt, 'time' ) }
   }
-  withName: multiqc {
-    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
+  withLabel:process_medium {
+    cpus = { check_max( 6 * task.attempt, 'cpus' ) }
+    memory = { check_max( 42.GB * task.attempt, 'memory' ) }
+    time = { check_max( 8.h * task.attempt, 'time' ) }
   }
-}
-
-params {
-  // Defaults only, expecting to be overwritten
-  max_memory = 128.GB
-  max_cpus = 16
-  max_time = 240.h
-  igenomes_base = 's3://ngi-igenomes/igenomes/'
+  withLabel:process_high {
+    cpus = { check_max( 12 * task.attempt, 'cpus' ) }
+    memory = { check_max( 84.GB * task.attempt, 'memory' ) }
+    time = { check_max( 10.h * task.attempt, 'time' ) }
+  }
+  withLabel:process_long {
+    time = { check_max( 20.h * task.attempt, 'time' ) }
+  }
+  withName:get_software_versions {
+    cache = false
+  }
+  
 }
diff --git a/conf/igenomes.config b/conf/igenomes.config
index d19e61f..2de9242 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -9,139 +9,412 @@
 
 params {
   // illumina iGenomes reference file paths
-  // TODO nf-core: Add new reference types and strip out those that are not needed
   genomes {
     'GRCh37' {
-      bed12   = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
+      mito_name   = "MT"
+      macs_gsize  = "2.7e9"
+      blacklist   = "${baseDir}/assets/blacklists/GRCh37-blacklist.bed"
+    }
+    'GRCh38' {
+      fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
+      mito_name   = "chrM"
+      macs_gsize  = "2.7e9"
+      blacklist   = "${baseDir}/assets/blacklists/hg38-blacklist.bed"
     }
     'GRCm38' {
-      bed12   = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
+      mito_name   = "MT"
+      macs_gsize  = "1.87e9"
+      blacklist   = "${baseDir}/assets/blacklists/GRCm38-blacklist.bed"
     }
     'TAIR10' {
-      bed12   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
+      mito_name   = "Mt"
     }
     'EB2' {
-      bed12   = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
     }
     'UMD3.1' {
-      bed12   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
+      mito_name   = "MT"
     }
     'WBcel235' {
-      bed12   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
+      mito_name   = "MtDNA"
+      macs_gsize  = "9e7"
     }
     'CanFam3.1' {
-      bed12   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
+      mito_name   = "MT"
     }
     'GRCz10' {
-      bed12   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
+      mito_name   = "MT"
     }
     'BDGP6' {
-      bed12   = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
+      mito_name   = "M"
+      macs_gsize  = "1.2e8"
     }
     'EquCab2' {
-      bed12   = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
+      mito_name   = "MT"
     }
     'EB1' {
-      bed12   = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
     }
     'Galgal4' {
-      bed12   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
+      mito_name   = "MT"
     }
     'Gm01' {
-      bed12   = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
     }
     'Mmul_1' {
-      bed12   = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
+      mito_name   = "MT"
     }
     'IRGSP-1.0' {
-      bed12   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
+      mito_name   = "Mt"
     }
     'CHIMP2.1.4' {
-      bed12   = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
+      mito_name   = "MT"
     }
     'Rnor_6.0' {
-      bed12   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
+      mito_name   = "MT"
     }
     'R64-1-1' {
-      bed12   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
+      mito_name   = "MT"
+      macs_gsize  = "1.2e7"
     }
     'EF2' {
-      bed12   = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
+      mito_name   = "MT"
+      macs_gsize  = "1.21e7"
     }
     'Sbi1' {
-      bed12   = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
     }
     'Sscrofa10.2' {
-      bed12   = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
+      mito_name   = "MT"
     }
     'AGPv3' {
-      bed12   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
-      fasta   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
-      gtf     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
-      star    = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
+      fasta       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
+      mito_name   = "Mt"
+    }
+    'hg38' {
+      fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
+      mito_name   = "chrM"
+      macs_gsize  = "2.7e9"
+      blacklist   = "${baseDir}/assets/blacklists/hg38-blacklist.bed"
+    }
+    'hg19' {
+      fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
+      mito_name   = "chrM"
+      macs_gsize  = "2.7e9"
+      blacklist   = "${baseDir}/assets/blacklists/hg19-blacklist.bed"
+    }
+    'mm10' {
+      fasta       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
+      mito_name   = "chrM"
+      macs_gsize  = "1.87e9"
+      blacklist   = "${baseDir}/assets/blacklists/mm10-blacklist.bed"
+    }
+    'bosTau8' {
+      fasta       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
+      mito_name   = "chrM"
+    }
+    'ce10' {
+      fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
+      mito_name   = "chrM"
+      macs_gsize  = "9e7"
+    }
+    'canFam3' {
+      fasta       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
+      mito_name   = "chrM"
+    }
+    'danRer10' {
+      fasta       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
+      mito_name   = "chrM"
+    }
+    'dm6' {
+      fasta       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
+      mito_name   = "chrM"
+      macs_gsize  = "1.2e8"
+    }
+    'equCab2' {
+      fasta       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
+      mito_name   = "chrM"
+    }
+    'galGal4' {
+      fasta       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
+      mito_name   = "chrM"
+    }
+    'panTro4' {
+      fasta       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
+      mito_name   = "chrM"
+    }
+    'rn6' {
+      fasta       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
+      mito_name   = "chrM"
+    }
+    'sacCer3' {
+      fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
+      readme      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
+      mito_name   = "chrM"
+      macs_gsize  = "1.2e7"
+    }
+    'susScr3' {
+      fasta       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
+      bwa         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa"
+      bowtie2     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
+      star        = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
+      bismark     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
+      gtf         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
+      bed12       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
+      readme      = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
+      mito_name   = "chrM"
     }
   }
 }
diff --git a/conf/test.config b/conf/test.config
index a03678b..4cd7b5f 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -4,18 +4,21 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/hic -profile test
+ *   nextflow run nf-core/hic -profile test,<docker/singularity>
  */
 
 params {
-  // Limit resources so that this can run on Travis
+  config_profile_name = 'Test profile'
+  config_profile_description = 'Minimal test dataset to check pipeline function'
+  // Limit resources so that this can run on GitHub Actions
   max_cpus = 2
   max_memory = 6.GB
   max_time = 48.h
+
   // Input data
   // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
   // TODO nf-core: Give any required params for the test so that command line flags are not needed
-  singleEnd = false
+  single_end = false
   readPaths = [
     ['Testdata', ['https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R1.tiny.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R2.tiny.fastq.gz']],
     ['SRR389222', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']]
diff --git a/docs/README.md b/docs/README.md
index d7dbdac..e160867 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -2,11 +2,11 @@
 
 The nf-core/hic documentation is split into the following files:
 
-1. [Installation](installation.md)
+1. [Installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration
-    * [Local installation](configuration/local.md)
-    * [Adding your own system](configuration/adding_your_own.md)
-    * [Reference genomes](configuration/reference_genomes.md)
+    * [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](usage.md)
 4. [Output and how to interpret the results](output.md)
-5. [Troubleshooting](troubleshooting.md)
+5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
diff --git a/docs/configuration/adding_your_own.md b/docs/configuration/adding_your_own.md
deleted file mode 100644
index bf7f808..0000000
--- a/docs/configuration/adding_your_own.md
+++ /dev/null
@@ -1,86 +0,0 @@
-# nf-core/hic: Configuration for other clusters
-
-It is entirely possible to run this pipeline on other clusters, though you will need to set up your own config file so that the pipeline knows how to work with your cluster.
-
-> If you think that there are other people using the pipeline who would benefit from your configuration (eg. other common cluster setups), please let us know. We can add a new configuration and profile which can used by specifying `-profile <name>` when running the pipeline. The config file will then be hosted at `nf-core/configs` and will be pulled automatically before the pipeline is executed.
-
-If you are the only person to be running this pipeline, you can create your config file as `~/.nextflow/config` and it will be applied every time you run Nextflow. Alternatively, save the file anywhere and reference it when running the pipeline with `-c path/to/config` (see the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more).
-
-A basic configuration comes with the pipeline, which loads the [`conf/base.config`](../../conf/base.config) by default. This means that you only need to configure the specifics for your system and overwrite any defaults that you want to change.
-
-## Cluster Environment
-By default, pipeline uses the `local` Nextflow executor - in other words, all jobs are run in the login session. If you're using a simple server, this may be fine. If you're using a compute cluster, this is bad as all jobs will run on the head node.
-
-To specify your cluster environment, add the following line to your config file:
-
-```nextflow
-process.executor = 'YOUR_SYSTEM_TYPE'
-```
-
-Many different cluster types are supported by Nextflow. For more information, please see the [Nextflow documentation](https://www.nextflow.io/docs/latest/executor.html).
-
-Note that you may need to specify cluster options, such as a project or queue. To do so, use the `clusterOptions` config option:
-
-```nextflow
-process {
-  executor = 'SLURM'
-  clusterOptions = '-A myproject'
-}
-```
-
-
-## Software Requirements
-To run the pipeline, several software packages are required. How you satisfy these requirements is essentially up to you and depends on your system. If possible, we _highly_ recommend using either Docker or Singularity.
-
-Please see the [`installation documentation`](../installation.md) for how to run using the below as a one-off. These instructions are about configuring a config file for repeated use.
-
-### Docker
-Docker is a great way to run nf-core/hic, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems.
-
-Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker, and beyond installing the two tools, not much else is required - nextflow will automatically fetch the [nfcore/hic](https://hub.docker.com/r/nfcore/hic/) image that we have created and is hosted at dockerhub at run time.
-
-To add docker support to your own config file, add the following:
-
-```nextflow
-docker.enabled = true
-process.container = "nfcore/hic"
-```
-
-Note that the dockerhub organisation name annoyingly can't have a hyphen, so is `nfcore` and not `nf-core`.
-
-
-### Singularity image
-Many HPC environments are not able to run Docker due to security issues.
-[Singularity](http://singularity.lbl.gov/) is a tool designed to run on such HPC systems which is very similar to Docker.
-
-To specify singularity usage in your pipeline config file, add the following:
-
-```nextflow
-singularity.enabled = true
-process.container = "shub://nf-core/hic"
-```
-
-If you intend to run the pipeline offline, nextflow will not be able to automatically download the singularity image for you.
-Instead, you'll have to do this yourself manually first, transfer the image file and then point to that.
-
-First, pull the image file where you have an internet connection:
-
-```bash
-singularity pull --name nf-core-hic.simg shub://nf-core/hic
-```
-
-Then transfer this file and point the config file to the image:
-
-```nextflow
-singularity.enabled = true
-process.container = "/path/to/nf-core-hic.simg"
-```
-
-
-### Conda
-If you're not able to use Docker or Singularity, you can instead use conda to manage the software requirements.
-To use conda in your own config file, add the following:
-
-```nextflow
-process.conda = "$baseDir/environment.yml"
-```
diff --git a/docs/configuration/local.md b/docs/configuration/local.md
deleted file mode 100644
index 657422f..0000000
--- a/docs/configuration/local.md
+++ /dev/null
@@ -1,46 +0,0 @@
-# nf-core/hic: Local Configuration
-
-If running the pipeline in a local environment, we highly recommend using either Docker or Singularity.
-
-## Docker
-Docker is a great way to run `nf-core/hic`, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems.
-
-Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker, and beyond installing the two tools, not much else is required. The `nf-core/hic` profile comes with a configuration profile for docker, making it very easy to use. This also comes with the required presets to use the AWS iGenomes resource, meaning that if using common reference genomes you just specify the reference ID and it will be automatically downloaded from AWS S3.
-
-First, install docker on your system: [Docker Installation Instructions](https://docs.docker.com/engine/installation/)
-
-Then, simply run the analysis pipeline:
-```bash
-nextflow run nf-core/hic -profile docker --genome '<genome ID>' --design '<path to your design file>'
-```
-
-Nextflow will recognise `nf-core/hic` and download the pipeline from GitHub. The `-profile docker` configuration lists the [nf-core/hic](https://hub.docker.com/r/nfcore/hic/) image that we have created and is hosted at dockerhub, and this is downloaded.
-
-For more information about how to work with reference genomes, see [`docs/configuration/reference_genomes.md`](reference_genomes.md).
-
-### Pipeline versions
-The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r 1.0`. This uses pipeline code and docker image from this tagged version.
-
-
-## Singularity image
-Many HPC environments are not able to run Docker due to security issues. [Singularity](http://singularity.lbl.gov/) is a tool designed to run on such HPC systems which is very similar to Docker. Even better, it can use create images directly from dockerhub.
-
-To use the singularity image for a single run, use `-with-singularity`. This will download the docker container from dockerhub and create a singularity image for you dynamically.
-
-If you intend to run the pipeline offline, nextflow will not be able to automatically download the singularity image for you. Instead, you'll have to do this yourself manually first, transfer the image file and then point to that.
-
-First, pull the image file where you have an internet connection:
-
-> NB: The "tag" at the end of this command corresponds to the pipeline version.
-> Here, we're pulling the docker image for version 1.0 of the nf-core/hic pipeline
-> Make sure that this tag corresponds to the version of the pipeline that you're using
-
-```bash
-singularity pull --name nf-core-hic-1.0.img docker://nf-core/hic:1.0
-```
-
-Then transfer this file and run the pipeline with this path:
-
-```bash
-nextflow run /path/to/nf-core-hic -with-singularity /path/to/nf-core-hic-1.0.img
-```
diff --git a/docs/configuration/reference_genomes.md b/docs/configuration/reference_genomes.md
deleted file mode 100644
index 1fafa8f..0000000
--- a/docs/configuration/reference_genomes.md
+++ /dev/null
@@ -1,49 +0,0 @@
-# nf-core/hic: Reference Genomes Configuration
-
-The nf-core/hic pipeline needs a reference genome for alignment and annotation.
-
-These paths can be supplied on the command line at run time (see the [usage docs](../usage.md)),
-but for convenience it's often better to save these paths in a nextflow config file.
-See below for instructions on how to do this.
-Read [Adding your own system](adding_your_own.md) to find out how to set up custom config files.
-
-## Adding paths to a config file
-Specifying long paths every time you run the pipeline is a pain.
-To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline.
-
-Note that this genome key can also be specified in a config file if you always use the same genome.
-
-To use this system, add paths to your config file using the following template:
-
-```nextflow
-params {
-  genomes {
-    'YOUR-ID' {
-      fasta  = '<PATH TO FASTA FILE>/genome.fa'
-    }
-    'OTHER-GENOME' {
-      // [..]
-    }
-  }
-  // Optional - default genome. Ignored if --genome 'OTHER-GENOME' specified on command line
-  genome = 'YOUR-ID'
-}
-```
-
-You can add as many genomes as you like as long as they have unique IDs.
-
-## illumina iGenomes
-To make the use of reference genomes easier, illumina has developed a centralised resource called [iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html).
-Multiple reference index types are held together with consistent structure for multiple genomes.
-
-We have put a copy of iGenomes up onto AWS S3 hosting and this pipeline is configured to use this by default.
-The hosting fees for AWS iGenomes are currently kindly funded by a grant from Amazon.
-The pipeline will automatically download the required reference files when you run the pipeline.
-For more information about the AWS iGenomes, see https://ewels.github.io/AWS-iGenomes/
-
-Downloading the files takes time and bandwidth, so we recommend making a local copy of the iGenomes resource.
-Once downloaded, you can customise the variable `params.igenomes_base` in your custom configuration file to point to the reference location.
-For example:
-```nextflow
-params.igenomes_base = '/path/to/data/igenomes/'
-```
diff --git a/docs/images/nf-core-hic_logo.png b/docs/images/nf-core-hic_logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..e5fead372861ff430d7f1428e15dad9b045523e8
GIT binary patch
literal 17777
zcmeAS@N?(olHy`uVBq!ia0y~yV2WU1U}WK7V_;zTa>(l}0|NtRfk$L90|Va?5N4dJ
z%_q&kpuphi;uumf=k49vIkQ9O{{Mg7@?^@g%P+S~Stz2jb;`miO&uL8RzyUk>=mEb
zw0(ubgS+d@*R0;H7yr6{{p(e)d3V)_ie8D0-LmP<$`_kDbd;17l#*61of74xxzum@
z<(DP1JkS07TR6!x&FZq+&UHTPQttW7B^oV1SvpsHr`mP(=g*2ATm}zVl`Iv@C@3iC
z+4uDH^v#ujtL7ONFDtzlnSWBI?#RTM+kB3F`<{P3_wJ_@Guua-A{W@sEwhi`yX#`8
zp9*V)l9CeB0q^N@sh&6En9~{bzii-{G2d(HE{4~8&s#lb<H=zPW8Pm>;C=nVg=e$n
ze-}Hyo@c_f!NtX8*~Z}bFG@N0gJ15+wU+)N&9Bd}X1Rn)#fN1gh86tB9(<e;FoSj9
zywj=nA6DDjzLF~B@m#{-?c$O$tLkZ>yWx~=>Xkc~EDl!ZR3-$7x%6%f-<f!zvi^sD
z`1+TttC!Ap*>zD=Ku~bv%I}L(-ES%;-+%qkSk8*Er!nZXs05GPF|jHx-H3<#3=?>+
zN2UK-{zE{>mvLH0#|e|q;of}PE0gVCK9v6$A>6cFX2UJ1;_mPN0uydXJbS#8<;Bfx
zWyKdoZ0ndmH#W<~t$laU2;!fK#?!vtvR%2YpYcCO#GwzXOb@i5_<cL=oWkzo+aIT&
zKlbJO?HIl41?Dvp8yqS>Uo&H#e`M!+{rVsNH>dJi&U$i5LPt<=V&)^!^%bnU&Hw#;
zDp#*OfzhC#`};p%XXEs*cdOs;t+stWW%2ZLTd)1Oa@ezVQC;$x{nqd8%q<?7-Q8dI
zRz%M6b3lWtl9G|{oT4v*cdy;DuXrym^o#ZVq0e3aWB-0Quy5Y?OUctpr4Fw?cze&|
zY5UjI?eM?3{u|WiAEw=loA)B)chBcPdpRF3|HWg|-^>?R|NHHB^IcWC?#UZmT$bD{
z4f}W_G2s^PvAB&)W^41TMb7W`RqUVI=+A#{#?F6stl^~#L9sOJ=E(!SA!WAG4D*<M
zcE|Y6ejn)(E&l$)g}2THTTfQ*tGr+P-E>!$t~V&qO*Vfw4CHF;T$?1t7S6D8-Aq}z
zdyl%;h96rKb$!2c<?2@+jA5&zb_&h=FT!IJdqO7s1e<xf;GB;;-LCt&sPJ_+7;D$$
z@cr=myJ}L*aoxzK#>b6I)p&Bs@BNlPGtYLm`n-xo2e)R&a&3q@xJpz<=GC&h+ivfX
zJyN#B+Qa_dVY#ZBv~Mwc-g8`*Jj38z8-4cc^L)b@jS~gi&z~tV{+^Tgb?0@nUm7kh
zt4bNC_V3>%Td|@p)N@_<+St?U`)z-Po@>9)oAc?O{f?@yhkMsXbO$$FJu+==RHO8q
zO!rGGE1x-3w|!UE-)dLPv_ay<p@xqwIlBWQ&NF;adz~1(OZjiZ#+&gxm;d@6N}8*r
zbas(&MR;p}Y0K7c%a+E=7xPqXzf+-eEZN}u7he9?#{18SB$zIqsvTMK<?+j$cFVbC
z_tI^aPcD`f5PQJV{4r6}ui??G=MN6oCR_C^7k^x}ce_4&vFwJWh3qOyL0dOBR*Kq{
z$rcpLzMhnE@A>njGn+QOzqS9hU;47UKBrbLV_1Ds=Idhb6Tj8tc)ne>DBo0m&q&H+
z>OcEkN$Hi5kvrLY<ZIjhU2s`4b4la(fS6sW|M#6T$y;iEOz+zd%YcYIH#hIIwY~Hr
zYpV@wgzuv7&-ORo-EH-$?t#&qYWsP74Tl<z2I(i<EIyUI=Hw|?msuB1PMMZ_bAIlD
z^4Ag5U7~jsD9Y_;*|79=!~GrFQ?p~1F5_g4IQzg@{^0wUv$HRKllt_IM}x(q?tQ|_
zTSbBs)si_^N^0fq{bi?kV%9XVGc%hDmG>U~!o$kE|L5Vyy=$&*33$n=#ar?u@bBDX
zv*aKAkzD%Vg#V@sfm@#{Dfy-vet5+tZ_N`Ed3=}3y=RS#4e27sABypqu5r5D!L+6&
z`qSF)kJtVeIX6Epr<Lh|{}q=|=barMpEra|pY<>-A!@y6O-A|luk(IBO)l9R{{Cu6
zK*Q98&-ptf$`5?dwD=$A_MC<3$EIobGC-Csk+xWW=(t$0vCnHyo43l$5;L45PsuUI
zYD-0}e(4yP(^R_ap~=c^{uS=WdX72m)6wgCy|2R~*n)dT{KMpM;Yr<o**CxF+=^Lu
zS={aeFI&&d{h23)B6d%6y*|(V_J+;XZTuxOf9_s$_W8_>w&&j*H{X2N+UU64*}jR4
zZyJp~-_CrxY3JN;6YrlbUlVil26HwO*9M`ipZe1_XQn@MnNx3Q_a{;0zr(5j@>^pL
zZ*p1UxnyNt!S8U+<PFQ#PQLe5?^AtMN6CFY?$r6;jo)ng=iL{5`S#~at`+-FZ2x%X
z%$$XCGPdV#@7&GjQTop6!v~&(@}0JkIcXPopKgEV^Iz;k|2Mnmou>bOeGcEg{LZz1
z6P@oov){6~Av>RIgV3veyysKu`123{_AwMaoN_QA=BbhrXBk&POl$vLu0QFruP+I>
z$8Mf<=RulWuJp3x*Txnp7cXbterEk~-{lDF_APG@UFiHQYjJ;P_UUhxoB4c7i&xJ~
zZ(H~y)wVw1)#S}`m5+jVyA{o}Wk1WenR~8w4ZnHC;{&4WM33e_vJ5Z#_(39@ee=C_
zFLQ2}dB5lUxBm{meoaBT{Lbb2|BhYRZ@{@UJJ(6J@NR47<WK#N{v6V{t$F55sl<U<
zGIHIYr#;&4kj=LDySq)*v(V_|727&IY$G1*Uy+lT&R)a#!y`7^#Fg*Yy~-`mH*HJ4
zc82HLm!z|v67zU<6yJ+aHYzUM$Nk*eU`LRiT>f76*{64Z+j{$L5Bu+o`X%z#bCmb1
zOfGIuz4SnGrtRd$WU)uLZlAhj;WNdtQ2yz$CmZfG8^$Zn-uv+7UFE~p_ihz^%)Kg-
zpn65nJf>ie;j_5+F;ZMN%Nq?m?greOZ<n~!JfR@s^8(MA?|;nMFMp%$yX56*QBU^P
z+g5&e>p7`)Kxkr1G}9kBr>3WWPcXSNzkVIH*sA*6RPjy4^IjjBWo)oV?tD=KV_wOG
z_Pf8M3_jNGIWFCN((+ar&(3fA8XtaJzHRwi5532RJNnFi`M*$|@0skAdV9`?eTIC=
zax8XNrk%R?@xy8{>ocb`E4EJZjBVje4gRJwzu4?gA;YocJ)Ff1hm+?1);ykg_W1Xd
z;QzmVe5>i}-WPf6$0||&3p*dQ#clq)S}k?`7v-O9vP(NWT=kZ0dcbvPR<rc0@TtG7
ze*M-ynPztO?#*MrPtNZC_%C3-em1Y+(RI5EmhX5HsUiROk9=^Sp#=XDUFG84Z%#DE
z&TV#=d30<0xAgS93az<Px02J>-t+kXv76g}W`*@{UH0zp$CH1|7o7g{(?fHce;<$6
z6?`*z9vA&QTzBS`rl}6+_der&Go$iA_{rbpzb|HP71q6H^RYI$Vaneiw&IhouGiIG
z(mZu~o#k{}<6Y0H)7h@g|LUtcPk5rrD>gaiXJH>A*!S@4Si8=2RrB+>O2OODC;LVI
z=X?KWc|o0=NL!`D%dA+Af+S7-Givic9@%#1%-85Q2Mo`vR6o$^HoUkkUS@mh*|o<C
z^1e^r_I|r~z3o2n)t(ysVNAK{dKUXjeB@Yz<+x|pPM0?JxK~>je^B(mEAzh%e>U^q
z-t?h?m1~`g%F25@XI6gL$j?-MWuxBLjajVL&z?Vzyi@;k&u*dT&mX!UU(#-K@#+5K
zp?wFX55GHHb?Nr}?MG6#@jvT27&PT=yOF=5<F{Vs_8neLkEbmbTf-7nb+^?_oNb4`
z)c^d+OT#p#{WjSBc%8}1>1!(QUSC$)WGk3imH8m<!4EF^dd7m%zpH}TSBG7&PCl13
zXTRX{{@e&#Cx<5+j`jV0B*&bccdGx%y$?5T-k%qy?X#LyyRoPI!OKPgi>do^r}%`)
zO*--MLSO7*u5~U;Zt5=obcJVj<1(o?pYQzETeN*`HDl%X$!%=m0#(jIX8#^=9r$^D
znbAvr`9JgDch=wLT*jc?=*DxmB0eH}^{%6{Z5vGgeooWeCp2+cS|fkJ&(c@74>;V-
z3TFR1`;+XFH}wx9UvU?IJe9xDf05;B#S-DF_uYs0+FiVAxvAu){yp*Aucw!AZ4f$9
zZMCuW`?6QAb8Xq~oOpM)Du1ciZ|nSJhbu!*2~YQ#d{y^k>AIsr4|=%dtvO;skMBD2
zuJwAIMDknv3FW61zt~Ag6l+g2i~X6gYfX^lx$;?4cAl{@y^;0&<&r2Z-@}Wd^%R;n
z?wo6xw#@qGT={oLW?0_)z4Jg!vd?tS+dhepSf0d+y=ULEkpIQu8T(44Bg?GI%G2&1
z3$I(Rcsy~9<{o{$Cn}mP|C5X2e8biymVOQU_t2o-U~^{N!@8d)pAr|y-(dS9`p$aN
z<_|d^Ep|1uI_N*NnCJL1!l?ClD))BB2c8Ms8zxRjUopd8SMzvi=cn%ldWpHaSzCY4
zopSGZVnRp3o!Q*m*ZSQ39kC{z{h@7C(2De*)l=AtT6gg=)U%lhUVC^u<j3~3s{B)X
z+Y9)@9vwFc%xe32zf#(NJFiUlXL;?Z@A6x6KTr9+SMIs<;)c)Z?`B>slhF>hGmxEj
zE%P43>#pyc-Ylr>Sz@+quVMS7ZQeKEPPa_%+xGIxq`N8NNxuBYN+f!YCV!N(f0T1`
z=R=Ozb4U5lG}iR>rUdb)70vzr?Owsbxtc|*=SN(hEd6KqdH;t8MW64T_BZa~-$TZ+
zdgi+$?L#K7;<ga1F#J%HAo=i643AU7o7US?|DF+STGM;L`M~>z-`wBXU&nqdd?s*g
z>mShqBgGA`QgZHo|H^w=^xs{<rgdiz*dF-Lw4Ld7()z-hXAJ5BeZMOYY&@{A<@~{<
z)mL5W&8Gz|*wp*s-rqR|f$NWdyybK^&d<ZLpl0E_-_`x6Ue8lzX)b57SA5d;YPECh
z>!s`!$)J{BDf{ea#`)*&OgUSr_qlSurvH`5d%73DJl%JrFk)A}Oy;F;wK88nv<mMt
z&|RiE%X(h*Q&%2a<Fo7L-Y~PilWV*(xlz30d3?un7M{<A`#!9_+|Tz<&-|Op4gZ~n
zM{DFPdm{S{uQUChnD4z_cIMpD*?xW3g!cYu<K7kY^2+(WpYJ~X{NJs<>XOC%*R?-A
z&#-Krzu-=TVVU%_++_Jslf3%2#OcNQ(f@y~-lq6CmE-mNy}bn+Un}m*lW^bh;I8uy
zhJQUDc=yPOcbX^~?3qv?^L3WdTveI#<s8kuzh7^e@3oYZ@yY4Na0Ye3BCVre<@lJ*
z8Kw*QFSyD(hd0KDgXQrbraSCwnDp4MP5P7Y<ZsKauupM!dH1vkgs9!Slt0h^okF$E
z2kH6cGe4dGkXd;DR_=rTnDS?#z5i-f>^{O4;l1y>TABQvWMk&t);_0X(sh<szxO{{
zEOYPt(d1gi%{ON#oSc1;@4>25wKH5Eo<7f^F-3Yq8b@;8vEQdpl-g{0$NN9*Gy9cC
zv+rHa?XA4>{FCkPd-;D)Zw$*8e7AP;hqphOTc)*C^-C7Cbbr0uQmA4suxr^OFX3Yw
zYUT*U_=I+ERo;>l%UIL9l6Q;Fh8Y4Y)+p?$pIT;o^_8Pjcf_`1&&wI!E3BEjz2n!s
z{N|Q}52gpcy5~EK=R@?N>hR9(jQ7{Zmp+=h^O=)a*~d`(N%i03?oT*gFP?YnQ|Bx_
zuEkq<63)E-E_0*w@MHadLThy*V_RD7Zr)3`z4!9cvnk(VcZW}SRI(@jL9yI{X}=Eo
zaMWn9`A#YQc`YFCkbZLdieHyFAJ?e=*lhT0>K5MmmEVtj){p+ayY+D3uZg}l|Eq!g
znabmx@%9JL)cPIAx8C=AVB+-s?(NRHgApDXj1{KA|I70@lUwb4GfaOAEVN!bZ>^f-
zq3Z8)hq5DHZqh33*tGsJ=iO-ij+J`9FS};QR+%nb`evHut$b5I^^$|(Ny-JWvaf}9
zA5Qy`CzIY+r#5@z>%ty4owIT0RFs?Mwoj>a{q=Hrp3+a<l@nEz4@7NkQeAfT*=@P_
zl;Cek@6XKsSjTuy{N5ggJ*7(%7G9APjj!DKDR^1P3+t1g`<J}ouJW%)a=os9|K|4t
z-upr?C;IRB%QnrwxVZ5=^Ye>0ZblTINvO75I6E)y%PW^{5<BF6)VGMudN^bIea91D
zYB{IIPnmo`C~ECKj~7yNvbr1O1)J`#pE!qmF6+OxQ~%l4Db2ffZ>8ZM{~6KqtXQ8v
z`)xS?z{9$m*Z)t`&@bV8`!#@BeR+`V<lf30$<7&iH)qeg`tWvo-D!!>8{|*^x2@d1
z;KpC^OMETSFP>}Nd88*F?zS*zQPH0EIo7;CP6o`M8=b9vE#>z7TSba0Mt@WvHcju?
z-zgROAof77it-MvO)X)Q=L_8bq0c?XbB4hO-dWl^yo7hXShvLRU}zxQ53Ub}lZx-j
zduN<ndqm(u2=^V`A2-Vy!dv}X9+|Ebnb-1LHz01$u^ER<m#<l45R@*cyiEPsbn`-?
zkM2)pWAFXmeDb#sM?UvV<C=$SKetBPp60f%HGHHu?d@ut_i+z;_7=V5^uKmPDB^Kl
zvX1yP=KTwH>Rp&zDZX&`%6rLuS*217ud4JZyykkazhSA$lj1c_(=M?7HJo&@Iib;C
z=-gbl%`JJSz0Tjy_IzitiSz84w|<ZRYEG$r&ueb~th)a4baCgkpR%=|UYEP?8NF)z
z)nHSV*Uc+`{QAA={_<6OK3o<#Ue=p`Y0e56h4<%9Nq&Fkq3*TyckjlUS<!wq;(y$#
zEfdd#3hCYYU1YTIw~?1X250m4$zOkl&g2)%^ITOu>q2OySMzJb_6v8TJ7s*Q&0<tY
zpV^-txI=8_A>BLXsoz)YeplnEJSiME!KO8)(=d1ct0IkUQ$^UePLIuVd;jC;dAn!)
zUuzFa>&%otHkp<2>mK{S4Tg~nM%(T@`lH@gaqY3WP1IW>-l@6uuTCwW{+Lr&A+~p&
z2alM*u9M4(63Ru^v;33$vA=iS2@&hL1|RG_4~7P+FFgIJ)kJUavC5Epsa58Rsvegk
z{&hdixs^G+l{5I`hlY>yTHi|k%lhV1e&~$k8NbM~C$i<dd>=QzwSN0;&+K3Qe>Tbf
zI<$VD&52JDJ&{|!zEtT=>4+Ele?j`t^uIdsE;}a`&56&sb;h#&?~6aHzDuU=FP!2Z
zY<s|Ti`(g`sxe!{O?D}TZfLn8sBW@LDR@P@0E_z8-(pVXuid4$yysb1y<t-JB;_92
z>{ZuR`!aXy%zOOk#|PfSwl=meMW)M@ZP=Z5GBKv+L(K0z>m<uO)7xv~uJimp=v?)N
zf11vd(BfS&GV^~fKL1_L{NUP(M#=s2J8v7<9GlUc(O-Sedy~p$*42#1=CGvY+^jpz
zX!Aa2{>0t0wEn%&zE>xEdilaf5;K<euJiEmV>*{vqMCKV@x?T&scO3et{o6!+p6DH
zIQwYNugQPoR(}^}I{4KvXSJ06@=yCuem&q@y2d+piP?L#|2^-NlYUmcw$*<z@1@<&
z4++mAc7GS+zFV^SvZh|F!Fjox7vJsM^i<!>|Lgq!^9qulHnQesmM2~3>6>-&oMLXK
z(Y1)@g|$0vUVlsZ`S`+yzmG4-Z92*sI{EEc>6&|It&@)B{Z8Tj|5sh_z^8lSpQ4Xe
z%nwRpivPCE|I3f0Z(mlOHdOy{a2spO9-UD6{IkD%BkXwRy1nSi5S3To7dG(```xfZ
zR%N$2l4EyqdY{r+vSp2rjGtmmM1EgpwP&eKVp~=SUxf3C*ss-I&O*By7jv$E?&(rp
zzl&pSgt+?+x2>02uJBAPXkpm!a+Y0D`<Vk4`z79MKI>yzVP?6_@R;tqH#^>OyUSE9
zKDqns%Pn)6pM^aCEB(3hdhngPpOe(`-^|RFy;qy*J>OS!d&t2$-8R1DinENH@4S9i
zR_x-Qc4lWP1HTy0wMRkM_}-j&8W#WW%C}zgZ*MIc_r#xJd7k_t@MH0{WuJAWV;nCr
z>BuuFzW4sjyJ}aw)Dhd9HFq0KUw^3UK4~oB$9y?+&D{3S-XHf}Pq=jSxtNy0GQFo~
zgMaIm+a+KA_QW;*&w*pS^1Ev6k8_G#v)5s>6lSsBcI}r$vYY>{liT9|?aqH0T+_qz
zLGxAdz3+n4yl)2Vh~L9dBDAYrOn6#uXYrZqMu#evS=e~&D7fpBd2-$(_T-N|n(LB(
zls)oJsNzhVxnQLockvXlNAHwbw4JA1i)guIHCeXhdm*3VjG4hZLW}-P+c3rN%Ev-}
z!MN4YGi&y`xN|(S^MAUMPpwF9;kjT_=l2$eDnmONXK7?tTW-I+`$~@Sd26oBqEl1%
z{h0RSQ{B!F8rhrFQtb^6r|-M>|BBr9C#>2Z>r``Q*WSJMFIN8ji7mBC(@+0jTm1BS
z8b|ZJJI2TDwxu8WyCQ$NtgMDn-tVKok2#-`3X`$89b0gLahrDPaaPa7+4m&Y80t+m
zGM7%?x69hPD7q}Wtm5g!yLUdkmX(~mEnoG${?XsAOZ9&~{8b!LtycRxKf79Yw(BOQ
zH5WB@?RmPgq<+(<LqTS*4ezu(UoKZa|Lm?t_5Kr2*#6rv*V$X={3|#i^IL^mPTn*6
z4O7sZ+&z`@=k&Fn8fr+|Uf0&%e(&?0clVZuZJgiTdU6-zd^30H_s4uPWai#|b++@^
zt^db*@A{~I)nxITZt?!#UB3?>k|IL)RQ<B~u_yDV=|ZkJ--r#Ce0>)}H+D@Zf2HUY
zV0yDU{>-&HnTL<QYk9psd-c+zgvRn~KkgJYAFvnr#MvAFD)rCCFT&G4?(Dn}RHXW_
zVv$Ab1=B57kIGgRntzZwbadAaiE`C0&xFe@--{R*zWY4$Pi?$g#?tObR)?zhuJ<%K
z`q$neqWojggS)2h*6%1epPpS)XWF$=QfseREO*Yz_|jMEwujU9d@nwf-|BMxS`K4f
zo9XvQe+-Vvb$(xe^k?cm8wM`NlLnf<&;99}`2PNvYx=$4CQ5DIw4=N6pS#{)4=vlz
z{twoDXjNE!qxo^8H{Z*R`)`|`S!Vk??&`}(W9uJ3jGuix^Q~v;o1e-1mPt2nedd^b
z_P)WS-Jk!xe|l$Sa{A@;pTAnezso&Yr#$u7io$oz_bxYnmtf8;u(@<=aig$k!qoLA
z-mcbqZuRNs_VX|1S(;ojd~$8ik5``GC$e61?whJ@t`qs|#QtZuZ?8AIR(H(e-1mF_
z6&q*05xKGZ{%qBq`_J5bZ~oCeJcf7j+MNGe!!K8V*weV`TXa~QM7HUcx|9w5#dSOO
zukul!wqaX>%-v||Mt^~()n1!Dtep&s!ykUrZwXtwxuKYoQ*8CmY9C>tT(^t<5$oSy
z)0+RB!|~M0mXl2BE-Rd+DufpvO<Bbw`0wAUT+`wyOq(7aGLyS={BgHq!IW#OtvPht
znnP{Wy-!@Y=RIR*M0atce!zd$DbEG3^{#OVUY4d&bS<st``uQyMqdfL=kA~W-@BH{
z{_Txa;l1Srmd@4f|CjjRESJc)bG>)=E5o&Kk1K!gT5Oe<bkbby?(sRw`o+7i)xDdY
zVqx_B?tRf;Oz!I?Wv>;yY-+x<`+EMiA0M+>oo1WHnB?o_znbZMtL6E$V}YWxEDueu
zxPEQgt}6esCzIxx87GMUy?jJ;*9+-2(K|Q&msHRDU9nt#pWI>df`{HS87t;BzQ6t<
z$*j|bHDambjivt*-hYpc`>}lO>vO-tOywOm6scx6CWozkaocwBZ(Fg+#(m}Dvkhxs
z&XKx2*EVzKcZuiXeP?cmg_?ddDnIt(Zr3;KbuntCI*RPUA=d@3?e4x+JBj(45Yt+H
zfv9VG%RVj0lvH$BJyn@y&Q-SXr@tDuGyM17;<9$Vs><#)-;dU;DivUQ5ydOSwB?oE
z?WRPh>5uYP=pL}{6Iifz<-?s<E3_Bx-YT?x^ZN#~i)$7hj%NN)ntx{LGTXghFJ7-J
zUewMf|4}~w=d8JxEBlYf<tyZ_iA>yF{VwTbOTYZ$&nMD%{X2fG_Egm8V>S2Qn(qGb
zW2W&N?Pn!B=YQkB^=N}kPh!}qPd8iHKhK$Ie9We<Np<$zjn6jU{PSVy=e|Ej{{2r2
zU-yKwpnHAYaocANU%Y)z#l8FdZqL3LJL~#~3B_jaVH$yq(=<z`1aizfy=?#6-Fw37
zdDhzOy!TrF2gfxX^U7&`l9xkn_`7y%NE?5jc+f(9xoZB$XUg?87hg(D3;Fe9E`MH9
z#o^1zr+lnhbMp^xTh6_G+ur)JmicO?`(EF_v+di|_|@N>?+Zm`Et>cKzhA_jiu-S0
zUp*a^bu-E#^=ph=;r#84|0N5h1&$fkc5LABTf6?f(IJLkE9dPD%U2iDtvz<V<J&A7
z7m52}-rnhkGqY`(*YK_KKYL+|<BrdE={>d0H<RB-lz*H0JEyh!OYZ&VtM7O3FOU7U
zp7GMlnb~r6XP@YXKkcz>KQ8xs`afo#aI17ZX0Q7vxU+xn`~HCW?OW#E5=9S_sw$TC
zp4YW%N#C+vblt|K$NQ&y-G0yi{L}Pv@7F5q(Axa(Pd+n`Ox<5=eV?U4^*0{g{mdUd
zd295nEv}n{I=MD@eU{|noxE()r;0;eZ`vZ8XWomQfBfgg%{$tTPO^UX_5Z#+W#`Eo
zDmI^gdjHv6`}{KsKRKh$@A>|wGReAm|8L`cIg2_rirv20_Ws0U_gf0@550P|?}Ae%
zuU)EQ`bSOidC@s*O^(ehdG+?nw}t;-&Enhf#P85ig?A6K_V|k0y>q>C@9s+uO`%7-
zBJR3X)K0tp<B!S0(v4S{*6d&Q?R&-ygJZf}>^1$jnAZe1>btKwyl>B}Q_+dng_@2o
zGyVNCWPfB*-v77RS~bzrV;#Tm6<^1=<9}uRs;u~S`G1D<;=Z51?-N<Pve@o%ujFN!
zi<hT8TC;QW-S6}6<xM|#;=@tbb_4afNhL?F?Km!O-x7Q+=j*-tl)CrFv;V!Rc=PrC
zDc!#>+4oP7mW$c(xMRA-kIJ>Pz4o}UMx>R@(pZ|Y@XsUL$Vwiwx)<JG;_46fZ%mu8
z=k+3!;L<a8-$VO8&YX8}&0VQz7rSp?SFEus<=fnIP{KZq>%)&@CJk?dZ@>KiG%8Oz
zc?xVTK*3VA44%}rVXe{2bnm#;^QWp!mb-gz$<7ch^ZpC25vvoOwkHHFYfJAavytY!
zt6O-I@xD^j>RX>PFWpT1y<yHR<~7wF>JRqJHF&mW+M9>!V)MdZS{%-baLQ`)ieA5N
z$-nr#SFiqcYiBn~eV+3?^#7bi^OQG5vzeXSadhXO)n_xBr!3zg_cppJ?RI<l`@;X5
zJ|tLcryhR3Mm;8A&&}5#TX(!J{+n|%rg$mWwLOo#15&*fr%hSo^UhTFlFa;^x?^EI
zHy`kZ?CmIuY4rVRa#y3<{Jkl!MO@;f{2T9YR2`V7zHRg0K7km<#S=GVYO@8jMpsJ(
zi$%;lbT%z$>GJ>yW`VaAaSmIGYeg6CR@L0qdF^Wn`^R{bdbceMUo0kls}%7Szu5HP
zf8R>E+ADSM<h=fdaac?|b=-wdXxH<lUdKK-GoPFNp;LC9^uztkmonE`{1LETZNRfQ
z;+<_zz0I-7o6@?AV`_gq{O#$ivUt+h#;`qZ{rM|zhFA6!9y!)pEpsp5Fj>rZ(GA<J
z?_H-n4%)ZY>znnunnQ1|G-{Sz6?@ghdAI5C>}{L>PS2LKcRso#c(LP^8`oBEWSpMs
z@BHxg6wNgvQGX;47AxDBv&V?0J}=$Sa4SkhVGG+It7E%Fa+RZ2wYr*|kLsHGLiJX4
ziTTG~-<72aJ5-}4>{$OcZ1Sv!yG`<Hk1R_)<Mr*$$-7CxWj6wT>FC~-_+EW8_s-*k
z6TEJ(=C`=wZ}U4=ZORJ0LxGdoc!lru8&9}#fq&+^OFeT>n%Rmr&s}vhU-?z=y@)Um
zpY7?v@_)<ig0gmMdEGQ*3|YB!)rF$aoRg=P7{0s`$M`z#XZWh^J-7Dz<S@SL-}d{4
zYi{U@<32j>Ck}?Z{?$~>xz_IMi@vOurC0v_oTa?yc;M%BQP-bJvHhw`t5(!hF4ys$
zGi%|+Amh!^XXi=sKeW_5)t;f1+E%RmPV3g~N2~9cOgO`^TFWq|?zH6NuCqzis*JkJ
zJZ3Dh5qrGrkk-xoIn95yL+8B_<v;A7v;6-#_YalfTod-NXK$Q&C4(VUE~8hreCn|+
zOVx9Ddn#h4U6>WHntes?tQuQgg<A~Yt9olIX56}d<h4Rf#d59cioLF$3nwb}WOjQ`
zVR(JwMpj^v-PG;x?s{$7^?bG$``w-y6L%ZT5lOXXE1rFRHt)4Mm36Cpxlg`Q@|kgI
z#iB#Co8Nz`D6=X{p896{o|=%k#}j({zJHo$JNvh{Zg}cf^J59dD-Cr+AG2?ozCC3s
z-=XQcl7V&m)iMt$e2?-?ZTskTcImhLFU>yFo|x@Ad*$EENoq3T+8Yie8s;dkix%Nd
zzTvhrD#+NQcV3mzbAxC1G_J33;(y4$Yumdp?WCzf;t5mZeYAJRPq*?3kbnQTrBotb
zuJ-xks0~_o^7qD1-rL&v{P67GFZVz8SG?=A;=~KX8QVe>8?vO0C)Cz>Ps{XAe)FTT
z%)oJWtgcmO*~2=cL&dLC&9?r3%NMji#wjp*{-c=X8z;&vG+ifproXZ}UFg{D&?Hku
z){ZMLK0L3RGI8RatYn{cI@)Ct%F%z;-1FaQm{yT;<gdl&M^k$(JJhDFVOX8B@wwOg
z<CZ7(u2E{8y!uL4P~36O(~no3n6X|;^iBDuPgZ<I`u}Xjnzi5mnbB}wy4mx#A>)-4
zWA<FNUeB8s{UYOMC`x_{-Xni1`-<y}qLr<S>(<%^Ua_i>dUgBmP5-yL*?rffp4`(~
zTUgxjzSfiZ{pv>_<CmTcHdZ;3mT)6@SBhBrKJoYdVRChk-_4Vpl@idM!Wyx7<_53J
z|9va98az+GUVQ54yw?GZ9A8(acTY2XQ<+qqv9pNp@!t&drG^P>ByR^zl@w1A-NoMB
zd`r_#JouYmd)VraPfcGa-D0?@Qg^^z(t76NI_9>;&p5NEGMp9)%G}cA_ozDFPi2YE
z$|GV<RU(}l{qLE7ofi5f;+9--Y<jOg`+*tO*Wc7Q-EB7YxT5eqO00Tb*VpfAySH3l
z{&CHk+v`vL?UQ^Lzh3;<@6~@i{!M58{(tA?B|2~RPVto}zj`rjN9w6})ALpyI=^??
zAx-Nx&i(@h@l#Fvs`}Jl<u6%qO>E~9??>6OtHUg(@qC<<KW)OA?U$}U{jIY3>yDo}
zvgc+x@A_q<)38@OU+>=h6?Yg`PTBeW#p3ld4smVoOR44P;k&i2X5;hDX_=jimG;f}
zwap@U{g3RIGBVNUR2Utv?lwz)r<S|%c_}yF?&fpL-#@UvyCJ)YJ>tQXPfYwNi5Awk
z_I>0@xOnlvo63;wZXe3bctiiXYMrv2cV$|K%C=RGU&KBxNjcT;yvZ&)JH7LHgjm4O
zNw!B*o33ODG1tGy$v*L2{P?E6_&t?h3WcXE4>p^9_Ss~Mi_0}tUO6vVc66TapSK=q
zU;fvX*iY5nB~$M^Y1<8B^>ugtCx0{6`Pz9Xx66gsZIZ<_H7|urj(^+OTx6HbyK-Qo
z*xDkULe_}qfj_5DoiBJzZi+<D5*^vf=Z932?wBTRa-CbdW7(6r@^T;TK3%f79J=UO
zLTh7b>fQs#LIUE>|C({}Z&*-VzUONH$r4JpD(fPSJimTeVQc;F_si;z8|xq1rn`1>
z%9V+G?qv2}VU3A+nB2Wm@=BHH<Tvv~9vIKKWV-oA-&5|@DLxT>igUL`|K6m$_EWj#
zQ=w~3rjGT|mDjJQJT?4$)UocV?8VgI^Gh~9ztKEr<9c@`vFbcK=9b30Tj#z0dLl*k
zYFQS4$}Udk>8~%!mTPQPmnz+Itw`gxlFfC&sKQAfsw@_<?@Jf_lo|Sn@le!Ep~;m$
z-#!U8wmM{bIXG(1&Wid^Mel3>8y;Vi6LEKT>>{Q$7a3ibt<m1_=XuLhyKgfNO}V~w
zLwC~uEi>2Htn=!Le^XiiTQ)q7Yu_u|qZ>1M1ldkso0U_dsi@(3=;%5PuYD`|oD@R(
z8IQOJRzH}&v~<&s=tZ*KswqYL_2#{D5!$MHGN>|(&E4Z{z<Qh9%R$!<*BAXgZ@15Q
z$?nFD@pldzr3+7OK4@*fqv)wu*t!_YucG;kCtv-Nn4f(qBqDD8t|@n~C!P1z_CCQJ
zyjt$Tj~TCoruVv>HV-{}rpYUE(O$o17444RLyY}ycaE)0y`A+$ch%&THMOU5TW&TB
zEnYsqw&Ygz{hi;F&R6Tdiiyi(c>ec;yL2ssuTCUm*u^D|hgH764sATiw4;ix?DwQC
zzf9QK*K~fU;hrNM9Q$Zf<E{NqqaXbI7@8VlevxTS@0M#jmab^t67QS6<Z*@k)bCSb
zd|&q*_U<WJxAt&#e0EXNZLi?!<xxh=Yg#nqUE<G_?OqSB4(>JojXv<c<6G{ZoJDKX
zCAR0fNIx#-`pD03(VC&DyNKnW=NE;GX+nAoanixDQcG`L;kob7d^`Dh?|YMDSElG(
zi@N-?;*RJnH<5(5&XtEJEWGmCEV9zZT6XtFuW#0g%+rn~Ox>;h=yP>L|D-wlrzbAb
zb*h#5$aio1f!oS?kK>|VKiVaDL*(I4u^m&M<sIEM<J9H@_gU7gPmW!-cFy9{62X@%
zQ+i)o`8{5rHEjy_F%8{sHtSfmH+I{aPyO9tx9|Dh1Kr6hyk%q_&dB2RFlt$It1yyn
zkI^HucRh=hI3G2D?1*rhFm=cIms}-`&%=M*kWn;kzTy~tN~hr5($#TqBtICGKj=I?
z`{N()mXy5(raIqZ=5JV3(bPNt*oh}k3$HHW6syj2ihS^_<Ms=Nbqn`pN?UO@-l-I|
z`Sx7!`&Yh4l5gg*+4*ky`pS%n|7gJUB|il(MnAP<n<MNTt7XU^A#-`#ImI(!Ymd|(
zxNG<}{M47V|4mkwtP<aFG*NY__OUv#>TmOE?tSgydEd2Z$Db|J)-ZIx60ct8tn@uF
z>dnqn3#S5+uSw+^AGjYpJ@R|Ial1goU&b9x7gTrJe;3fb>ZG1%Icdes>-YV?Tw6Um
zb8Tu-SDtd!t4<Te)Wg45`bW(*S(y4w>w*7)mxei;XNd(ZO<S?}U5R?d|20lY-we%f
z{7*W+a*A*D^T{UvwyadqIv}-s#pd;k_T2lrYMsrkbEo>(@A})P8P0vJV!P1!Ptu<o
zr5pb%oSC)y>7sN_@r9EcPB*r5Hinw6Wp8dtnGz_Xzh)~-q*#Uc!mnDVo_iSn$aQT#
zu+=bUd2_+MKNBwGN<96lH?R6Q<A3%awhz4z|2(q&U7G1iNi#<CBU|Dnm)E}zzE;`S
zoWvb!82RYN)c`f^^Uq_CNr?GW9*uTc#I)woZ|hn2S5CN9U;p&$iVpqTWtD4;GAna-
zn+e}tyUT9Vbe#{Ck0d?jGT!6)!}cTI$^6{OmTAj7cb(E%cr-&WG3@Ho7Vg{Y8}_TR
z<X$amQP5vi%yG9@J@DuAgEdaCuZMSDGv!#Ay&-gWd)Hdy!Y$__5AFOc?X;j&?P1O8
zC$^hgOilfjS&n=c%bTxKB7FR&Q5xsk@Tv2>@2joZrcnA|*KVT&M#oHje6Cm+2JZZR
z;oiM%E6!cbiR?V}B<^z3`O*w`qs9NfFaCWo>Adbk`$m3&D8@$<6j{R5#p~o3O>s(W
zC`ddjpqKZVYrDn&XL+hD8iD=KRUS-lefzgT;6u)`DQOD6FOJ#pRmdu8bY}~`S%1Nb
zTiHK_cSF~yV^>2LP2TY3Ok_)OPVU2Pj6b-SUf(2a(IIf<yHJ$-<E(|ZrXLNtmulmY
z;W*W5qh?j(yi4HfB);2LJjMN!yY1gE_5~Ll=dVi-jSgDGv?hr|)M<8*z{dBVezl73
z)48&0$)0<Y!se@)u++3%I2zvn^8MTv)9YHX<+@t#854i-FWT;w&LMtmx_I6D<y%&i
zuq!U`I=*3k(d&ly$9C*hDQcOv=(<qT6^l}4b+Npo({4Wc9sGLMguqybr?Ka*3#wUo
z$fj)8zWF)i*Am<6qHEH|>ns;t@Y*=Ph#}ke{k7%k{)uO!-52fR;I-pP{JwPFLxb!B
z`KP549H9~ZGLH|ht(pH@YrVU#*3I`fif;BtH`M2ss3w)@7S#9L-aKX36fvPFhiAe}
z8!YVgWfZqZX!GUC=i7eJd^P*|>L2^2{<pjOOdxG}nA1whS8wM3myEeLmn$N8hmFYk
zna5^d`dTdil;PaZWbq|6i;`N?Caw`bJG(%8-NX=?ge~hoSs5JN6>!VHQ0n!Pr-fVP
zd!aRv-NUjabCkCv+1_~3bwq``rsElRNZ7=lqdm({O>eZ8itV(jR-W3gzK6SFL0{?2
zZ|5pwk6E2BVu<gUaj10hhxzN*$V6<pZB}~dcAIBdLuilavG0H1uHG}RRCD+Gqw}J@
z>=SDb>Vjr&-ZAaF^1>@5Q8!WNPRS(Il->QCK2%Ivx>B$5t*C~n^W7ive;O(`M?Bjb
z&(O+f7OMA6<`m-#lOJ*K?eAYm&T>1+wV_LmS4wS1{PM__#rA5q>h7lLzjMFz>hhgy
z0&F?%Csn7494)j9oV?PnHTS^mj(PH{By*RPp4<6xTJX=5?%tNAg-iUt?Mc(k&0TqU
zZuh;(5BI9i-FDpW&+f3O?%FIB;{#qDp8|c4=4}71)t|on@v@U)8{&KSt-5J@V0A|C
zv^9xN+@6zy<wT<S9?KYC%X!Cq&tc2aU6WtbhSb^aob>GVr93U?+qc&i|6Bj~#<cGV
zYb=)~`$c_pn);;)R|OOLD(^u^)Z<0_doMT@RX4vjoaoz<@NJu0xC&z)dz_=k+6!E(
ze9sn?%Dz@|$g5a#ySo0<Klw<-^Ow$?yA{2m@86;L;wQRO^?Ywy35h3!?!Qs|r#AU%
z^!23kmk&ufP57ERt3KvLn3F=W>DRei!+Li&h>O;F705p{?VQzX&w0=JX{P@^|LiRi
z>emi9&sS`%WSsY|ORRL=f;*PiZ(A;3y{#hgDwi8yyutnVp0&?TglY?k7heh9#J8>O
z=)Bj{<Q%(g{mq$M8n5fCvM}{>_{nUTb)i)9sDPsU#hoT*=PxjP;BR>l`m^ubwwVGv
z``e$CNQPD4JFlv<Ik;0tar53Q7r)Kbob9(fZsPZ&d*1wxyt1>YDETbYrmN>wY~I}B
zFG_jNsGe|kec`{oc2{LfpSCZX1g&Gz5BnY#t6o>MKkAKTSh--+n(M;5ik2yzuGqF=
zy*cA~)^|ObyRS2yXS8$7FrBe#K_SBrs}DI3;xpd*ybZK`kbS`LK>EyIj34?0CfsM*
zGx@@ykY4kk%CP^|0a<N<r|UP$gstnT-EI8r>7{$WFZbv#TX66HqI18s%g>!RU3q2U
zxzM=#>9N1VZrx@(|FQDBy~TEp7l$^y=?K+MvN-i@LWj@0V-21+bMO5)m!&2!?QVa5
zRkLBU+T2@QH&(q)I&<LLwv65OCR3S{=Xl=Ey*D!}uKAMwx%8_|qMm&Qr(dQWI<sQC
zfKlOhq5IP($t=wNq;@Fjc=iha?<w*h{xkk(o8!BqW1hpGnQvqtN~}{<DZ1-Y%e<>D
zEB~wKqg&<CoSotOIrfNFNM95$o7bbfr>vaWUa2HFZ`rT!tC@G~=&G&T+E%+|S*Ui!
zp89Ktl>P6_xmop<{n}fL|DPhve!tG&)BVjv{n_Wb%$KJE_8nSq{7S^TkH_tPrd;3k
zH!SHYSKpa4=iY3q5qfU_X6|_jhUarL{papT{@(cgYF*1&RYAsS=V#lweLBCY)@Ew=
zbLmf(_ARgVEBI%WWT<LiS%2ua-Sdi1`uZgw?wf`uewLqiR`C3-3j3RXCf<_>&y{7!
z?vZ>nNB&w2yW~{mn#XkvJ47P9X7v55Ikc;$U1-{IO+7{9e~%KmZ=Vp_$C9I>V)55>
z;nXbIVDo3I`!B5e;_I}aLTcgCcPw7V18v$)>b-h;+}vk}hrLV0hh01L9))ZPvvk^?
zJmtCiSEv1~Kf(`H97t_h+U=*x5?w4QE#d#guGfCuqn+CuFZ}%z?IivsYZ3db(<^OE
z4_ieg?}^kA>s_Ll?DyeZY+b<lb>?Sx|NC2R|LIqKca5K1?I~m3dHfd7FF#ET`ms;;
zQ&j6k)9UX9K3f<{Hr}z!QJY+KQn8)q-iGym<v&jTo?LXed+$T7Pjx%_GatFH54L;X
zXPM$C?eA`JENxL5-^5p<(^X%xRdIA%lnd{>D6U_1xHVdSVd<jz7etv)?%W~XznDG3
zfn&=v@w)k*FO%YUg#J5mFl-ahyAjR()YEcaSSsi9YYPu7I&|K-F>=a1W%mmGvcRZ<
z8tH|q8~cN_>to(eWnHJf<xSWlp$FWCZ+E}c{rA#!$)|sN^Hl0v4a)>hFTMBs|MatE
z>GJU(kIvfm^52*Gm-*gvpV``fz1N?)aND(%>+dCRmc;%)cd-1+nRoND-zY6GnX;tG
zb-`NG*>gXifA#Y3@x8k?_D61QdU)o{mW?mXAOD<FUU#oWQ~L6^<8zgNUjO@V&FbYx
z)7zMI1O-=KGjhs~P;H*}yK(W1c_&lVzpS}^Kck%g%rEu%r|XMK5>vDDj?dudIrD-4
zTTc9eSH)prd-iV4-hW1B_vYogQ-6i(J)bsXLdRUe^VjC{@O+EiTw48n@!^|4GyT=3
zZn_<&XH)U|bXuw2N4qacQ_DHU4l^0AyOZFt{O$Dex8LNej$Qo!fT3?!nySCtrpcAe
z%-tXV70sz%s-GQc+Uode@y^|AD>deyw|%~G^S--pHgDCQ)S>4jD43}w9voS~`XN>%
zruU+~MRVDEey#Ylv)0@1NEGLP-w<nR^tkhM|Nf_YzdtYI`FNo#|NZu@&l|oZEL*(x
zt@Y12(I!cMj>Yrvq~_n;IN6%Lt!mA8@426s_;5@v`dM?{KDVOi+}F)k*XxrG?m6>k
z+ZU(jdt`fCdY124w^nkm{Hf2C-~X+X{C2T7`~S=Pe!mXKpP23Y`T1Lu=@0(w-dj93
zai(m1*BP$BS&dF_(suREx8w8{P3Y|KFs<TX{;0k13XiZyzV|`Kl3z(50((4cB==OW
zHh<RJyn8eMrF&(`?|a|xI$XV7ZSMK}(`QcXTKGmL=qJzNm5JA<olec^`Z>RL(|f1>
z`Ss@yT)3saNtyfdymfQFi@kSmUpf67>x0YtWhJ7Dp3So7*PDNN>n~gO^IO}?Q^cMY
zt-JhNz-Q*gkcg$K&U=nO`#Asp3}4y1H_av;E|#;r9(yb2qu;|7r_y$ar~NOln7-u=
z>(|AgeL<@}hH3eqEznLZTRG+Bn>#1v(o(&6Ba+j59@k18=ai^tVoNtT{4?bCfp-(P
z)g`;P&5_+G>93yotSWie`un?T&&*hD(<+c&!v6HO{@v5o_e-PipG*Fq{`=fR=Ucb0
z?a#{l{-Jxf)#YyE+}OF-%9gM3tbTv@+{8V9FMpWVcmM6Jx&N*nnDF=UJKOhi@~Sg8
z)rwY29Y0gXe=v;i&lZV#R?t4KB}I~2{%08qSZA?poWAgmPSD$w<37yt>rHI$FwK2n
z{qfBG*M*PMSi+1q?D}zI%JSsbA5Lt_&;7?8K6{@`+d)Z9>j~S`Uhg^oMy}BI-0!|e
z5o`XwTl|J`u`vg)#QXL=q2TRV_aqNY;*#IpHsL_Xv5jvd6)sOdl9_hwx5+%q!+Q4V
zK9x8Buf7%c)Bo_ZZ)Z+y;oPvyH-1G&hs!rRt^Ij5Q=i4(-mGVI&T8@||10^H6Ii&K
zUtBLcH^(@aNoOl4QK(L1Tpk=bJzidM@qV9#Bg+)uoAv2^PwVPFI5X(b`9lex({$!<
z5We`J=V>_e>fo(=GkiTjd$2;1q(2<ulDBp^QLic-@x7f@rtr>V{#jER_h@IIklMT;
z=km1bKN;65G<vpfH+#P6=X}|+GdXgpRUQfa8#+2XvZMFBa>~B_SJ>{o8~eI`-*=Ih
zdY&e~lV-klCnbHy_4T&NRVjt+y$6K^1!oq;uDr{4Sa<T-leh0bIkaSYe{}%gkDBQJ
z=Q4$38bRg9M9uFHr1y0jKCAM{^ocgitTLP$@_E|qi}m_j;?^43)jpR$|MOv8{PeIz
zpd__~u}Jw{dc@{T6S<GA9Y?1Nm768+{5WNiZnjy%8`b_fKeuLHtpdlbi&RpD_w5ZE
zpJ^w^91}?rVm>CaNlN6MdF0O*o7%2@nY=0gWa-<RMy~pqi!vtc?&$DnmMQ$pdiU6@
z`w#A1+S}gg9I5x^ndWzgQ+cM>))d?>zyI+?<^8+&PhXgHrAbvu>5{_Fn|Tb$_u35)
zKb|D-pm;l^c&fC=O?HDlCC<lBY~fw!019Z2!#NgjqaVD@RZF$c<5_26wZ~%9$tidH
zBjU{1R_Wb79%1Zps^;30V*O0{dmGc9q~7m)8JgwyN=ZaeFmuD=JS+RT>ZOvE-@hNZ
z`6KZx+nS$xmER>^hVY-;EAo8$<Ci_@>~cMl$7ap`5c90<^6KmJt^cxZ@pl1R%%t=8
zqpR8TKldNqS^lx4=kN88$@9L2^DTLE_TJC!_OHZqlCM?0i00|%y|{bJdhs1B@6T(q
zMuq0zPdsb(AnL)Xg|Xijo{hGak^fV~>TYGLaX?5=(6i%S==+wwD<=<xpZNWF@Aqpn
z4&AD6-NI2<vgPuVr%T@U$LiIu%bjnz<=xcyo7wiq|G&two-u#3$myjO=Z^g3d;hoP
zwz-_avBX|xv*aDTXL{?7+<lgIR-)ofs%=7;-&yV}E+Pq?9UUqj@6XmZpXDpJI34}*
zpK`_iB{wEKsXfspP?z{cD=seY(l<5ZNB6dTTeG_D+t&F{_eY$(w)}t2X4#d=hR>Mh
z)a!1TkR-nJ`(cUAY}xP3kNr9J^i%ory^+n*CwaGQ-K`$~`|FMVy;C6`S~OKVvgXdQ
zExxxef0)BPr!SrHUiACI2GeCa=QgEr9G>3ud4A24GpjdUeZ&4>!SprDtKDzceE7`E
zQ~ln|rs~O}#J*@rx!{U9A#UIxZ_@pJu==Ls?zeAl%=|Vljz>M|?8S=xCn9EltTgX2
z{r+pu{)MN@^8WnI-oM828Rr6Ua`x2uf7Hv&=Bvrvw|}oav%2fNZ+?2I{ubx7-LHQa
z^WWD0m9u!YhLVz!Qjol7_CYJL2)TzpuQSemyt1nUlo2cR7iX7TFRA``B|Or_#U*7;
z$zpAV<QPU7@rOU<S>JW7)B|Z%W{o&mBy%z9Vb!Bm9UUDVSNytdyE{5Mj`)Dw-QjTt
z9PVUtw}kj@ieV^mt@!tAhZe}CTZ0>>>SRmDf_52q`o*?@#0-N$WucOgF)L^fv6A8J
zbIBWYE-<EWeb;@^AY;IjA|1YU*>tr%>mJA7e)M{_>-zN_9a}cM6iSFpu=~LDp!I-J
zf}sKXi)A7lPZ|^x7;Z4FVSC5=j^Ucfzu0516!y&1XPC$Pg^8PEeXjV@>)Rw^c*XK=
zH}JO1?5}5#Q{nj}Kkw45?v4&0=J%{MEw{Um=jL;MsONCJ<Z&eTKj#mXf{Z)tcU!C)
zHaBE9EbsWXYuf#POn>-47(Qsxw3ZSSoG2#l-Y}K%9NRzhN88kPzh&FU^ySLKANovk
z{ROkb+pVTri~JDzVDhyx_xOD|-8bvEpF0jJATBLpi->2D>)X-mmG956zUSu;dzp=X
zpOe@52bwEhxGA`?ZtJ~o49~B;yy4>Fl5{<5GlxBg&fG<{vRpC#99@$>SzTK!m(H-C
z_1{E+3{$5zgJs?>E=x33R1Gr1Bp(zXxNo*gsdNIP9&=sGt`{yYE~^$XXj^gDNLj4C
zDB2k){=xRae2&Ix9UUDZj*MY8Rt@W!=7QF&T5-nCPdDEMij=cnjA1p?7~W?U$S&G9
zKhx<|>*eGX-5nh#wk&1Pj+0-sbMp2$wmsV}P8ARo%q-*D@MtSX#JvYrS6=ZvcrO*p
zDJVEGYypFI-TM3z)~pM@9`kOUS(~q<q||9BtG6O@0sjq_FXE?maaOK*Ciq`xXRyZF
zz2;Z5cxT-Amv9y{caOMUD7|6ohI5ORd6vxgKhbvo=obrqSC<s2%&Xkd@&&>lf*;5^
z6`0m7Oyky3;d!x7!oqM_t-h+t(Kp?h)nBhM*C-r&o66ap9M6BpGvZ8T!KCA5Lc2o!
zS^jlh@U`UMx~8k6<A~O)AWMJYNp)ef3-1V}F}&;A@&D0V*3fr9__!Du7+ASIT^vL9
zYrG1w<j%hFoL%|d=8DtI_m!f&Bianw-g+H6bpGk>{TheLTwPq2ZC$|_b|q#0a$)}o
zUyn(Bx4+65CiNrvNNv@F^DXNxT9h*6tLfaD>ki6KCKJP6cS-jB_!G_9E#)4%-gWx-
z<+r|nW?8iU?hdI6!G+NVeuod#Gc9L2uUhi8tE0oDHH>@1BZ-KA`7MUgfie=#w#yE^
z?kMB?BDziR>(^W2>^1>AI$_ET7-GZ=rO$3kIVUMN|9@aYtc<9jpkSuzTCs$qQ>7l(
zE7|RrOiMq<+SmKxkLiK!;BvwvJFvlYV|&uAb0Mpr{k559Fkw&F{e<^d#FdnknwZv{
z<Pn&Zv~AO4B^z_@KNjmi1<RIMASX>yW)WQb<^;$2yG_U9Iy*XiR$XOUV=;Ys=8+)t
z;LO05=j)bzjh7b`oH$GKK$h;+J@Y>+y;(jlQ_{u7Wmep3)`*~;^El4uPAe62b#ake
zbd_n%%X>|sz3Vv6_s%kmcX3&=RP(^BeMW-wZu3;`b8&HzS_V?GZq|2WuL)OlX1;>z
z(%G62s^=xurSW*Xi;GLtJf<}-wY`+CvTnTU<l?e~6=cSuGc0dhA8&ARaZ$UP#dxhG
z{Os?YribdDF>)*0fGye@)v#1-&8fBhAMWsccmyt{E@egO9+-5>R_5c+=f{G$LAm@&
z7UQ(24O->(N1o5;)9G9c$|Gx+O=Z$y4Zpf~K0i~l;J2xadc7ZN1O+EfyXwU_EhL>`
zhxH?~dpvur+IDqxbZnUt#=YT6SLj@6WxM-K_nG?o7wS#+WY%Xtx9+hWD3gOUHLZRX
z>%OIBvB0KX|IHOSx`Jn2u=-Z~K>fhxq<i~1Iy~-f32I>F+O(?H-kjO|=!W~12l^Y{
z3rw2eW+?x|;KT1jX8sGmo(mQf%q%>0On1I|$$nQ`@k<9P4@5UcH@<GPZru8&`tD)9
z1j!9D6|9Q;r=9Z_6wJ(8TcSAo-P-W2yZCpARV4e|-h4o^b+&SeW1h;EX}khWYk4mC
zMqDmXywDi6(#2&-E5r#|UkeXOtg<xBzaEseFiPz6HdhxHA@8+pYnNX8UTmv)LP$_>
zqQsV<hNah5XYBKPp(P?HII$y2^8gcTWZ;tq?gn<LSV2L-iD}op7^gL@e!<poT_EjW
zXGe!eZ<OYNNfr0b`yM#WkuBQQ(c!@xrF$SqJIuz6X}OTUP!Q;BgyrCX|M-eIjA1%M
zGw-_Yjt-CD%%u$8kEXNkW3ZWiVb;{_0NZO!`*SYrb9Hf9bqy5r`A1h>|GiVJLU!Tp
z4{YD|e({ZwDd7KL_TXmA({fO<bka^On*Z+L)sP*V3!-`UNLq+nm_4gqqyFUaFUErU
zGq=SA1!oE^yC^zg*>(vF-U`72nG4<#=^KRp9$<5NxAs26_JtyXN=lcQL=rsb=p-sW
zmrJO7n4Z2+$Nfc=49hmgXimm3v8{HXECi}&hX{Ui|3Clq7jKx?7IU;QFfcH9y85}S
Ib4q9e0K5l;WB>pF

literal 0
HcmV?d00001

diff --git a/docs/installation.md b/docs/installation.md
deleted file mode 100644
index 70c4a6d..0000000
--- a/docs/installation.md
+++ /dev/null
@@ -1,110 +0,0 @@
-# nf-core/hic: Installation
-
-To start using the nf-core/hic pipeline, follow the steps below:
-
-1. [Install Nextflow](#1-install-nextflow)
-2. [Install the pipeline](#2-install-the-pipeline)
-    * [Automatic](#21-automatic)
-    * [Offline](#22-offline)
-    * [Development](#23-development)
-3. [Pipeline configuration](#3-pipeline-configuration)
-    * [Software deps: Docker and Singularity](#31-software-deps-docker-and-singularity)
-    * [Software deps: Bioconda](#32-software-deps-bioconda)
-    * [Configuration profiles](#33-configuration-profiles)
-4. [Reference genomes](#4-reference-genomes)
-
-## 1) Install NextFlow
-Nextflow runs on most POSIX systems (Linux, Mac OSX etc). It can be installed by running the following commands:
-
-```bash
-# Make sure that Java v8+ is installed:
-java -version
-
-# Install Nextflow
-curl -fsSL get.nextflow.io | bash
-
-# Add Nextflow binary to your PATH:
-mv nextflow ~/bin/
-# OR system-wide installation:
-# sudo mv nextflow /usr/local/bin
-```
-
-See [nextflow.io](https://www.nextflow.io/) for further instructions on how to install and configure Nextflow.
-
-## 2) Install the pipeline
-
-#### 2.1) Automatic
-This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if `nf-core/hic` is specified as the pipeline name.
-
-#### 2.2) Offline
-The above method requires an internet connection so that Nextflow can download the pipeline files. If you're running on a system that has no internet connection, you'll need to download and transfer the pipeline files manually:
-
-```bash
-wget https://github.com/nf-core/hic/archive/master.zip
-mkdir -p ~/my-pipelines/nf-core/
-unzip master.zip -d ~/my-pipelines/nf-core/
-cd ~/my_data/
-nextflow run ~/my-pipelines/nf-core/hic-master
-```
-
-To stop nextflow from looking for updates online, you can tell it to run in offline mode by specifying the following environment variable in your ~/.bashrc file:
-
-```bash
-export NXF_OFFLINE='TRUE'
-```
-
-#### 2.3) Development
-
-If you would like to make changes to the pipeline, it's best to make a fork on GitHub and then clone the files. Once cloned you can run the pipeline directly as above.
-
-
-## 3) Pipeline configuration
-By default, the pipeline loads a basic server configuration [`conf/base.config`](../conf/base.config)
-This uses a number of sensible defaults for process requirements and is suitable for running
-on a simple (if powerful!) local server.
-
-Be warned of two important points about this default configuration:
-
-1. The default profile uses the `local` executor
-    * All jobs are run in the login session. If you're using a simple server, this may be fine. If you're using a compute cluster, this is bad as all jobs will run on the head node.
-    * See the [nextflow docs](https://www.nextflow.io/docs/latest/executor.html) for information about running with other hardware backends. Most job scheduler systems are natively supported.
-2. Nextflow will expect all software to be installed and available on the `PATH`
-    * It's expected to use an additional config profile for docker, singularity or conda support. See below.
-
-#### 3.1) Software deps: Docker
-First, install docker on your system: [Docker Installation Instructions](https://docs.docker.com/engine/installation/)
-
-Then, running the pipeline with the option `-profile docker` tells Nextflow to enable Docker for this run. An image containing all of the software requirements will be automatically fetched and used from dockerhub (https://hub.docker.com/r/nfcore/hic).
-
-#### 3.1) Software deps: Singularity
-If you're not able to use Docker then [Singularity](http://singularity.lbl.gov/) is a great alternative.
-The process is very similar: running the pipeline with the option `-profile singularity` tells Nextflow to enable singularity for this run. An image containing all of the software requirements will be automatically fetched and used from singularity hub.
-
-If running offline with Singularity, you'll need to download and transfer the Singularity image first:
-
-```bash
-singularity pull --name nf-core-hic.simg shub://nf-core/hic
-```
-
-Once transferred, use `-with-singularity` and specify the path to the image file:
-
-```bash
-nextflow run /path/to/nf-core-hic -with-singularity nf-core-hic.simg
-```
-
-Remember to pull updated versions of the singularity image if you update the pipeline.
-
-
-#### 3.2) Software deps: conda
-If you're not able to use Docker _or_ Singularity, you can instead use conda to manage the software requirements.
-This is slower and less reproducible than the above, but is still better than having to install all requirements yourself!
-The pipeline ships with a conda environment file and nextflow has built-in support for this.
-To use it first ensure that you have conda installed (we recommend [miniconda](https://conda.io/miniconda.html)), then follow the same pattern as above and use the flag `-profile conda`
-
-#### 3.3) Configuration profiles
-
-See [`docs/configuration/adding_your_own.md`](configuration/adding_your_own.md)
-
-## 4) Reference genomes
-
-See [`docs/configuration/reference_genomes.md`](configuration/reference_genomes.md)
diff --git a/docs/output.md b/docs/output.md
index 9de7067..2ae1070 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -5,6 +5,7 @@ This document describes the output produced by the pipeline. Most of the plots a
 <!-- TODO nf-core: Write this documentation describing your workflow's output -->
 
 ## Pipeline overview
+
 The pipeline is built using [Nextflow](https://www.nextflow.io/)
 and processes data using the following steps:
 
@@ -12,6 +13,7 @@ and processes data using the following steps:
 * [MultiQC](#multiqc) - aggregate report, describing results of the whole pipeline
 
 ## FastQC
+
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your reads. It provides information about the quality score distribution across your reads, the per base sequence content (%T/A/G/C). You get information about adapter contamination and other overrepresented sequences.
 
 For further reading and documentation see the [FastQC help](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
@@ -25,8 +27,8 @@ For further reading and documentation see the [FastQC help](http://www.bioinform
 * `zips/sample_fastqc.zip`
   * zip file containing the FastQC report, tab-delimited data file and plot images
 
-
 ## MultiQC
+
 [MultiQC](http://multiqc.info) is a visualisation tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in within the report data directory.
 
 The pipeline has special steps which allow the software versions used to be reported in the MultiQC output for future traceability.
@@ -38,4 +40,4 @@ The pipeline has special steps which allow the software versions used to be repo
 * `Project_multiqc_data/`
   * Directory containing parsed statistics from the different tools used in the pipeline
 
-For more information about how to use MultiQC reports, see http://multiqc.info
+For more information about how to use MultiQC reports, see [http://multiqc.info](http://multiqc.info)
diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md
deleted file mode 100644
index 927d1b7..0000000
--- a/docs/troubleshooting.md
+++ /dev/null
@@ -1,30 +0,0 @@
-# nf-core/hic: Troubleshooting
-
-<!-- TODO nf-core: Change this documentation if these parameters/errors are not relevant for your workflow -->
-
-## Input files not found
-
-If only no file, only one input file , or only read one and not read two is picked up then something is wrong with your input file declaration
-
-1. The path must be enclosed in quotes (`'` or `"`)
-2. The path must have at least one `*` wildcard character. This is even if you are only running one paired end sample.
-3. When using the pipeline with paired end data, the path must use `{1,2}` or `{R1,R2}` notation to specify read pairs.
-4.  If you are running Single end data make sure to specify `--singleEnd`
-
-If the pipeline can't find your files then you will get the following error
-
-```
-ERROR ~ Cannot find any reads matching: *{1,2}.fastq.gz
-```
-
-Note that if your sample name is "messy" then you have to be very particular with your glob specification. A file name like `L1-1-D-2h_S1_L002_R1_001.fastq.gz` can be difficult enough for a human to read. Specifying `*{1,2}*.gz` wont work give you what you want Whilst `*{R1,R2}*.gz` will.
-
-
-## Data organization
-The pipeline can't take a list of multiple input files - it takes a glob expression. If your input files are scattered in different paths then we recommend that you generate a directory with symlinked files. If running in paired end mode please make sure that your files are sensibly named so that they can be properly paired. See the previous point.
-
-## Extra resources and getting help
-If you still have an issue with running the pipeline then feel free to contact us.
-Have a look at the [pipeline website](https://github.com/nf-core/hic) to find out how.
-
-If you have problems that are related to Nextflow and not our pipeline then check out the [Nextflow gitter channel](https://gitter.im/nextflow-io/nextflow) or the [google group](https://groups.google.com/forum/#!forum/nextflow).
diff --git a/docs/usage.md b/docs/usage.md
index 95d863f..00541b2 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -2,45 +2,45 @@
 
 ## Table of contents
 
-* [Introduction](#general-nextflow-info)
+* [Table of contents](#table-of-contents)
+* [Introduction](#introduction)
 * [Running the pipeline](#running-the-pipeline)
-* [Updating the pipeline](#updating-the-pipeline)
-* [Reproducibility](#reproducibility)
+  * [Updating the pipeline](#updating-the-pipeline)
+  * [Reproducibility](#reproducibility)
 * [Main arguments](#main-arguments)
-    * [`-profile`](#-profile-single-dash)
-        * [`awsbatch`](#awsbatch)
-        * [`conda`](#conda)
-        * [`docker`](#docker)
-        * [`singularity`](#singularity)
-        * [`test`](#test)
-    * [`--reads`](#--reads)
-    * [`--singleEnd`](#--singleend)
+  * [`-profile`](#-profile)
+  * [`--reads`](#--reads)
+  * [`--single_end`](#--single_end)
 * [Reference genomes](#reference-genomes)
-    * [`--genome`](#--genome)
-    * [`--fasta`](#--fasta)
-    * [`--igenomesIgnore`](#--igenomesignore)
+  * [`--genome` (using iGenomes)](#--genome-using-igenomes)
+  * [`--fasta`](#--fasta)
+  * [`--igenomes_ignore`](#--igenomes_ignore)
 * [Job resources](#job-resources)
-* [Automatic resubmission](#automatic-resubmission)
-* [Custom resource requests](#custom-resource-requests)
-* [AWS batch specific parameters](#aws-batch-specific-parameters)
-    * [`-awsbatch`](#-awsbatch)
-    * [`--awsqueue`](#--awsqueue)
-    * [`--awsregion`](#--awsregion)
+  * [Automatic resubmission](#automatic-resubmission)
+  * [Custom resource requests](#custom-resource-requests)
+* [AWS Batch specific parameters](#aws-batch-specific-parameters)
+  * [`--awsqueue`](#--awsqueue)
+  * [`--awsregion`](#--awsregion)
+  * [`--awscli`](#--awscli)
 * [Other command line parameters](#other-command-line-parameters)
-    * [`--outdir`](#--outdir)
-    * [`--email`](#--email)
-    * [`-name`](#-name-single-dash)
-    * [`-resume`](#-resume-single-dash)
-    * [`-c`](#-c-single-dash)
-    * [`--custom_config_version`](#--custom_config_version)
-    * [`--max_memory`](#--max_memory)
-    * [`--max_time`](#--max_time)
-    * [`--max_cpus`](#--max_cpus)
-    * [`--plaintext_email`](#--plaintext_email)
-    * [`--multiqc_config`](#--multiqc_config)
-
-
-## General Nextflow info
+  * [`--outdir`](#--outdir)
+  * [`--email`](#--email)
+  * [`--email_on_fail`](#--email_on_fail)
+  * [`--max_multiqc_email_size`](#--max_multiqc_email_size)
+  * [`-name`](#-name)
+  * [`-resume`](#-resume)
+  * [`-c`](#-c)
+  * [`--custom_config_version`](#--custom_config_version)
+  * [`--custom_config_base`](#--custom_config_base)
+  * [`--max_memory`](#--max_memory)
+  * [`--max_time`](#--max_time)
+  * [`--max_cpus`](#--max_cpus)
+  * [`--plaintext_email`](#--plaintext_email)
+  * [`--monochrome_logs`](#--monochrome_logs)
+  * [`--multiqc_config`](#--multiqc_config)
+
+## Introduction
+
 Nextflow handles job submissions on SLURM or other environments, and supervises running the jobs. Thus the Nextflow process must run until the pipeline is finished. We recommend that you put the process running in the background through `screen` / `tmux` or similar tool. Alternatively you can run nextflow within a cluster job submitted your job scheduler.
 
 It is recommended to limit the Nextflow Java virtual machines memory. We recommend adding the following line to your environment (typically in `~/.bashrc` or `~./bash_profile`):
@@ -48,9 +48,13 @@ It is recommended to limit the Nextflow Java virtual machines memory. We recomme
 ```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
+
 <!-- TODO nf-core: Document required command line parameters to run the pipeline-->
+
 ## Running the pipeline
+
 The typical command for running the pipeline is as follows:
+
 ```bash
 nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile docker
 ```
@@ -67,6 +71,7 @@ results         # Finished results (configurable, see below)
 ```
 
 ### Updating the pipeline
+
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
 ```bash
@@ -74,37 +79,48 @@ nextflow pull nf-core/hic
 ```
 
 ### Reproducibility
+
 It's a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
 First, go to the [nf-core/hic releases page](https://github.com/nf-core/hic/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
 
-
 ## Main arguments
 
 ### `-profile`
-Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. Note that multiple profiles can be loaded, for example: `-profile docker` - the order of arguments is important!
 
-If `-profile` is not specified at all the pipeline will be run locally and expects all software to be installed and available on the `PATH`.
+Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
+
+Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Conda) - see below.
+
+> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+
+Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
+They are loaded in sequence, so later profiles can overwrite earlier profiles.
+
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended.
 
-* `awsbatch`
-    * A generic configuration profile to be used with AWS Batch.
-* `conda`
-    * A generic configuration profile to be used with [conda](https://conda.io/docs/)
-    * Pulls most software from [Bioconda](https://bioconda.github.io/)
 * `docker`
-    * A generic configuration profile to be used with [Docker](http://docker.com/)
-    * Pulls software from dockerhub: [`nfcore/hic`](http://hub.docker.com/r/nfcore/hic/)
+  * A generic configuration profile to be used with [Docker](http://docker.com/)
+  * Pulls software from dockerhub: [`nfcore/hic`](http://hub.docker.com/r/nfcore/hic/)
 * `singularity`
-    * A generic configuration profile to be used with [Singularity](http://singularity.lbl.gov/)
-    * Pulls software from singularity-hub
+  * A generic configuration profile to be used with [Singularity](http://singularity.lbl.gov/)
+  * Pulls software from DockerHub: [`nfcore/hic`](http://hub.docker.com/r/nfcore/hic/)
+* `conda`
+  * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker or Singularity.
+  * A generic configuration profile to be used with [Conda](https://conda.io/docs/)
+  * Pulls most software from [Bioconda](https://bioconda.github.io/)
 * `test`
-    * A profile with a complete configuration for automated testing
-    * Includes links to test data so needs no other parameters
+  * A profile with a complete configuration for automated testing
+  * Includes links to test data so needs no other parameters
 
 <!-- TODO nf-core: Document required command line parameters -->
+
 ### `--reads`
+
 Use this to specify the location of your input FastQ files. For example:
 
 ```bash
@@ -119,21 +135,22 @@ Please note the following requirements:
 
 If left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`
 
-### `--singleEnd`
-By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--singleEnd` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
+### `--single_end`
+
+By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--single_end` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
 
 ```bash
---singleEnd --reads '*.fastq'
+--single_end --reads '*.fastq'
 ```
 
 It is not possible to run a mixture of single-end and paired-end files in one run.
 
-
 ## Reference genomes
 
 The pipeline config files come bundled with paths to the illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.
 
 ### `--genome` (using iGenomes)
+
 There are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.
 
 You can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:
@@ -154,6 +171,7 @@ Note that you can use the same configuration setup to save sets of reference fil
 The syntax for this reference configuration is as follows:
 
 <!-- TODO nf-core: Update reference genome example according to what is needed -->
+
 ```nextflow
 params {
   genomes {
@@ -166,33 +184,48 @@ params {
 ```
 
 <!-- TODO nf-core: Describe reference path flags -->
+
 ### `--fasta`
+
 If you prefer, you can specify the full path to your reference genome when you run the pipeline:
 
 ```bash
 --fasta '[path to Fasta reference]'
 ```
 
-### `--igenomesIgnore`
+### `--igenomes_ignore`
+
 Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.
 
 ## Job resources
+
 ### Automatic resubmission
+
 Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.
 
 ### Custom resource requests
+
 Wherever process-specific requirements are set in the pipeline, the default value can be changed by creating a custom config file. See the files hosted at [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
 
 If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition below). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
 
-If you have any questions or issues please send us a message on [`Slack`](https://nf-core-invite.herokuapp.com/).
+If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).
 
 ## AWS Batch specific parameters
-Running the pipeline on AWS Batch requires a couple of specific parameters to be set according to your AWS Batch configuration. Please use the `-awsbatch` profile and then specify all of the following parameters.
+
+Running the pipeline on AWS Batch requires a couple of specific parameters to be set according to your AWS Batch configuration. Please use [`-profile awsbatch`](https://github.com/nf-core/configs/blob/master/conf/awsbatch.config) and then specify all of the following parameters.
+
 ### `--awsqueue`
+
 The JobQueue that you intend to use on AWS Batch.
+
 ### `--awsregion`
-The AWS region to run your job in. Default is set to `eu-west-1` but can be adjusted to your needs.
+
+The AWS region in which to run your job. Default is set to `eu-west-1` but can be adjusted to your needs.
+
+### `--awscli`
+
+The [AWS CLI](https://www.nextflow.io/docs/latest/awscloud.html#aws-cli-installation) path in your custom AMI. Default: `/home/ec2-user/miniconda/bin/aws`.
 
 Please make sure to also set the `-w/--work-dir` and `--outdir` parameters to a S3 storage bucket of your choice - you'll get an error message notifying you if you didn't.
 
@@ -201,12 +234,23 @@ Please make sure to also set the `-w/--work-dir` and `--outdir` parameters to a
 <!-- TODO nf-core: Describe any other command line flags here -->
 
 ### `--outdir`
+
 The output directory where the results will be saved.
 
 ### `--email`
-Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to speicfy this on the command line for every run.
+
+Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.
+
+### `--email_on_fail`
+
+This works exactly as with `--email`, except emails are only sent if the workflow is not successful.
+
+### `--max_multiqc_email_size`
+
+Threshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB).
 
 ### `-name`
+
 Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
 
 This is used in the MultiQC report (if not default) and in the summary HTML / e-mail (always).
@@ -214,6 +258,7 @@ This is used in the MultiQC report (if not default) and in the summary HTML / e-
 **NB:** Single hyphen (core Nextflow option)
 
 ### `-resume`
+
 Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously.
 
 You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names.
@@ -221,6 +266,7 @@ You can also supply a run name to resume a specific run: `-resume [run-name]`. U
 **NB:** Single hyphen (core Nextflow option)
 
 ### `-c`
+
 Specify the path to a specific config file (this is a core NextFlow command).
 
 **NB:** Single hyphen (core Nextflow option)
@@ -228,27 +274,58 @@ Specify the path to a specific config file (this is a core NextFlow command).
 Note - you can use this to override pipeline defaults.
 
 ### `--custom_config_version`
-Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default is set to `master`.
+
+Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default: `master`.
 
 ```bash
 ## Download and use config file with following git commid id
 --custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
 ```
 
+### `--custom_config_base`
+
+If you're running offline, nextflow will not be able to fetch the institutional config files
+from the internet. If you don't need them, then this is not a problem. If you do need them,
+you should download the files from the repo and tell nextflow where to find them with the
+`custom_config_base` option. For example:
+
+```bash
+## Download and unzip the config files
+cd /path/to/my/configs
+wget https://github.com/nf-core/configs/archive/master.zip
+unzip master.zip
+
+## Run the pipeline
+cd /path/to/my/data
+nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
+```
+
+> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
+> files + singularity containers + institutional configs in one go for you, to make this process easier.
+
 ### `--max_memory`
+
 Use to set a top-limit for the default memory requirement for each process.
 Should be a string in the format integer-unit. eg. `--max_memory '8.GB'`
 
 ### `--max_time`
+
 Use to set a top-limit for the default time requirement for each process.
 Should be a string in the format integer-unit. eg. `--max_time '2.h'`
 
 ### `--max_cpus`
+
 Use to set a top-limit for the default CPU requirement for each process.
 Should be a string in the format integer-unit. eg. `--max_cpus 1`
 
 ### `--plaintext_email`
+
 Set to receive plain-text e-mails instead of HTML formatted.
 
+### `--monochrome_logs`
+
+Set to disable colourful command line output and live life in monochrome.
+
 ### `--multiqc_config`
+
 Specify a path to a custom MultiQC configuration file.
diff --git a/environment.yml b/environment.yml
index 42c74b4..d082016 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,9 +1,15 @@
-name: nf-core-hic-1.0dev
+# You can use this file to create a conda environment for this pipeline:
+#   conda env create -f environment.yml
+name: nf-core-hic-1.1.1dev
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
+  - conda-forge::python=3.7.3
+  - conda-forge::markdown=3.1.1
+  - conda-forge::pymdown-extensions=6.0
+  - conda-forge::pygments=2.5.2
   # TODO nf-core: Add required software dependencies here
-  - fastqc=0.11.8
-  - multiqc=1.6
+  - bioconda::fastqc=0.11.8
+  - bioconda::multiqc=1.7
diff --git a/main.nf b/main.nf
index 97a07de..7b273a2 100644
--- a/main.nf
+++ b/main.nf
@@ -9,19 +9,10 @@
 ----------------------------------------------------------------------------------------
 */
 
-
 def helpMessage() {
     // TODO nf-core: Add to this help message with new command line parameters
+    log.info nfcoreHeader()
     log.info"""
-    =======================================================
-                                              ,--./,-.
-              ___     __   __   __   ___     /,-._.--~\'
-        |\\ | |__  __ /  ` /  \\ |__) |__         }  {
-        | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
-                                              `._,._,\'
-
-     nf-core/hic v${workflow.manifest.version}
-    =======================================================
 
     Usage:
 
@@ -30,143 +21,143 @@ def helpMessage() {
     nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile docker
 
     Mandatory arguments:
-      --reads                       Path to input data (must be surrounded with quotes)
-      --genome                      Name of iGenomes reference
-      -profile                      Configuration profile to use. Can use multiple (comma separated)
-                                    Available: conda, docker, singularity, awsbatch, test and more.
+      --reads [file]                Path to input data (must be surrounded with quotes)
+      -profile [str]                Configuration profile to use. Can use multiple (comma separated)
+                                    Available: conda, docker, singularity, test, awsbatch, <institute> and more
 
     Options:
-      --singleEnd                   Specifies that the input is single end reads
+      --genome [str]                  Name of iGenomes reference
+      --single_end [bool]             Specifies that the input is single-end reads
 
-    References                      If not specified in the configuration file or you wish to overwrite any of the references.
-      --fasta                       Path to Fasta reference
+    References                        If not specified in the configuration file or you wish to overwrite any of the references
+      --fasta [file]                  Path to fasta reference
 
     Other options:
-      --outdir                      The output directory where the results will be saved
-      --email                       Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
-      -name                         Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
+      --outdir [file]                 The output directory where the results will be saved
+      --email [email]                 Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
+      --email_on_fail [email]         Same as --email, except only send mail if the workflow is not successful
+      --max_multiqc_email_size [str]  Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
+      -name [str]                     Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic
 
     AWSBatch options:
-      --awsqueue                    The AWSBatch JobQueue that needs to be set when running on AWSBatch
-      --awsregion                   The AWS Region for your AWS Batch job to run on
+      --awsqueue [str]                The AWSBatch JobQueue that needs to be set when running on AWSBatch
+      --awsregion [str]               The AWS Region for your AWS Batch job to run on
+      --awscli [str]                  Path to the AWS CLI tool
     """.stripIndent()
 }
 
+// Show help message
+if (params.help) {
+    helpMessage()
+    exit 0
+}
+
 /*
  * SET UP CONFIGURATION VARIABLES
  */
 
-// Show help emssage
-if (params.help){
-    helpMessage()
-    exit 0
+// Check if genome exists in the config file
+if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+    exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
 }
 
 // TODO nf-core: Add any reference files that are needed
 // Configurable reference genomes
-fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
-if ( params.fasta ){
-    fasta = file(params.fasta)
-    if( !fasta.exists() ) exit 1, "Fasta file not found: ${params.fasta}"
-}
 //
 // NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
-// If you want to use the above in a process, define the following:
+// If you want to use the channel below in a process, define the following:
 //   input:
-//   file fasta from fasta
+//   file fasta from ch_fasta
 //
-
+params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
+if (params.fasta) { ch_fasta = file(params.fasta, checkIfExists: true) }
 
 // Has the run name been specified by the user?
 //  this has the bonus effect of catching both -name and --name
 custom_runName = params.name
-if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){
-  custom_runName = workflow.runName
+if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
+    custom_runName = workflow.runName
 }
 
-
-if( workflow.profile == 'awsbatch') {
-  // AWSBatch sanity checking
-  if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
-  if (!workflow.workDir.startsWith('s3') || !params.outdir.startsWith('s3')) exit 1, "Specify S3 URLs for workDir and outdir parameters on AWSBatch!"
-  // Check workDir/outdir paths to be S3 buckets if running on AWSBatch
-  // related: https://github.com/nextflow-io/nextflow/issues/813
-  if (!workflow.workDir.startsWith('s3:') || !params.outdir.startsWith('s3:')) exit 1, "Workdir or Outdir not on S3 - specify S3 Buckets for each to run on AWSBatch!"
+if (workflow.profile.contains('awsbatch')) {
+    // AWSBatch sanity checking
+    if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
+    // Check outdir paths to be S3 buckets if running on AWSBatch
+    // related: https://github.com/nextflow-io/nextflow/issues/813
+    if (!params.outdir.startsWith('s3:')) exit 1, "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
+    // Prevent trace files to be stored on S3 since S3 does not support rolling files.
+    if (params.tracedir.startsWith('s3:')) exit 1, "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."
 }
 
 // Stage config files
-ch_multiqc_config = Channel.fromPath(params.multiqc_config)
-ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
+ch_multiqc_config = file("$baseDir/assets/multiqc_config.yaml", checkIfExists: true)
+ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
+ch_output_docs = file("$baseDir/docs/output.md", checkIfExists: true)
 
 /*
  * Create a channel for input read files
  */
- if(params.readPaths){
-     if(params.singleEnd){
-         Channel
-             .from(params.readPaths)
-             .map { row -> [ row[0], [file(row[1][0])]] }
-             .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
-             .into { read_files_fastqc; read_files_trimming }
-     } else {
-         Channel
-             .from(params.readPaths)
-             .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
-             .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
-             .into { read_files_fastqc; read_files_trimming }
-     }
- } else {
-     Channel
-         .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
-         .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --singleEnd on the command line." }
-         .into { read_files_fastqc; read_files_trimming }
- }
-
+if (params.readPaths) {
+    if (params.single_end) {
+        Channel
+            .from(params.readPaths)
+            .map { row -> [ row[0], [ file(row[1][0], checkIfExists: true) ] ] }
+            .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
+            .into { ch_read_files_fastqc; ch_read_files_trimming }
+    } else {
+        Channel
+            .from(params.readPaths)
+            .map { row -> [ row[0], [ file(row[1][0], checkIfExists: true), file(row[1][1], checkIfExists: true) ] ] }
+            .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
+            .into { ch_read_files_fastqc; ch_read_files_trimming }
+    }
+} else {
+    Channel
+        .fromFilePairs(params.reads, size: params.single_end ? 1 : 2)
+        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --single_end on the command line." }
+        .into { ch_read_files_fastqc; ch_read_files_trimming }
+}
 
 // Header log info
-log.info """=======================================================
-                                          ,--./,-.
-          ___     __   __   __   ___     /,-._.--~\'
-    |\\ | |__  __ /  ` /  \\ |__) |__         }  {
-    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
-                                          `._,._,\'
-
-nf-core/hic v${workflow.manifest.version}"
-======================================================="""
+log.info nfcoreHeader()
 def summary = [:]
-summary['Pipeline Name']  = 'nf-core/hic'
-summary['Pipeline Version'] = workflow.manifest.version
-summary['Run Name']     = custom_runName ?: workflow.runName
+if (workflow.revision) summary['Pipeline Release'] = workflow.revision
+summary['Run Name']         = custom_runName ?: workflow.runName
 // TODO nf-core: Report custom parameters here
-summary['Reads']        = params.reads
-summary['Fasta Ref']    = params.fasta
-summary['Data Type']    = params.singleEnd ? 'Single-End' : 'Paired-End'
-summary['Max Memory']   = params.max_memory
-summary['Max CPUs']     = params.max_cpus
-summary['Max Time']     = params.max_time
-summary['Output dir']   = params.outdir
-summary['Working dir']  = workflow.workDir
-summary['Container Engine'] = workflow.containerEngine
-if(workflow.containerEngine) summary['Container'] = workflow.container
-summary['Current home']   = "$HOME"
-summary['Current user']   = "$USER"
-summary['Current path']   = "$PWD"
-summary['Working dir']    = workflow.workDir
-summary['Output dir']     = params.outdir
-summary['Script dir']     = workflow.projectDir
+summary['Reads']            = params.reads
+summary['Fasta Ref']        = params.fasta
+summary['Data Type']        = params.single_end ? 'Single-End' : 'Paired-End'
+summary['Max Resources']    = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
+if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
+summary['Output dir']       = params.outdir
+summary['Launch dir']       = workflow.launchDir
+summary['Working dir']      = workflow.workDir
+summary['Script dir']       = workflow.projectDir
+summary['User']             = workflow.userName
+if (workflow.profile.contains('awsbatch')) {
+    summary['AWS Region']   = params.awsregion
+    summary['AWS Queue']    = params.awsqueue
+    summary['AWS CLI']      = params.awscli
+}
 summary['Config Profile'] = workflow.profile
-if(workflow.profile == 'awsbatch'){
-   summary['AWS Region'] = params.awsregion
-   summary['AWS Queue'] = params.awsqueue
+if (params.config_profile_description) summary['Config Description'] = params.config_profile_description
+if (params.config_profile_contact)     summary['Config Contact']     = params.config_profile_contact
+if (params.config_profile_url)         summary['Config URL']         = params.config_profile_url
+if (params.email || params.email_on_fail) {
+    summary['E-mail Address']    = params.email
+    summary['E-mail on failure'] = params.email_on_fail
+    summary['MultiQC maxsize']   = params.max_multiqc_email_size
 }
-if(params.email) summary['E-mail Address'] = params.email
-log.info summary.collect { k,v -> "${k.padRight(15)}: $v" }.join("\n")
-log.info "========================================="
+log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
+log.info "-\033[2m--------------------------------------------------\033[0m-"
 
+// Check the hostnames against configured profiles
+checkHostname()
 
-def create_workflow_summary(summary) {
-    def yaml_file = workDir.resolve('workflow_summary_mqc.yaml')
-    yaml_file.text  = """
+Channel.from(summary.collect{ [it.key, it.value] })
+    .map { k,v -> "<dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }
+    .reduce { a, b -> return [a, b].join("\n            ") }
+    .map { x -> """
     id: 'nf-core-hic-summary'
     description: " - this information is collected when the pipeline is started."
     section_name: 'nf-core/hic Workflow Summary'
@@ -174,21 +165,24 @@ def create_workflow_summary(summary) {
     plot_type: 'html'
     data: |
         <dl class=\"dl-horizontal\">
-${summary.collect { k,v -> "            <dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }.join("\n")}
+            $x
         </dl>
-    """.stripIndent()
-
-   return yaml_file
-}
-
+    """.stripIndent() }
+    .set { ch_workflow_summary }
 
 /*
  * Parse software version numbers
  */
 process get_software_versions {
+    publishDir "${params.outdir}/pipeline_info", mode: 'copy',
+        saveAs: { filename ->
+                      if (filename.indexOf(".csv") > 0) filename
+                      else null
+                }
 
     output:
-    file 'software_versions_mqc.yaml' into software_versions_yaml
+    file 'software_versions_mqc.yaml' into ch_software_versions_yaml
+    file "software_versions.csv"
 
     script:
     // TODO nf-core: Get all tools to print their version number here
@@ -197,34 +191,33 @@ process get_software_versions {
     echo $workflow.nextflow.version > v_nextflow.txt
     fastqc --version > v_fastqc.txt
     multiqc --version > v_multiqc.txt
-    scrape_software_versions.py > software_versions_mqc.yaml
+    scrape_software_versions.py &> software_versions_mqc.yaml
     """
 }
 
-
-
 /*
  * STEP 1 - FastQC
  */
 process fastqc {
     tag "$name"
+    label 'process_medium'
     publishDir "${params.outdir}/fastqc", mode: 'copy',
-        saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
+        saveAs: { filename ->
+                      filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"
+                }
 
     input:
-    set val(name), file(reads) from read_files_fastqc
+    set val(name), file(reads) from ch_read_files_fastqc
 
     output:
-    file "*_fastqc.{zip,html}" into fastqc_results
+    file "*_fastqc.{zip,html}" into ch_fastqc_results
 
     script:
     """
-    fastqc -q $reads
+    fastqc --quiet --threads $task.cpus $reads
     """
 }
 
-
-
 /*
  * STEP 2 - MultiQC
  */
@@ -232,32 +225,33 @@ process multiqc {
     publishDir "${params.outdir}/MultiQC", mode: 'copy'
 
     input:
-    file multiqc_config from ch_multiqc_config
+    file (multiqc_config) from ch_multiqc_config
+    file (mqc_custom_config) from ch_multiqc_custom_config.collect().ifEmpty([])
     // TODO nf-core: Add in log files from your new processes for MultiQC to find!
-    file ('fastqc/*') from fastqc_results.collect().ifEmpty([])
-    file ('software_versions/*') from software_versions_yaml
-    file workflow_summary from create_workflow_summary(summary)
+    file ('fastqc/*') from ch_fastqc_results.collect().ifEmpty([])
+    file ('software_versions/*') from ch_software_versions_yaml.collect()
+    file workflow_summary from ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml")
 
     output:
-    file "*multiqc_report.html" into multiqc_report
+    file "*multiqc_report.html" into ch_multiqc_report
     file "*_data"
+    file "multiqc_plots"
 
     script:
     rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
     rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
+    custom_config_file = params.multiqc_config ? "--config $mqc_custom_config" : ''
     // TODO nf-core: Specify which MultiQC modules to use with -m for a faster run time
     """
-    multiqc -f $rtitle $rfilename --config $multiqc_config .
+    multiqc -f $rtitle $rfilename $custom_config_file .
     """
 }
 
-
-
 /*
  * STEP 3 - Output Description HTML
  */
 process output_documentation {
-    publishDir "${params.outdir}/Documentation", mode: 'copy'
+    publishDir "${params.outdir}/pipeline_info", mode: 'copy'
 
     input:
     file output_docs from ch_output_docs
@@ -267,12 +261,10 @@ process output_documentation {
 
     script:
     """
-    markdown_to_html.r $output_docs results_description.html
+    markdown_to_html.py $output_docs -o results_description.html
     """
 }
 
-
-
 /*
  * Completion e-mail notification
  */
@@ -280,8 +272,8 @@ workflow.onComplete {
 
     // Set up the e-mail variables
     def subject = "[nf-core/hic] Successful: $workflow.runName"
-    if(!workflow.success){
-      subject = "[nf-core/hic] FAILED: $workflow.runName"
+    if (!workflow.success) {
+        subject = "[nf-core/hic] FAILED: $workflow.runName"
     }
     def email_fields = [:]
     email_fields['version'] = workflow.manifest.version
@@ -299,13 +291,34 @@ workflow.onComplete {
     email_fields['summary']['Date Completed'] = workflow.complete
     email_fields['summary']['Pipeline script file path'] = workflow.scriptFile
     email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId
-    if(workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
-    if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
-    if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
+    if (workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
+    if (workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
+    if (workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
     email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
     email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
     email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
+    // TODO nf-core: If not using MultiQC, strip out this code (including params.max_multiqc_email_size)
+    // On success try attach the multiqc report
+    def mqc_report = null
+    try {
+        if (workflow.success) {
+            mqc_report = ch_multiqc_report.getVal()
+            if (mqc_report.getClass() == ArrayList) {
+                log.warn "[nf-core/hic] Found multiple reports from process 'multiqc', will use only one"
+                mqc_report = mqc_report[0]
+            }
+        }
+    } catch (all) {
+        log.warn "[nf-core/hic] Could not attach MultiQC report to summary email"
+    }
+
+    // Check if we are only sending emails on failure
+    email_address = params.email
+    if (!params.email && params.email_on_fail && !workflow.success) {
+        email_address = params.email_on_fail
+    }
+
     // Render the TXT template
     def engine = new groovy.text.GStringTemplateEngine()
     def tf = new File("$baseDir/assets/email_template.txt")
@@ -318,35 +331,96 @@ workflow.onComplete {
     def email_html = html_template.toString()
 
     // Render the sendmail template
-    def smail_fields = [ email: params.email, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir" ]
+    def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
     def sf = new File("$baseDir/assets/sendmail_template.txt")
     def sendmail_template = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html = sendmail_template.toString()
 
     // Send the HTML e-mail
-    if (params.email) {
+    if (email_address) {
         try {
-          if( params.plaintext_email ){ throw GroovyException('Send plaintext e-mail, not HTML') }
-          // Try to send HTML e-mail using sendmail
-          [ 'sendmail', '-t' ].execute() << sendmail_html
-          log.info "[nf-core/hic] Sent summary e-mail to $params.email (sendmail)"
+            if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            // Try to send HTML e-mail using sendmail
+            [ 'sendmail', '-t' ].execute() << sendmail_html
+            log.info "[nf-core/hic] Sent summary e-mail to $email_address (sendmail)"
         } catch (all) {
-          // Catch failures and try with plaintext
-          [ 'mail', '-s', subject, params.email ].execute() << email_txt
-          log.info "[nf-core/hic] Sent summary e-mail to $params.email (mail)"
+            // Catch failures and try with plaintext
+            [ 'mail', '-s', subject, email_address ].execute() << email_txt
+            log.info "[nf-core/hic] Sent summary e-mail to $email_address (mail)"
         }
     }
 
     // Write summary e-mail HTML to a file
-    def output_d = new File( "${params.outdir}/Documentation/" )
-    if( !output_d.exists() ) {
-      output_d.mkdirs()
+    def output_d = new File("${params.outdir}/pipeline_info/")
+    if (!output_d.exists()) {
+        output_d.mkdirs()
     }
-    def output_hf = new File( output_d, "pipeline_report.html" )
+    def output_hf = new File(output_d, "pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    def output_tf = new File( output_d, "pipeline_report.txt" )
+    def output_tf = new File(output_d, "pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
 
-    log.info "[nf-core/hic] Pipeline Complete"
+    c_green = params.monochrome_logs ? '' : "\033[0;32m";
+    c_purple = params.monochrome_logs ? '' : "\033[0;35m";
+    c_red = params.monochrome_logs ? '' : "\033[0;31m";
+    c_reset = params.monochrome_logs ? '' : "\033[0m";
+
+    if (workflow.stats.ignoredCount > 0 && workflow.success) {
+        log.info "-${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}-"
+        log.info "-${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCount} ${c_reset}-"
+        log.info "-${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}-"
+    }
+
+    if (workflow.success) {
+        log.info "-${c_purple}[nf-core/hic]${c_green} Pipeline completed successfully${c_reset}-"
+    } else {
+        checkHostname()
+        log.info "-${c_purple}[nf-core/hic]${c_red} Pipeline completed with errors${c_reset}-"
+    }
+
+}
+
 
+def nfcoreHeader() {
+    // Log colors ANSI codes
+    c_black = params.monochrome_logs ? '' : "\033[0;30m";
+    c_blue = params.monochrome_logs ? '' : "\033[0;34m";
+    c_cyan = params.monochrome_logs ? '' : "\033[0;36m";
+    c_dim = params.monochrome_logs ? '' : "\033[2m";
+    c_green = params.monochrome_logs ? '' : "\033[0;32m";
+    c_purple = params.monochrome_logs ? '' : "\033[0;35m";
+    c_reset = params.monochrome_logs ? '' : "\033[0m";
+    c_white = params.monochrome_logs ? '' : "\033[0;37m";
+    c_yellow = params.monochrome_logs ? '' : "\033[0;33m";
+
+    return """    -${c_dim}--------------------------------------------------${c_reset}-
+                                            ${c_green},--.${c_black}/${c_green},-.${c_reset}
+    ${c_blue}        ___     __   __   __   ___     ${c_green}/,-._.--~\'${c_reset}
+    ${c_blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${c_yellow}}  {${c_reset}
+    ${c_blue}  | \\| |       \\__, \\__/ |  \\ |___     ${c_green}\\`-._,-`-,${c_reset}
+                                            ${c_green}`._,._,\'${c_reset}
+    ${c_purple}  nf-core/hic v${workflow.manifest.version}${c_reset}
+    -${c_dim}--------------------------------------------------${c_reset}-
+    """.stripIndent()
+}
+
+def checkHostname() {
+    def c_reset = params.monochrome_logs ? '' : "\033[0m"
+    def c_white = params.monochrome_logs ? '' : "\033[0;37m"
+    def c_red = params.monochrome_logs ? '' : "\033[1;91m"
+    def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m"
+    if (params.hostnames) {
+        def hostname = "hostname".execute().text.trim()
+        params.hostnames.each { prof, hnames ->
+            hnames.each { hname ->
+                if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
+                    log.error "====================================================\n" +
+                            "  ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" +
+                            "  but your machine hostname is ${c_white}'$hostname'${c_reset}\n" +
+                            "  ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" +
+                            "============================================================"
+                }
+            }
+        }
+    }
 }
diff --git a/nextflow.config b/nextflow.config
index 5f363c6..7338b5a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -3,83 +3,104 @@
  *  nf-core/hic Nextflow config file
  * -------------------------------------------------
  * Default config options for all environments.
- * Cluster-specific config options should be saved
- * in the conf folder and imported under a profile
- * name here.
  */
 
 // Global default params, used in configs
 params {
 
-  // Container slug. Stable releases should specify release tag!
-  //   Developmental code should specify :latest
-  container = 'nfcore/hic:latest'
-
   // Workflow flags
   // TODO nf-core: Specify your pipeline's command line flags
+  genome = false
   reads = "data/*{1,2}.fastq.gz"
-  singleEnd = false
+  single_end = false
   outdir = './results'
 
   // Boilerplate options
   name = false
-  multiqc_config = "$baseDir/conf/multiqc_config.yaml"
+  multiqc_config = false
   email = false
+  email_on_fail = false
+  max_multiqc_email_size = 25.MB
   plaintext_email = false
+  monochrome_logs = false
   help = false
-  igenomes_base = "./iGenomes"
+  igenomes_base = 's3://ngi-igenomes/igenomes/'
   tracedir = "${params.outdir}/pipeline_info"
-  clusterOptions = false
-  awsqueue = false
-  awsregion = 'eu-west-1'
-  igenomesIgnore = false
+  igenomes_ignore = false
   custom_config_version = 'master'
+  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+  hostnames = false
+  config_profile_description = false
+  config_profile_contact = false
+  config_profile_url = false
+
+  // Defaults only, expecting to be overwritten
+  max_memory = 128.GB
+  max_cpus = 16
+  max_time = 240.h
+
 }
 
+// Container slug. Stable releases should specify release tag!
+// Developmental code should specify :dev
+process.container = 'nfcore/hic:dev'
+
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
 // Load nf-core custom profiles from different Institutions
-includeConfig "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/nfcore_custom.config"
+try {
+  includeConfig "${params.custom_config_base}/nfcore_custom.config"
+} catch (Exception e) {
+  System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
+}
 
 profiles {
-  awsbatch { includeConfig 'conf/awsbatch.config' }
   conda { process.conda = "$baseDir/environment.yml" }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   docker {
     docker.enabled = true
-    process.container = params.container
+    // Avoid this error:
+    //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
+    // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
+    // once this is established and works well, nextflow might implement this behavior as new default.
+    docker.runOptions = '-u \$(id -u):\$(id -g)'
   }
   singularity {
     singularity.enabled = true
-    process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"}
+    singularity.autoMounts = true
   }
   test { includeConfig 'conf/test.config' }
 }
 
 // Load igenomes.config if required
-if(!params.igenomesIgnore){
+if (!params.igenomes_ignore) {
   includeConfig 'conf/igenomes.config'
 }
 
+// Export this variable to prevent local Python libraries from conflicting with those in the container
+env {
+  PYTHONNOUSERSITE = 1
+}
+
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 timeline {
   enabled = true
-  file = "${params.tracedir}/nf-core/hic_timeline.html"
+  file = "${params.tracedir}/execution_timeline.html"
 }
 report {
   enabled = true
-  file = "${params.tracedir}/nf-core/hic_report.html"
+  file = "${params.tracedir}/execution_report.html"
 }
 trace {
   enabled = true
-  file = "${params.tracedir}/nf-core/hic_trace.txt"
+  file = "${params.tracedir}/execution_trace.txt"
 }
 dag {
   enabled = true
-  file = "${params.tracedir}/nf-core/hic_dag.svg"
+  file = "${params.tracedir}/pipeline_dag.svg"
 }
 
 manifest {
@@ -88,16 +109,16 @@ manifest {
   homePage = 'https://github.com/nf-core/hic'
   description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
   mainScript = 'main.nf'
-  nextflowVersion = '>=0.32.0'
-  version = '1.0dev'
+  nextflowVersion = '>=19.10.0'
+  version = '1.1.1dev'
 }
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {
-  if(type == 'memory'){
+  if (type == 'memory') {
     try {
-      if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+      if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
         return params.max_memory as nextflow.util.MemoryUnit
       else
         return obj
@@ -105,9 +126,9 @@ def check_max(obj, type) {
       println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
       return obj
     }
-  } else if(type == 'time'){
+  } else if (type == 'time') {
     try {
-      if(obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+      if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
         return params.max_time as nextflow.util.Duration
       else
         return obj
@@ -115,7 +136,7 @@ def check_max(obj, type) {
       println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
       return obj
     }
-  } else if(type == 'cpus'){
+  } else if (type == 'cpus') {
     try {
       return Math.min( obj, params.max_cpus as int )
     } catch (all) {
-- 
GitLab