diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000000000000000000000000000000000000..afb20bb1ec9082b031f37fdd2c339df8c33b030e
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,24 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{yml,yaml}]
+indent_size = 2
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 284970f00a1e6d4fa739c1faa0805642fdc0668f..c8351e2bb0a3c584c07cf391bccb2c6be68c60ce 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -74,7 +74,7 @@ If you wish to contribute a new step, please use the following coding standards:
 7. Add sanity checks for all relevant parameters.
 8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
 9. Do local tests that the new code works properly and as expected.
-10. Add a new test command in `.github/workflow/ci.yaml`.
+10. Add a new test command in `.github/workflow/ci.yml`.
 11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
 12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
 13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index eeaa8479de91fb0b11752b812570bdb062fd1b40..bc2507dad1513181e12d0d3f6aacf7efc804afde 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -18,7 +18,7 @@ Please delete this text and anything that's not relevant from the template below
 I have checked the following places for your error:
 
 - [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-- [ ] [nf-core/hic pipeline documentation](https://nf-co.re/nf-core/hic/usage)
+- [ ] [nf-core/hic pipeline documentation](https://nf-co.re/hic/usage)
 
 ## Description of the bug
 
@@ -51,13 +51,12 @@ Have you provided the following extra information/files:
 
 ## Nextflow Installation
 
-- Version: <!-- [e.g. 19.10.0] -->
+- Version: <!-- [e.g. 21.04.0] -->
 
 ## Container engine
 
 - Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
-- Image tag: <!-- [e.g. nfcore/hic:1.0.0] -->
 
 ## Additional context
 
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index f94b9a453d3e42987ffbdd9a2d2be99e9e2b70ac..693558cb6d3d1acc19f8625cd5407d3fae60db38 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -16,8 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-    - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
-    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](<https://github.com/>nf-core/hic/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
     - [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint .`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 685ae01217ed0ffc1101589d1faad35b1edfbcf7..caa6a1c08a82dfe09fc2e465e4d994ce112c9a5b 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,46 +1,34 @@
 name: nf-core AWS full size tests
 # This workflow is triggered on published releases.
-# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  workflow_run:
-    workflows: ["nf-core Docker push (release)"]
-    types: [completed]
+  release:
+    types: [published]
   workflow_dispatch:
-
-
-env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
-
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS full tests
     if: github.repository == 'nf-core/hic'
     runs-on: ubuntu-latest
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
-        # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
-        run: |
-          aws batch submit-job \
-            --region eu-west-1 \
-            --job-name nf-core-hic \
-            --job-queue $AWS_JOB_QUEUE \
-            --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+        
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/hic/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hic/results-${{ github.sha }}"
+            }
+          profiles: '[ "test_full", "aws_tower" ]'
+
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index d8ab46bc220758ab7c72f0a261e88ce03670bf46..654e7b637fa1f1ac0a521b2425c9ef3d7c4ea019 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -1,42 +1,28 @@
 name: nf-core AWS test
-# This workflow is triggered on push to the master branch.
-# It can be additionally triggered manually with GitHub actions workflow dispatch.
-# It runs the -profile 'test' on AWS batch.
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
 
 on:
   workflow_dispatch:
-
-
-env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
-
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS tests
     if: github.repository == 'nf-core/hic'
     runs-on: ubuntu-latest
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
+        
         with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
-        run: |
-          aws batch submit-job \
-          --region eu-west-1 \
-          --job-name nf-core-hic \
-          --job-queue $AWS_JOB_QUEUE \
-          --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/hic/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hic/results-${{ github.sha }}"
+            }
+          profiles: '[ "test", "aws_tower" ]'
+
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c126d3e34c3d385c0f7b6c4b7950da0f4007fe60..3c0b4e6f58188d5a5e4fcff1caba3d5371baa773 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,28 +23,11 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.04.0', '']
+        nxf_ver: ['21.04.0', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
-      - name: Check if Dockerfile or Conda environment changed
-        uses: technote-space/get-diff-action@v4
-        with:
-          FILES: |
-            Dockerfile
-            environment.yml
-
-      - name: Build new docker image
-        if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/hic:dev
-
-      - name: Pull docker image
-        if: ${{ !env.MATCHED_FILES }}
-        run: |
-          docker pull nfcore/hic:dev
-          docker tag nfcore/hic:dev nfcore/hic:dev
-
       - name: Install Nextflow
         env:
           CAPSULE_LOG: none
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index fcde400cedbc1566f84e8a811e0b45a1c113df60..13b4fc818b3a5a1f77db9b994b275a4585074243 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -18,7 +18,7 @@ jobs:
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
-        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+        run: markdownlint .
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -35,8 +35,8 @@ jobs:
                 * On Mac: `brew install markdownlint-cli`
                 * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
             * Fix the markdown errors
-                * Automatically: `markdownlint . --config .github/markdownlint.yml --fix`
-                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
+                * Automatically: `markdownlint . --fix`
+                * Manually resolve anything left from `markdownlint .`
 
             Once you push these changes the test should pass, and you can hide this comment :+1:
 
@@ -46,6 +46,20 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
+  EditorConfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-node@v1
+        with:
+          node-version: "10"
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
 
   YAML:
     runs-on: ubuntu-latest
@@ -84,7 +98,6 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
-
   nf-core:
     runs-on: ubuntu-latest
     steps:
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
deleted file mode 100644
index d6fc716fb947d262e0613ccab07655d387a98d1f..0000000000000000000000000000000000000000
--- a/.github/workflows/push_dockerhub_dev.yml
+++ /dev/null
@@ -1,28 +0,0 @@
-name: nf-core Docker push (dev)
-# This builds the docker image and pushes it to DockerHub
-# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
-on:
-  push:
-    branches:
-      - dev
-
-jobs:
-  push_dockerhub:
-    name: Push new Docker image to Docker Hub (dev)
-    runs-on: ubuntu-latest
-    # Only run for the nf-core repo, for releases and merged PRs
-    if: ${{ github.repository == 'nf-core/hic' }}
-    env:
-      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
-      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Build new docker image
-        run: docker build --no-cache . -t nfcore/hic:dev
-
-      - name: Push Docker image to DockerHub (dev)
-        run: |
-          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push nfcore/hic:dev
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
deleted file mode 100644
index eda09ccfb6fcdd5791c56b6875343dc2bbf9c8c0..0000000000000000000000000000000000000000
--- a/.github/workflows/push_dockerhub_release.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-name: nf-core Docker push (release)
-# This builds the docker image and pushes it to DockerHub
-# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
-on:
-  release:
-    types: [published]
-
-jobs:
-  push_dockerhub:
-    name: Push new Docker image to Docker Hub (release)
-    runs-on: ubuntu-latest
-    # Only run for the nf-core repo, for releases and merged PRs
-    if: ${{ github.repository == 'nf-core/hic' }}
-    env:
-      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
-      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Build new docker image
-        run: docker build --no-cache . -t nfcore/hic:latest
-
-      - name: Push Docker image to DockerHub (release)
-        run: |
-          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push nfcore/hic:latest
-          docker tag nfcore/hic:latest nfcore/hic:${{ github.event.release.tag_name }}
-          docker push nfcore/hic:${{ github.event.release.tag_name }}
diff --git a/.gitignore b/.gitignore
index aa4bb5b375a9021f754dbd91d2321d16d1c0afc7..5124c9ac77e036998a69ae8e8e89f9ff6f9bcdb3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,7 +3,6 @@ work/
 data/
 results/
 .DS_Store
-tests/
 testing/
 testing*
 *.pyc
diff --git a/.github/markdownlint.yml b/.markdownlint.yml
similarity index 90%
rename from .github/markdownlint.yml
rename to .markdownlint.yml
index 8d7eb53b07463c24bd981a479a7d0591fabf7463..9e605fcfabe5a2024128aab62da6425ad7f1ee54 100644
--- a/.github/markdownlint.yml
+++ b/.markdownlint.yml
@@ -1,6 +1,8 @@
 # Markdownlint configuration file
 default: true
 line-length: false
+ul-indent:
+    indent: 4
 no-duplicate-header:
     siblings_only: true
 no-inline-html:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d11259a2ad55442ea006ced96d7821314349d9e8..fcf522d7d2038c7f1fd424fb82478a325f3db82e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.3.0dev - [date]
+## v1.3.0 - [date]
 
 Initial release of nf-core/hic, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/CITATIONS.md b/CITATIONS.md
new file mode 100644
index 0000000000000000000000000000000000000000..da253d248988442de777df56482ff1333cd7dce5
--- /dev/null
+++ b/CITATIONS.md
@@ -0,0 +1,32 @@
+# nf-core/hic: Citations
+
+## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
+
+> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
+
+## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+
+> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+
+## Pipeline tools
+
+* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+
+* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/)
+    > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+
+## Software packaging/containerisation tools
+
+* [Anaconda](https://anaconda.com)
+    > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+
+* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
+    > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+
+* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+    > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+
+* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+
+* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+    > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index c17398f9dbdef1c56ae1979789d843be3b707934..0000000000000000000000000000000000000000
--- a/Dockerfile
+++ /dev/null
@@ -1,13 +0,0 @@
-FROM nfcore/base:1.14
-LABEL authors="Nicolas Servant" \
-      description="Docker image containing all software requirements for the nf-core/hic pipeline"
-
-# Install the conda environment
-COPY environment.yml /
-RUN conda env create --quiet -f /environment.yml && conda clean -a
-
-# Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-hic-1.3.0dev/bin:$PATH
-
-# Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-hic-1.3.0dev > nf-core-hic-1.3.0dev.yml
diff --git a/README.md b/README.md
index 7e5298f1f5a41b11dbe5d922072dc4e55b488e36..ce38d720537f443a842d5fff0cfce2f7d170efd4 100644
--- a/README.md
+++ b/README.md
@@ -1,67 +1,69 @@
 # ![nf-core/hic](docs/images/nf-core-hic_logo.png)
 
-**Analysis of Chromosome Conformation Capture data (Hi-C)**.
+[![GitHub Actions CI Status](https://github.com/nf-core/hic/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/nf-core/hic/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+linting%22)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/hic/results)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
-[![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%A520.04.0-brightgreen.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
+[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
+[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
-[![Docker](https://img.shields.io/docker/automated/nfcore/hic.svg)](https://hub.docker.com/r/nfcore/hic)
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hic-4A154B?logo=slack)](https://nfcore.slack.com/channels/hic)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hic-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/hic)
+[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)
+[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
 <!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
-**nf-core/hic** is a bioinformatics best-practise analysis pipeline for
+**nf-core/hic** is a bioinformatics best-practice analysis pipeline for Analysis of Chromosome Conformation Capture data (Hi-C).
 
-The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
+The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
+
+<!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
+On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/hic/results).
+
+## Pipeline summary
+
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+
+1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Quick Start
 
-1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=20.04.0`)
+1. Install [`Nextflow`](https://nf-co.re/usage/installation) (`>=21.04.0`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-    ```bash
+    ```console
     nextflow run nf-core/hic -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
-    > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) 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.
+    > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+    > * If you are using `singularity` then the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, it is highly recommended to use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to pre-download all of the required containers before running the pipeline and to set the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options to be able to store and re-use the images from a central location for future pipeline runs.
+    > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
 
 4. Start running your own analysis!
 
     <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
-    ```bash
-    nextflow run nf-core/hic -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
+    ```console
+    nextflow run nf-core/hic -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --genome GRCh37
     ```
 
-See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running the pipeline.
-
-## Pipeline Summary
-
-By default, the pipeline currently performs the following:
-
-<!-- TODO nf-core: Fill in short bullet-pointed list of default steps of pipeline -->
-
-* Sequencing quality control (`FastQC`)
-* Overall pipeline run summaries (`MultiQC`)
-
 ## Documentation
 
-The nf-core/hic pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/hic/usage) and [output](https://nf-co.re/hic/output).
-
-<!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works -->
+The nf-core/hic pipeline comes with documentation about the pipeline [usage](https://nf-co.re/hic/usage), [parameters](https://nf-co.re/hic/parameters) and [output](https://nf-co.re/hic/output).
 
 ## Credits
 
 nf-core/hic was originally written by Nicolas Servant.
 
-We thank the following people for their extensive assistance in the development
-of this pipeline:
+We thank the following people for their extensive assistance in the development of this pipeline:
 
 <!-- TODO nf-core: If applicable, make list of people who have also contributed -->
 
@@ -73,9 +75,12 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. -->
+<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use  nf-core/hic for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
+<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+
 You can cite the `nf-core` publication as follows:
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
@@ -83,7 +88,3 @@ You can cite the `nf-core` publication as follows:
 > 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).
-
-In addition, references of tools and data used in this pipeline are as follows:
-
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
new file mode 100644
index 0000000000000000000000000000000000000000..5f653ab7bfc86c905b720d2bb8708646bb66366e
--- /dev/null
+++ b/assets/samplesheet.csv
@@ -0,0 +1,3 @@
+sample,fastq_1,fastq_2
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
diff --git a/assets/schema_input.json b/assets/schema_input.json
new file mode 100644
index 0000000000000000000000000000000000000000..1c3f0f7be19d1d007f3a5ab083adf91cb5cf72dc
--- /dev/null
+++ b/assets/schema_input.json
@@ -0,0 +1,39 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/hic/master/assets/schema_input.json",
+    "title": "nf-core/hic pipeline - params.input schema",
+    "description": "Schema for the file provided with params.input",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "sample": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Sample name must be provided and cannot contain spaces"
+            },
+            "fastq_1": {
+                "type": "string",
+                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+            },
+            "fastq_2": {
+                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
+                "anyOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+\\.f(ast)?q\\.gz$"
+                    },
+                    {
+                        "type": "string",
+                        "maxLength": 0
+                    }
+                ]
+            }
+        },
+        "required": [
+            "sample",
+            "fastq_1"
+        ]
+    }
+}
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
index bdf905878111122e2d6b6983f72e6a04c78e97b5..6213286c8a3c027fb1fb4496c938fbe3ed7909d3 100644
--- a/assets/sendmail_template.txt
+++ b/assets/sendmail_template.txt
@@ -15,15 +15,15 @@ Content-ID: <nfcorepipelinelogo>
 Content-Disposition: inline; filename="nf-core-hic_logo.png"
 
 <% out << new File("$projectDir/assets/nf-core-hic_logo.png").
-  bytes.
-  encodeBase64().
-  toString().
-  tokenize( '\n' )*.
-  toList()*.
-  collate( 76 )*.
-  collect { it.join() }.
-  flatten().
-  join( '\n' ) %>
+    bytes.
+    encodeBase64().
+    toString().
+    tokenize( '\n' )*.
+    toList()*.
+    collate( 76 )*.
+    collect { it.join() }.
+    flatten().
+    join( '\n' ) %>
 
 <%
 if (mqcFile){
@@ -37,15 +37,15 @@ Content-ID: <mqcreport>
 Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
 
 ${mqcFileObj.
-  bytes.
-  encodeBase64().
-  toString().
-  tokenize( '\n' )*.
-  toList()*.
-  collate( 76 )*.
-  collect { it.join() }.
-  flatten().
-  join( '\n' )}
+    bytes.
+    encodeBase64().
+    toString().
+    tokenize( '\n' )*.
+    toList()*.
+    collate( 76 )*.
+    collect { it.join() }.
+    flatten().
+    join( '\n' )}
 """
 }}
 %>
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
new file mode 100755
index 0000000000000000000000000000000000000000..9f6aaa35eeecaa04a4f33b9b8bdf0aa303936362
--- /dev/null
+++ b/bin/check_samplesheet.py
@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+
+# TODO nf-core: Update the script to check the samplesheet
+# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
+
+import os
+import sys
+import errno
+import argparse
+
+
+def parse_args(args=None):
+    Description = "Reformat nf-core/hic samplesheet file and check its contents."
+    Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
+
+    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
+    parser.add_argument("FILE_IN", help="Input samplesheet file.")
+    parser.add_argument("FILE_OUT", help="Output file.")
+    return parser.parse_args(args)
+
+
+def make_dir(path):
+    if len(path) > 0:
+        try:
+            os.makedirs(path)
+        except OSError as exception:
+            if exception.errno != errno.EEXIST:
+                raise exception
+
+
+def print_error(error, context="Line", context_str=""):
+    error_str = "ERROR: Please check samplesheet -> {}".format(error)
+    if context != "" and context_str != "":
+        error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format(
+            error, context.strip(), context_str.strip()
+        )
+    print(error_str)
+    sys.exit(1)
+
+
+# TODO nf-core: Update the check_samplesheet function
+def check_samplesheet(file_in, file_out):
+    """
+    This function checks that the samplesheet follows the following structure:
+
+    sample,fastq_1,fastq_2
+    SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
+    SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
+    SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
+
+    For an example see:
+    https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
+    """
+
+    sample_mapping_dict = {}
+    with open(file_in, "r") as fin:
+
+        ## Check header
+        MIN_COLS = 2
+        # TODO nf-core: Update the column names for the input samplesheet
+        HEADER = ["sample", "fastq_1", "fastq_2"]
+        header = [x.strip('"') for x in fin.readline().strip().split(",")]
+        if header[: len(HEADER)] != HEADER:
+            print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER)))
+            sys.exit(1)
+
+        ## Check sample entries
+        for line in fin:
+            lspl = [x.strip().strip('"') for x in line.strip().split(",")]
+
+            # Check valid number of columns per row
+            if len(lspl) < len(HEADER):
+                print_error(
+                    "Invalid number of columns (minimum = {})!".format(len(HEADER)),
+                    "Line",
+                    line,
+                )
+            num_cols = len([x for x in lspl if x])
+            if num_cols < MIN_COLS:
+                print_error(
+                    "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
+                    "Line",
+                    line,
+                )
+
+            ## Check sample name entries
+            sample, fastq_1, fastq_2 = lspl[: len(HEADER)]
+            sample = sample.replace(" ", "_")
+            if not sample:
+                print_error("Sample entry has not been specified!", "Line", line)
+
+            ## Check FastQ file extension
+            for fastq in [fastq_1, fastq_2]:
+                if fastq:
+                    if fastq.find(" ") != -1:
+                        print_error("FastQ file contains spaces!", "Line", line)
+                    if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
+                        print_error(
+                            "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
+                            "Line",
+                            line,
+                        )
+
+            ## Auto-detect paired-end/single-end
+            sample_info = []  ## [single_end, fastq_1, fastq_2]
+            if sample and fastq_1 and fastq_2:  ## Paired-end short reads
+                sample_info = ["0", fastq_1, fastq_2]
+            elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
+                sample_info = ["1", fastq_1, fastq_2]
+            else:
+                print_error("Invalid combination of columns provided!", "Line", line)
+
+            ## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 ] }
+            if sample not in sample_mapping_dict:
+                sample_mapping_dict[sample] = [sample_info]
+            else:
+                if sample_info in sample_mapping_dict[sample]:
+                    print_error("Samplesheet contains duplicate rows!", "Line", line)
+                else:
+                    sample_mapping_dict[sample].append(sample_info)
+
+    ## Write validated samplesheet with appropriate columns
+    if len(sample_mapping_dict) > 0:
+        out_dir = os.path.dirname(file_out)
+        make_dir(out_dir)
+        with open(file_out, "w") as fout:
+            fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n")
+            for sample in sorted(sample_mapping_dict.keys()):
+
+                ## Check that multiple runs of the same sample are of the same datatype
+                if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]):
+                    print_error("Multiple runs of a sample must be of the same datatype!", "Sample: {}".format(sample))
+
+                for idx, val in enumerate(sample_mapping_dict[sample]):
+                    fout.write(",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n")
+    else:
+        print_error("No entries to process!", "Samplesheet: {}".format(file_in))
+
+
+def main(args=None):
+    args = parse_args(args)
+    check_samplesheet(args.FILE_IN, args.FILE_OUT)
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/bin/markdown_to_html.py b/bin/markdown_to_html.py
deleted file mode 100755
index a26d1ff5e6de3c09385760e76cc40f11a512b3a4..0000000000000000000000000000000000000000
--- a/bin/markdown_to_html.py
+++ /dev/null
@@ -1,91 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-import argparse
-import markdown
-import os
-import sys
-import io
-
-
-def convert_markdown(in_fn):
-    input_md = io.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/scrape_software_versions.py b/bin/scrape_software_versions.py
index feb158ae01211f5e71e63c8c74a3573882f9a6a4..f6a861b36a065664348822185d4039f4ec556db3 100755
--- a/bin/scrape_software_versions.py
+++ b/bin/scrape_software_versions.py
@@ -1,36 +1,18 @@
 #!/usr/bin/env python
 from __future__ import print_function
-from collections import OrderedDict
-import re
+import os
 
-# TODO nf-core: Add additional regexes for new tools in process get_software_versions
-regexes = {
-    "nf-core/hic": ["v_pipeline.txt", r"(\S+)"],
-    "Nextflow": ["v_nextflow.txt", r"(\S+)"],
-    "FastQC": ["v_fastqc.txt", r"FastQC v(\S+)"],
-    "MultiQC": ["v_multiqc.txt", r"multiqc, version (\S+)"],
-}
-results = OrderedDict()
-results["nf-core/hic"] = '<span style="color:#999999;">N/A</span>'
-results["Nextflow"] = '<span style="color:#999999;">N/A</span>'
-results["FastQC"] = '<span style="color:#999999;">N/A</span>'
-results["MultiQC"] = '<span style="color:#999999;">N/A</span>'
+results = {}
+version_files = [x for x in os.listdir(".") if x.endswith(".version.txt")]
+for version_file in version_files:
 
-# Search each file using its regex
-for k, v in regexes.items():
-    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
+    software = version_file.replace(".version.txt", "")
+    if software == "pipeline":
+        software = "nf-core/hic"
 
-# Remove software set to false in results
-for k in list(results):
-    if not results[k]:
-        del results[k]
+    with open(version_file) as fin:
+        version = fin.read().strip()
+    results[software] = version
 
 # Dump to YAML
 print(
@@ -44,11 +26,11 @@ data: |
     <dl class="dl-horizontal">
 """
 )
-for k, v in results.items():
+for k, v in sorted(results.items()):
     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():
+with open("software_versions.tsv", "w") as f:
+    for k, v in sorted(results.items()):
         f.write("{}\t{}\n".format(k, v))
diff --git a/conf/base.config b/conf/base.config
index 07aaa866f6c83b96dda659d3253e6a31e71900a7..2e7db0c1db87efe04da28a0914de2e9130a1c112 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -1,51 +1,57 @@
 /*
- * -------------------------------------------------
- *  nf-core/hic Nextflow base config file
- * -------------------------------------------------
- * A 'blank slate' config file, appropriate for general
- * use on most high performace compute environments.
- * Assumes that all software is installed and available
- * on the PATH. Runs in `local` mode - all jobs will be
- * run on the logged in environment.
- */
+========================================================================================
+    nf-core/hic Nextflow base config file
+========================================================================================
+    A 'blank slate' config file, appropriate for general use on most high performance
+    compute environments. Assumes that all software is installed and available on
+    the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.
+----------------------------------------------------------------------------------------
+*/
 
 process {
 
-  // TODO nf-core: Check the defaults for all processes
-  cpus = { check_max( 1 * task.attempt, 'cpus' ) }
-  memory = { check_max( 7.GB * task.attempt, 'memory' ) }
-  time = { check_max( 4.h * task.attempt, 'time' ) }
+    // TODO nf-core: Check the defaults for all processes
+    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
+    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
+    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
-  errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
-  maxRetries = 1
-  maxErrors = '-1'
-
-  // Process-specific resource requirements
-  // 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' ) }
-  }
-  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' ) }
-  }
-  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
-  }
+    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+    maxRetries    = 1
+    maxErrors     = '-1'
 
+    // Process-specific resource requirements
+    // NOTE - Please try and re-use the labels below as much as possible.
+    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
+    //        If possible, it would be nice to keep the same label naming convention when
+    //        adding in your local modules too.
+    // 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( 12.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_medium {
+        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high {
+        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
+        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_long {
+        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high_memory {
+        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+    }
+    withLabel:error_ignore {
+        errorStrategy = 'ignore'
+    }
+    withLabel:error_retry {
+        errorStrategy = 'retry'
+        maxRetries    = 2
+    }
 }
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 31b7ee6130c97ff9ea026fa312e8a2354dac565c..855948def19c408aa81e133a0b297e3d2a1cc299 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -1,421 +1,432 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for iGenomes paths
- * -------------------------------------------------
- * Defines reference genomes, using iGenome paths
- * Can be used by any config that customises the base
- * path using $params.igenomes_base / --igenomes_base
- */
+========================================================================================
+    Nextflow config file for iGenomes paths
+========================================================================================
+    Defines reference genomes using iGenome paths.
+    Can be used by any config that customises the base path using:
+        $params.igenomes_base / --igenomes_base
+----------------------------------------------------------------------------------------
+*/
 
 params {
-  // illumina iGenomes reference file paths
-  genomes {
-    'GRCh37' {
-      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   = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
+    // illumina iGenomes reference file paths
+    genomes {
+        'GRCh37' {
+            fasta       = "${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      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
+            mito_name   = "MT"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/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       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
+        }
+        'GRCm38' {
+            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   = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
+        }
+        'TAIR10' {
+            fasta       = "${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      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
+            mito_name   = "Mt"
+        }
+        'EB2' {
+            fasta       = "${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      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
+        }
+        'UMD3.1' {
+            fasta       = "${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      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
+            mito_name   = "MT"
+        }
+        'WBcel235' {
+            fasta       = "${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' {
+            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' {
+            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       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+        }
+        'BDGP6' {
+            fasta       = "${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' {
+            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' {
+            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' {
+            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       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+        }
+        'Gm01' {
+            fasta       = "${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      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
+        }
+        'Mmul_1' {
+            fasta       = "${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      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
+            mito_name   = "MT"
+        }
+        'IRGSP-1.0' {
+            fasta       = "${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' {
+            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_5.0' {
+            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/genome.fa"
+            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+        }
+        'Rnor_6.0' {
+            fasta       = "${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' {
+            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       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+            macs_gsize  = "1.2e7"
+        }
+        'EF2' {
+            fasta       = "${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      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
+            mito_name   = "MT"
+            macs_gsize  = "1.21e7"
+        }
+        'Sbi1' {
+            fasta       = "${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      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
+        }
+        'Sscrofa10.2' {
+            fasta       = "${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      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
+            mito_name   = "MT"
+        }
+        'AGPv3' {
+            fasta       = "${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       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/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   = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
+        }
+        'mm10' {
+            fasta       = "${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      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
+            mito_name   = "chrM"
+            macs_gsize  = "1.87e9"
+            blacklist   = "${projectDir}/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"
+            macs_gsize  = "1.37e9"
+        }
+        '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"
+        }
     }
-    '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       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
-      mito_name   = "chrM"
-      macs_gsize  = "2.7e9"
-      blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-    }
-    'GRCm38' {
-      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   = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
-    }
-    'TAIR10' {
-      fasta       = "${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      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
-      mito_name   = "Mt"
-    }
-    'EB2' {
-      fasta       = "${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      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
-    }
-    'UMD3.1' {
-      fasta       = "${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      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
-      mito_name   = "MT"
-    }
-    'WBcel235' {
-      fasta       = "${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' {
-      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' {
-      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       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
-      mito_name   = "MT"
-    }
-    'BDGP6' {
-      fasta       = "${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' {
-      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' {
-      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' {
-      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       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
-      mito_name   = "MT"
-    }
-    'Gm01' {
-      fasta       = "${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      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
-    }
-    'Mmul_1' {
-      fasta       = "${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      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
-      mito_name   = "MT"
-    }
-    'IRGSP-1.0' {
-      fasta       = "${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' {
-      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' {
-      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       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
-      mito_name   = "MT"
-    }
-    'R64-1-1' {
-      fasta       = "${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' {
-      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' {
-      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' {
-      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' {
-      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   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-    }
-    'hg19' {
-      fasta       = "${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      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
-      mito_name   = "chrM"
-      macs_gsize  = "2.7e9"
-      blacklist   = "${projectDir}/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   = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
-    }
-    'bosTau8' {
-      fasta       = "${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       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
-      mito_name   = "chrM"
-      macs_gsize  = "1.37e9"
-    }
-    'dm6' {
-      fasta       = "${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/modules.config b/conf/modules.config
new file mode 100644
index 0000000000000000000000000000000000000000..0b1bfdec2050c7ba17ab39188d89ced8973ea549
--- /dev/null
+++ b/conf/modules.config
@@ -0,0 +1,32 @@
+/*
+========================================================================================
+    Config file for defining DSL2 per module options
+========================================================================================
+    Available keys to override module options:
+        args            = Additional arguments appended to command in module.
+        args2           = Second set of arguments appended to command in module (multi-tool modules).
+        args3           = Third set of arguments appended to command in module (multi-tool modules).
+        publish_dir     = Directory to publish results.
+        publish_by_meta = Groovy list of keys available in meta map to append as directories to "publish_dir" path
+                            If publish_by_meta = true                 - Value of ${meta['id']} is appended as a directory to "publish_dir" path
+                            If publish_by_meta = ['id', 'custompath'] - If "id" is in meta map and "custompath" isn't then "${meta['id']}/custompath/"
+                                                                        is appended as a directory to "publish_dir" path
+                            If publish_by_meta = false / null         - No directories are appended to "publish_dir" path
+        publish_files   = Groovy map where key = "file_ext" and value = "directory" to publish results for that file extension
+                            The value of "directory" is appended to the standard "publish_dir" path as defined above.
+                            If publish_files = null (unspecified)     - All files are published.
+                            If publish_files = false                  - No files are published.
+        suffix          = File name suffix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    modules {
+        'fastqc' {
+            args = "--quiet"
+        }
+        'multiqc' {
+            args = ""
+        }
+    }
+}
diff --git a/conf/test.config b/conf/test.config
index 6fb6dcef9ca689e80f9bd04fccb0ced82d289504..d117e413a738899ff73b5ed900a52ced8c5986f9 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -1,28 +1,29 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/hic -profile test,<docker/singularity>
- */
+========================================================================================
+    Nextflow config file for running minimal tests
+========================================================================================
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/hic -profile test,<docker/singularity>
+
+----------------------------------------------------------------------------------------
+*/
 
 params {
-  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
+    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   = 6.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
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
-  // 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
-  single_end = false
-  input_paths = [
-    ['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']]
-  ]
-  // Ignore `--input` as otherwise the parameter validation will throw an error
-  schema_ignore_params = 'genomes,input_paths,input'
+    // Genome references
+    genome = 'R64-1-1'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index b5fabaab29f342773efc5558bc2c2d8715908bde..749878333105099f6ec556853fa2b404e1a28cbb 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -1,24 +1,24 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running full-size tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a full size pipeline test. Use as follows:
- *   nextflow run nf-core/hic -profile test_full,<docker/singularity>
- */
+========================================================================================
+    Nextflow config file for running full-size tests
+========================================================================================
+    Defines input files and everything required to run a full size pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/hic -profile test_full,<docker/singularity>
+
+----------------------------------------------------------------------------------------
+*/
 
 params {
-  config_profile_name = 'Full test profile'
-  config_profile_description = 'Full test dataset to check pipeline function'
+    config_profile_name        = 'Full test profile'
+    config_profile_description = 'Full test dataset to check pipeline function'
+
+    // Input data for full size test
+    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
+    // TODO nf-core: Give any required params for the test so that command line flags are not needed
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
 
-  // Input data for full size test
-  // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-  // TODO nf-core: Give any required params for the test so that command line flags are not needed
-  single_end = false
-  input_paths = [
-    ['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']]
-  ]
-  // Ignore `--input` as otherwise the parameter validation will throw an error
-  schema_ignore_params = 'genomes,input_paths,input'
+    // Genome references
+    genome = 'R64-1-1'
 }
diff --git a/docs/README.md b/docs/README.md
index a6889549c7f27bda0aed81947685713781fe2d1b..112811ae596b875a989ea77d0671e97ee1125a7c 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -3,8 +3,8 @@
 The nf-core/hic documentation is split into the following pages:
 
 * [Usage](usage.md)
-  * An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
+    * An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
 * [Output](output.md)
-  * An overview of the different results produced by the pipeline and how to interpret them.
+    * An overview of the different results produced by the pipeline and how to interpret them.
 
 You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)
diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png
new file mode 100755
index 0000000000000000000000000000000000000000..361d0e47acfb424dea1f326590d1eb2f6dfa26b5
Binary files /dev/null and b/docs/images/mqc_fastqc_adapter.png differ
diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png
new file mode 100755
index 0000000000000000000000000000000000000000..cb39ebb80a71dc4cdeee076c107e30a6c944441b
Binary files /dev/null and b/docs/images/mqc_fastqc_counts.png differ
diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png
new file mode 100755
index 0000000000000000000000000000000000000000..a4b89bf56ab2ba88cab87841916eb680a816deae
Binary files /dev/null and b/docs/images/mqc_fastqc_quality.png differ
diff --git a/docs/output.md b/docs/output.md
index 238d7eb935a46e1fb58d79895a10913bf55a50aa..e2d35a1b9c9b5bd3b6c2f7948a3cf5bb469e0c62 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -10,50 +10,59 @@ The directories listed below will be created in the results directory after the
 
 ## Pipeline overview
 
-The pipeline is built using [Nextflow](https://www.nextflow.io/)
-and processes data using the following steps:
+The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-* [FastQC](#fastqc) - Read quality control
-* [MultiQC](#multiqc) - Aggregate report describing results from the whole pipeline
+* [FastQC](#fastqc) - Raw read QC
+* [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 * [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
-## FastQC
+### FastQC
 
-[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences.
+<details markdown="1">
+<summary>Output files</summary>
 
-For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
+* `fastqc/`
+    * `*_fastqc.html`: FastQC report containing quality metrics.
+    * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
 
-**Output files:**
+</details>
 
-* `fastqc/`
-  * `*_fastqc.html`: FastQC report containing quality metrics for your untrimmed raw fastq files.
-* `fastqc/zips/`
-  * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
 
-## MultiQC
+![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
 
-[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarizing all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
+![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
 
-The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability.
+> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
 
-For more information about how to use MultiQC reports, see [https://multiqc.info](https://multiqc.info).
+### MultiQC
 
-**Output files:**
+<details markdown="1">
+<summary>Output files</summary>
 
 * `multiqc/`
-  * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-  * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-  * `multiqc_plots/`: directory containing static images from the report in various formats.
+    * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+    * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+    * `multiqc_plots/`: directory containing static images from the report in various formats.
 
-## Pipeline information
+</details>
 
-[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
+[MultiQC](http://multiqc.info) is a visualization 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 the report data directory.
 
-**Output files:**
+Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+
+### Pipeline information
+
+<details markdown="1">
+<summary>Output files</summary>
 
 * `pipeline_info/`
-  * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-  * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.csv`.
-  * Documentation for interpretation of results in HTML format: `results_description.html`.
+    * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
+    * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.tsv`.
+    * Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
+
+</details>
+
+[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
diff --git a/docs/usage.md b/docs/usage.md
index 45a94e94cd157b813ddf6076a6c6c2b8eadfb221..79b33ec2f74790ac27c2c883fe932dfa222f63e6 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -8,19 +8,63 @@
 
 <!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
 
+## Samplesheet input
+
+You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+
+```console
+--input '[path to samplesheet file]'
+```
+
+### Multiple runs of the same sample
+
+The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:
+
+```console
+sample,fastq_1,fastq_2
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
+CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz
+```
+
+### Full samplesheet
+
+The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below.
+
+A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice.
+
+```console
+sample,fastq_1,fastq_2
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
+CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz
+TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,
+TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,
+TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,
+TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,
+```
+
+| Column         | Description                                                                                                                                                                            |
+|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `sample`       | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
+| `fastq_1`      | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
+| `fastq_2`      | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
+
+An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:
 
-```bash
-nextflow run nf-core/hic --input '*_R{1,2}.fastq.gz' -profile docker
+```console
+nextflow run nf-core/hic --input samplesheet.csv --genome GRCh37 -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
 
 Note that the pipeline will create the following files in your working directory:
 
-```bash
+```console
 work            # Directory containing the nextflow working files
 results         # Finished results (configurable, see below)
 .nextflow_log   # Log file from Nextflow
@@ -31,13 +75,13 @@ results         # Finished results (configurable, see below)
 
 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
+```console
 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.
+It is 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`.
 
@@ -51,7 +95,7 @@ This version number will be logged in reports when you run the pipeline, so that
 
 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, Podman, Shifter, Charliecloud, Conda) - see below.
+Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. When using Biocontainers, most of these software packaging methods pull Docker containers from quay.io e.g [FastQC](https://quay.io/repository/biocontainers/fastqc) except for Singularity which directly downloads Singularity images via https hosted by the [Galaxy project](https://depot.galaxyproject.org/singularity/) and Conda which downloads and installs software locally from [Bioconda](https://bioconda.github.io/).
 
 > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
@@ -63,27 +107,20 @@ 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.
 
 * `docker`
-  * A generic configuration profile to be used with [Docker](https://docker.com/)
-  * Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
+    * A generic configuration profile to be used with [Docker](https://docker.com/)
 * `singularity`
-  * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
-  * Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
+    * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
 * `podman`
-  * A generic configuration profile to be used with [Podman](https://podman.io/)
-  * Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
+    * A generic configuration profile to be used with [Podman](https://podman.io/)
 * `shifter`
-  * A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
-  * Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
+    * A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
 * `charliecloud`
-  * A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
-  * Pulls software from Docker Hub: [`nfcore/hic`](https://hub.docker.com/r/nfcore/hic/)
+    * A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 * `conda`
-  * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
-  * A generic configuration profile to be used with [Conda](https://conda.io/docs/)
-  * Pulls most software from [Bioconda](https://bioconda.github.io/)
+    * A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
 * `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
 
 ### `-resume`
 
@@ -95,29 +132,140 @@ You can also supply a run name to resume a specific run: `-resume [run-name]`. U
 
 Specify the path to a specific config file (this is a core Nextflow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information.
 
-#### Custom resource requests
+## Custom configuration
+
+### Resource requests
+
+Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. 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 any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
+
+For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue:
+
+```console
+[62/149eb0] NOTE: Process `RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1)
+Error executing process > 'RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)'
+
+Caused by:
+    Process `RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137)
 
-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.
+Command executed:
+    STAR \
+        --genomeDir star \
+        --readFilesIn WT_REP1_trimmed.fq.gz  \
+        --runThreadN 2 \
+        --outFileNamePrefix WT_REP1. \
+        <TRUNCATED>
 
-Whilst these default requirements will hopefully work for most people with most data, you may find that you want to customise the compute resources that the pipeline requests. You can do this by creating a custom config file. For example, to give the workflow process `star` 32GB of memory, you could use the following config:
+Command exit status:
+    137
+
+Command output:
+    (empty)
+
+Command error:
+    .command.sh: line 9:  30 Killed    STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. <TRUNCATED>
+Work dir:
+    /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb
+
+Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
+```
+
+To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so based on the search results the file we want is `modules/nf-core/software/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. Providing you haven't set any other standard nf-core parameters to __cap__ the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
 
 ```nextflow
 process {
-  withName: star {
-    memory = 32.GB
-  }
+    withName: STAR_ALIGN {
+        memory = 100.GB
+    }
 }
 ```
 
-To find the exact name of a process you wish to modify the compute resources, check the live-status of a nextflow run displayed on your terminal or check the nextflow error for a line like so: `Error executing process > 'bwa'`. In this case the name to specify in the custom config file is `bwa`.
+> **NB:** We specify just the process name i.e. `STAR_ALIGN` in the config file and not the full task name string that is printed to screen in the error message or on the terminal whilst the pipeline is running i.e. `RNASEQ:ALIGN_STAR:STAR_ALIGN`. You may get a warning suggesting that the process selector isn't recognised but you can ignore that if the process name has been specified correctly. This is something that needs to be fixed upstream in core Nextflow.
+
+### Tool-specific options
+
+For the ultimate flexibility, we have implemented and are using Nextflow DSL2 modules in a way where it is possible for both developers and users to change tool-specific command-line arguments (e.g. providing an additional command-line argument to the `STAR_ALIGN` process) as well as publishing options (e.g. saving files produced by the `STAR_ALIGN` process that aren't saved by default by the pipeline). In the majority of instances, as a user you won't have to change the default options set by the pipeline developer(s), however, there may be edge cases where creating a simple custom config file can improve the behaviour of the pipeline if for example it is failing due to a weird error that requires setting a tool-specific parameter to deal with smaller / larger genomes.
+
+The command-line arguments passed to STAR in the `STAR_ALIGN` module are a combination of:
+
+* Mandatory arguments or those that need to be evaluated within the scope of the module, as supplied in the [`script`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L49-L55) section of the module file.
+
+* An [`options.args`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L56) string of non-mandatory parameters that is set to be empty by default in the module but can be overwritten when including the module in the sub-workflow / workflow context via the `addParams` Nextflow option.
+
+The nf-core/rnaseq pipeline has a sub-workflow (see [terminology](https://github.com/nf-core/modules#terminology)) specifically to align reads with STAR and to sort, index and generate some basic stats on the resulting BAM files using SAMtools. At the top of this file we import the `STAR_ALIGN` module via the Nextflow [`include`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/subworkflows/nf-core/align_star.nf#L10) keyword and by default the options passed to the module via the `addParams` option are set as an empty Groovy map [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/subworkflows/nf-core/align_star.nf#L5); this in turn means `options.args` will be set to empty by default in the module file too. This is an intentional design choice and allows us to implement well-written sub-workflows composed of a chain of tools that by default run with the bare minimum parameter set for any given tool in order to make it much easier to share across pipelines and to provide the flexibility for users and developers to customise any non-mandatory arguments.
+
+When including the sub-workflow above in the main pipeline workflow we use the same `include` statement, however, we now have the ability to overwrite options for each of the tools in the sub-workflow including the [`align_options`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/workflows/rnaseq.nf#L225) variable that will be used specifically to overwrite the optional arguments passed to the `STAR_ALIGN` module. In this case, the options to be provided to `STAR_ALIGN` have been assigned sensible defaults by the developer(s) in the pipeline's [`modules.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/modules.config#L70-L74) and can be accessed and customised in the [workflow context](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/workflows/rnaseq.nf#L201-L204) too before eventually passing them to the sub-workflow as a Groovy map called `star_align_options`. These options will then be propagated from `workflow -> sub-workflow -> module`.
+
+As mentioned at the beginning of this section it may also be necessary for users to overwrite the options passed to modules to be able to customise specific aspects of the way in which a particular tool is executed by the pipeline. Given that all of the default module options are stored in the pipeline's `modules.config` as a [`params` variable](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/modules.config#L24-L25) it is also possible to overwrite any of these options via a custom config file.
+
+Say for example we want to append an additional, non-mandatory parameter (i.e. `--outFilterMismatchNmax 16`) to the arguments passed to the `STAR_ALIGN` module. Firstly, we need to copy across the default `args` specified in the [`modules.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/modules.config#L71) and create a custom config file that is a composite of the default `args` as well as the additional options you would like to provide. This is very important because Nextflow will overwrite the default value of `args` that you provide via the custom config.
+
+As you will see in the example below, we have:
+
+* appended `--outFilterMismatchNmax 16` to the default `args` used by the module.
+* changed the default `publish_dir` value to where the files will eventually be published in the main results directory.
+* appended `'bam':''` to the default value of `publish_files` so that the BAM files generated by the process will also be saved in the top-level results directory for the module. Note: `'out':'log'` means any file/directory ending in `out` will now be saved in a separate directory called `my_star_directory/log/`.
+
+```nextflow
+params {
+    modules {
+        'star_align' {
+            args          = "--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outFilterMismatchNmax 16"
+            publish_dir   = "my_star_directory"
+            publish_files = ['out':'log', 'tab':'log', 'bam':'']
+        }
+    }
+}
+```
+
+### Updating containers
+
+The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`.
+
+1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19)
+2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags)
+3. Create the custom config accordingly:
+
+    * For Docker:
+
+        ```nextflow
+        process {
+            withName: PANGOLIN {
+                container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
+            }
+        }
+        ```
+
+    * For Singularity:
+
+        ```nextflow
+        process {
+            withName: PANGOLIN {
+                container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
+            }
+        }
+        ```
+
+    * For Conda:
+
+        ```nextflow
+        process {
+            withName: PANGOLIN {
+                conda = 'bioconda::pangolin=3.0.5'
+            }
+        }
+        ```
+
+> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch.
+
+### nf-core/configs
 
-See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information.
+In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings 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. 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 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 above). 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.
+See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files.
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
-### Running in the background
+## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
 
@@ -126,11 +274,11 @@ The Nextflow `-bg` flag launches Nextflow in the background, detached from your
 Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time.
 Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs).
 
-#### Nextflow memory requirements
+## Nextflow memory requirements
 
 In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
 We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
 
-```bash
+```console
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index cde6a0c58bdaea5d3a9c55b167d26df11441799e..0000000000000000000000000000000000000000
--- a/environment.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-# You can use this file to create a conda environment for this pipeline:
-#   conda env create -f environment.yml
-name: nf-core-hic-1.3.0dev
-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
-  - bioconda::fastqc=0.11.8
-  - bioconda::multiqc=1.7
diff --git a/lib/Headers.groovy b/lib/Headers.groovy
deleted file mode 100644
index 15d1d388006df42e226aea961f0d21dbdabaa8cb..0000000000000000000000000000000000000000
--- a/lib/Headers.groovy
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * This file holds several functions used to render the nf-core ANSI header.
- */
-
-class Headers {
-
-    private static Map log_colours(Boolean monochrome_logs) {
-        Map colorcodes = [:]
-        colorcodes['reset']       = monochrome_logs ? '' : "\033[0m"
-        colorcodes['dim']         = monochrome_logs ? '' : "\033[2m"
-        colorcodes['black']       = monochrome_logs ? '' : "\033[0;30m"
-        colorcodes['green']       = monochrome_logs ? '' : "\033[0;32m"
-        colorcodes['yellow']      = monochrome_logs ? '' :  "\033[0;33m"
-        colorcodes['yellow_bold'] = monochrome_logs ? '' : "\033[1;93m"
-        colorcodes['blue']        = monochrome_logs ? '' : "\033[0;34m"
-        colorcodes['purple']      = monochrome_logs ? '' : "\033[0;35m"
-        colorcodes['cyan']        = monochrome_logs ? '' : "\033[0;36m"
-        colorcodes['white']       = monochrome_logs ? '' : "\033[0;37m"
-        colorcodes['red']         = monochrome_logs ? '' : "\033[1;91m"
-        return colorcodes
-    }
-
-    static String dashed_line(monochrome_logs) {
-        Map colors = log_colours(monochrome_logs)
-        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-    }
-
-    static String nf_core(workflow, monochrome_logs) {
-        Map colors = log_colours(monochrome_logs)
-        String.format(
-            """\n
-            ${dashed_line(monochrome_logs)}
-                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                    ${colors.green}`._,._,\'${colors.reset}
-            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
-            ${dashed_line(monochrome_logs)}
-            """.stripIndent()
-        )
-    }
-}
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
old mode 100644
new mode 100755
index 52ee730432905c5f6dc3e2c89352bbaee6ea145b..8d6920dd645644e70e8bce260022e7e70be97788
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -1,6 +1,6 @@
-/*
- * This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
- */
+//
+// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
+//
 
 import org.everit.json.schema.Schema
 import org.everit.json.schema.loader.SchemaLoader
@@ -13,16 +13,23 @@ import groovy.json.JsonBuilder
 
 class NfcoreSchema {
 
-    /*
-    * Function to loop over all parameters defined in schema and check
-    * whether the given paremeters adhere to the specificiations
-    */
+    //
+    // Resolve Schema path relative to main workflow directory
+    //
+    public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') {
+        return "${workflow.projectDir}/${schema_filename}"
+    }
+
+    //
+    // Function to loop over all parameters defined in schema and check
+    // whether the given parameters adhere to the specifications
+    //
     /* groovylint-disable-next-line UnusedPrivateMethodParameter */
-    private static void validateParameters(params, jsonSchema, log) {
+    public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') {
         def has_error = false
         //=====================================================================//
         // Check for nextflow core params and unexpected params
-        def json = new File(jsonSchema).text
+        def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text
         def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions')
         def nf_params = [
             // Options for base `nextflow` command
@@ -114,7 +121,8 @@ class NfcoreSchema {
             def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
             def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }
             def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
-            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !expectedParamsLowerCase.contains(specifiedParamLowerCase)) {
+            def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase))
+            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
                 // Temporarily remove camelCase/camel-case params #1035
                 def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}
                 if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){
@@ -125,36 +133,36 @@ class NfcoreSchema {
 
         //=====================================================================//
         // Validate parameters against the schema
-        InputStream inputStream = new File(jsonSchema).newInputStream()
-        JSONObject rawSchema = new JSONObject(new JSONTokener(inputStream))
+        InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream()
+        JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream))
 
         // Remove anything that's in params.schema_ignore_params
-        rawSchema = removeIgnoredParams(rawSchema, params)
+        raw_schema = removeIgnoredParams(raw_schema, params)
 
-        Schema schema = SchemaLoader.load(rawSchema)
+        Schema schema = SchemaLoader.load(raw_schema)
 
         // Clean the parameters
         def cleanedParams = cleanParameters(params)
 
         // Convert to JSONObject
         def jsonParams = new JsonBuilder(cleanedParams)
-        JSONObject paramsJSON = new JSONObject(jsonParams.toString())
+        JSONObject params_json = new JSONObject(jsonParams.toString())
 
         // Validate
         try {
-            schema.validate(paramsJSON)
+            schema.validate(params_json)
         } catch (ValidationException e) {
             println ''
             log.error 'ERROR: Validation of pipeline parameters failed!'
             JSONObject exceptionJSON = e.toJSON()
-            printExceptions(exceptionJSON, paramsJSON, log)
+            printExceptions(exceptionJSON, params_json, log)
             println ''
             has_error = true
         }
 
         // Check for unexpected parameters
         if (unexpectedParams.size() > 0) {
-            Map colors = log_colours(params.monochrome_logs)
+            Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
             println ''
             def warn_msg = 'Found unexpected parameters:'
             for (unexpectedParam in unexpectedParams) {
@@ -170,266 +178,17 @@ class NfcoreSchema {
         }
     }
 
-    // Loop over nested exceptions and print the causingException
-    private static void printExceptions(exJSON, paramsJSON, log) {
-        def causingExceptions = exJSON['causingExceptions']
-        if (causingExceptions.length() == 0) {
-            def m = exJSON['message'] =~ /required key \[([^\]]+)\] not found/
-            // Missing required param
-            if (m.matches()) {
-                log.error "* Missing required parameter: --${m[0][1]}"
-            }
-            // Other base-level error
-            else if (exJSON['pointerToViolation'] == '#') {
-                log.error "* ${exJSON['message']}"
-            }
-            // Error with specific param
-            else {
-                def param = exJSON['pointerToViolation'] - ~/^#\//
-                def param_val = paramsJSON[param].toString()
-                log.error "* --${param}: ${exJSON['message']} (${param_val})"
-            }
-        }
-        for (ex in causingExceptions) {
-            printExceptions(ex, paramsJSON, log)
-        }
-    }
-
-    // Remove an element from a JSONArray
-    private static JSONArray removeElement(jsonArray, element){
-        def list = []
-        int len = jsonArray.length()
-        for (int i=0;i<len;i++){
-            list.add(jsonArray.get(i).toString())
-        }
-        list.remove(element)
-        JSONArray jsArray = new JSONArray(list)
-        return jsArray
-    }
-
-    private static JSONObject removeIgnoredParams(rawSchema, params){
-        // Remove anything that's in params.schema_ignore_params
-        params.schema_ignore_params.split(',').each{ ignore_param ->
-            if(rawSchema.keySet().contains('definitions')){
-                rawSchema.definitions.each { definition ->
-                    for (key in definition.keySet()){
-                        if (definition[key].get("properties").keySet().contains(ignore_param)){
-                            // Remove the param to ignore
-                            definition[key].get("properties").remove(ignore_param)
-                            // If the param was required, change this
-                            if (definition[key].has("required")) {
-                                def cleaned_required = removeElement(definition[key].required, ignore_param)
-                                definition[key].put("required", cleaned_required)
-                            }
-                        }
-                    }
-                }
-            }
-            if(rawSchema.keySet().contains('properties') && rawSchema.get('properties').keySet().contains(ignore_param)) {
-                rawSchema.get("properties").remove(ignore_param)
-            }
-            if(rawSchema.keySet().contains('required') && rawSchema.required.contains(ignore_param)) {
-                def cleaned_required = removeElement(rawSchema.required, ignore_param)
-                rawSchema.put("required", cleaned_required)
-            }
-        }
-        return rawSchema
-    }
-
-    private static Map cleanParameters(params) {
-        def new_params = params.getClass().newInstance(params)
-        for (p in params) {
-            // remove anything evaluating to false
-            if (!p['value']) {
-                new_params.remove(p.key)
-            }
-            // Cast MemoryUnit to String
-            if (p['value'].getClass() == nextflow.util.MemoryUnit) {
-                new_params.replace(p.key, p['value'].toString())
-            }
-            // Cast Duration to String
-            if (p['value'].getClass() == nextflow.util.Duration) {
-                new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
-            }
-            // Cast LinkedHashMap to String
-            if (p['value'].getClass() == LinkedHashMap) {
-                new_params.replace(p.key, p['value'].toString())
-            }
-        }
-        return new_params
-    }
-
-     /*
-     * This method tries to read a JSON params file
-     */
-    private static LinkedHashMap params_load(String json_schema) {
-        def params_map = new LinkedHashMap()
-        try {
-            params_map = params_read(json_schema)
-        } catch (Exception e) {
-            println "Could not read parameters settings from JSON. $e"
-            params_map = new LinkedHashMap()
-        }
-        return params_map
-    }
-
-    private static Map log_colours(Boolean monochrome_logs) {
-        Map colorcodes = [:]
-
-        // Reset / Meta
-        colorcodes['reset']       = monochrome_logs ? '' : "\033[0m"
-        colorcodes['bold']        = monochrome_logs ? '' : "\033[1m"
-        colorcodes['dim']         = monochrome_logs ? '' : "\033[2m"
-        colorcodes['underlined']  = monochrome_logs ? '' : "\033[4m"
-        colorcodes['blink']       = monochrome_logs ? '' : "\033[5m"
-        colorcodes['reverse']     = monochrome_logs ? '' : "\033[7m"
-        colorcodes['hidden']      = monochrome_logs ? '' : "\033[8m"
-
-        // Regular Colors
-        colorcodes['black']       = monochrome_logs ? '' : "\033[0;30m"
-        colorcodes['red']         = monochrome_logs ? '' : "\033[0;31m"
-        colorcodes['green']       = monochrome_logs ? '' : "\033[0;32m"
-        colorcodes['yellow']      = monochrome_logs ? '' : "\033[0;33m"
-        colorcodes['blue']        = monochrome_logs ? '' : "\033[0;34m"
-        colorcodes['purple']      = monochrome_logs ? '' : "\033[0;35m"
-        colorcodes['cyan']        = monochrome_logs ? '' : "\033[0;36m"
-        colorcodes['white']       = monochrome_logs ? '' : "\033[0;37m"
-
-        // Bold
-        colorcodes['bblack']      = monochrome_logs ? '' : "\033[1;30m"
-        colorcodes['bred']        = monochrome_logs ? '' : "\033[1;31m"
-        colorcodes['bgreen']      = monochrome_logs ? '' : "\033[1;32m"
-        colorcodes['byellow']     = monochrome_logs ? '' : "\033[1;33m"
-        colorcodes['bblue']       = monochrome_logs ? '' : "\033[1;34m"
-        colorcodes['bpurple']     = monochrome_logs ? '' : "\033[1;35m"
-        colorcodes['bcyan']       = monochrome_logs ? '' : "\033[1;36m"
-        colorcodes['bwhite']      = monochrome_logs ? '' : "\033[1;37m"
-
-        // Underline
-        colorcodes['ublack']      = monochrome_logs ? '' : "\033[4;30m"
-        colorcodes['ured']        = monochrome_logs ? '' : "\033[4;31m"
-        colorcodes['ugreen']      = monochrome_logs ? '' : "\033[4;32m"
-        colorcodes['uyellow']     = monochrome_logs ? '' : "\033[4;33m"
-        colorcodes['ublue']       = monochrome_logs ? '' : "\033[4;34m"
-        colorcodes['upurple']     = monochrome_logs ? '' : "\033[4;35m"
-        colorcodes['ucyan']       = monochrome_logs ? '' : "\033[4;36m"
-        colorcodes['uwhite']      = monochrome_logs ? '' : "\033[4;37m"
-
-        // High Intensity
-        colorcodes['iblack']      = monochrome_logs ? '' : "\033[0;90m"
-        colorcodes['ired']        = monochrome_logs ? '' : "\033[0;91m"
-        colorcodes['igreen']      = monochrome_logs ? '' : "\033[0;92m"
-        colorcodes['iyellow']     = monochrome_logs ? '' : "\033[0;93m"
-        colorcodes['iblue']       = monochrome_logs ? '' : "\033[0;94m"
-        colorcodes['ipurple']     = monochrome_logs ? '' : "\033[0;95m"
-        colorcodes['icyan']       = monochrome_logs ? '' : "\033[0;96m"
-        colorcodes['iwhite']      = monochrome_logs ? '' : "\033[0;97m"
-
-        // Bold High Intensity
-        colorcodes['biblack']     = monochrome_logs ? '' : "\033[1;90m"
-        colorcodes['bired']       = monochrome_logs ? '' : "\033[1;91m"
-        colorcodes['bigreen']     = monochrome_logs ? '' : "\033[1;92m"
-        colorcodes['biyellow']    = monochrome_logs ? '' : "\033[1;93m"
-        colorcodes['biblue']      = monochrome_logs ? '' : "\033[1;94m"
-        colorcodes['bipurple']    = monochrome_logs ? '' : "\033[1;95m"
-        colorcodes['bicyan']      = monochrome_logs ? '' : "\033[1;96m"
-        colorcodes['biwhite']     = monochrome_logs ? '' : "\033[1;97m"
-
-        return colorcodes
-    }
-
-    static String dashed_line(monochrome_logs) {
-        Map colors = log_colours(monochrome_logs)
-        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-    }
-
-    /*
-    Method to actually read in JSON file using Groovy.
-    Group (as Key), values are all parameters
-        - Parameter1 as Key, Description as Value
-        - Parameter2 as Key, Description as Value
-        ....
-    Group
-        -
-    */
-    private static LinkedHashMap params_read(String json_schema) throws Exception {
-        def json = new File(json_schema).text
-        def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions')
-        def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties')
-        /* Tree looks like this in nf-core schema
-         * definitions <- this is what the first get('definitions') gets us
-             group 1
-               title
-               description
-                 properties
-                   parameter 1
-                     type
-                     description
-                   parameter 2
-                     type
-                     description
-             group 2
-               title
-               description
-                 properties
-                   parameter 1
-                     type
-                     description
-         * properties <- parameters can also be ungrouped, outside of definitions
-            parameter 1
-             type
-             description
-        */
-
-        // Grouped params
-        def params_map = new LinkedHashMap()
-        schema_definitions.each { key, val ->
-            def Map group = schema_definitions."$key".properties // Gets the property object of the group
-            def title = schema_definitions."$key".title
-            def sub_params = new LinkedHashMap()
-            group.each { innerkey, value ->
-                sub_params.put(innerkey, value)
-            }
-            params_map.put(title, sub_params)
-        }
-
-        // Ungrouped params
-        def ungrouped_params = new LinkedHashMap()
-        schema_properties.each { innerkey, value ->
-            ungrouped_params.put(innerkey, value)
-        }
-        params_map.put("Other parameters", ungrouped_params)
-
-        return params_map
-    }
-
-    /*
-     * Get maximum number of characters across all parameter names
-     */
-    private static Integer params_max_chars(params_map) {
-        Integer max_chars = 0
-        for (group in params_map.keySet()) {
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            for (param in group_params.keySet()) {
-                if (param.size() > max_chars) {
-                    max_chars = param.size()
-                }
-            }
-        }
-        return max_chars
-    }
-
-    /*
-     * Beautify parameters for --help
-     */
-    private static String params_help(workflow, params, json_schema, command) {
-        Map colors = log_colours(params.monochrome_logs)
+    //
+    // Beautify parameters for --help
+    //
+    public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') {
+        Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
         Integer num_hidden = 0
         String output  = ''
         output        += 'Typical pipeline command:\n\n'
         output        += "  ${colors.cyan}${command}${colors.reset}\n\n"
-        Map params_map = params_load(json_schema)
-        Integer max_chars  = params_max_chars(params_map) + 1
+        Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
+        Integer max_chars  = paramsMaxChars(params_map) + 1
         Integer desc_indent = max_chars + 14
         Integer dec_linewidth = 160 - desc_indent
         for (group in params_map.keySet()) {
@@ -469,18 +228,17 @@ class NfcoreSchema {
                 output += group_output
             }
         }
-        output += dashed_line(params.monochrome_logs)
         if (num_hidden > 0){
-            output += colors.dim + "\n Hiding $num_hidden params, use --show_hidden_params to show.\n" + colors.reset
-            output += dashed_line(params.monochrome_logs)
+            output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset
         }
+        output += NfcoreTemplate.dashedLine(params.monochrome_logs)
         return output
     }
 
-    /*
-     * Groovy Map summarising parameters/workflow options used by the pipeline
-     */
-    private static LinkedHashMap params_summary_map(workflow, params, json_schema) {
+    //
+    // Groovy Map summarising parameters/workflow options used by the pipeline
+    //
+    public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') {
         // Get a selection of core Nextflow workflow options
         def Map workflow_summary = [:]
         if (workflow.revision) {
@@ -503,7 +261,7 @@ class NfcoreSchema {
         // Get pipeline parameters defined in JSON Schema
         def Map params_summary = [:]
         def blacklist  = ['hostnames']
-        def params_map = params_load(json_schema)
+        def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
         for (group in params_map.keySet()) {
             def sub_params = new LinkedHashMap()
             def group_params = params_map.get(group)  // This gets the parameters of that particular group
@@ -546,14 +304,14 @@ class NfcoreSchema {
         return [ 'Core Nextflow options' : workflow_summary ] << params_summary
     }
 
-    /*
-     * Beautify parameters for summary and return as string
-     */
-    private static String params_summary_log(workflow, params, json_schema) {
-        Map colors = log_colours(params.monochrome_logs)
+    //
+    // Beautify parameters for summary and return as string
+    //
+    public static String paramsSummaryLog(workflow, params) {
+        Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
         String output  = ''
-        def params_map = params_summary_map(workflow, params, json_schema)
-        def max_chars  = params_max_chars(params_map)
+        def params_map = paramsSummaryMap(workflow, params)
+        def max_chars  = paramsMaxChars(params_map)
         for (group in params_map.keySet()) {
             def group_params = params_map.get(group)  // This gets the parameters of that particular group
             if (group_params) {
@@ -564,10 +322,196 @@ class NfcoreSchema {
                 output += '\n'
             }
         }
-        output += dashed_line(params.monochrome_logs)
-        output += colors.dim + "\n Only displaying parameters that differ from defaults.\n" + colors.reset
-        output += dashed_line(params.monochrome_logs)
+        output += "!! Only displaying parameters that differ from the pipeline defaults !!\n"
+        output += NfcoreTemplate.dashedLine(params.monochrome_logs)
         return output
     }
 
+    //
+    // Loop over nested exceptions and print the causingException
+    //
+    private static void printExceptions(ex_json, params_json, log) {
+        def causingExceptions = ex_json['causingExceptions']
+        if (causingExceptions.length() == 0) {
+            def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
+            // Missing required param
+            if (m.matches()) {
+                log.error "* Missing required parameter: --${m[0][1]}"
+            }
+            // Other base-level error
+            else if (ex_json['pointerToViolation'] == '#') {
+                log.error "* ${ex_json['message']}"
+            }
+            // Error with specific param
+            else {
+                def param = ex_json['pointerToViolation'] - ~/^#\//
+                def param_val = params_json[param].toString()
+                log.error "* --${param}: ${ex_json['message']} (${param_val})"
+            }
+        }
+        for (ex in causingExceptions) {
+            printExceptions(ex, params_json, log)
+        }
+    }
+
+    //
+    // Remove an element from a JSONArray
+    //
+    private static JSONArray removeElement(json_array, element) {
+        def list = []
+        int len = json_array.length()
+        for (int i=0;i<len;i++){
+            list.add(json_array.get(i).toString())
+        }
+        list.remove(element)
+        JSONArray jsArray = new JSONArray(list)
+        return jsArray
+    }
+
+    //
+    // Remove ignored parameters
+    //
+    private static JSONObject removeIgnoredParams(raw_schema, params) {
+        // Remove anything that's in params.schema_ignore_params
+        params.schema_ignore_params.split(',').each{ ignore_param ->
+            if(raw_schema.keySet().contains('definitions')){
+                raw_schema.definitions.each { definition ->
+                    for (key in definition.keySet()){
+                        if (definition[key].get("properties").keySet().contains(ignore_param)){
+                            // Remove the param to ignore
+                            definition[key].get("properties").remove(ignore_param)
+                            // If the param was required, change this
+                            if (definition[key].has("required")) {
+                                def cleaned_required = removeElement(definition[key].required, ignore_param)
+                                definition[key].put("required", cleaned_required)
+                            }
+                        }
+                    }
+                }
+            }
+            if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) {
+                raw_schema.get("properties").remove(ignore_param)
+            }
+            if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) {
+                def cleaned_required = removeElement(raw_schema.required, ignore_param)
+                raw_schema.put("required", cleaned_required)
+            }
+        }
+        return raw_schema
+    }
+
+    //
+    // Clean and check parameters relative to Nextflow native classes
+    //
+    private static Map cleanParameters(params) {
+        def new_params = params.getClass().newInstance(params)
+        for (p in params) {
+            // remove anything evaluating to false
+            if (!p['value']) {
+                new_params.remove(p.key)
+            }
+            // Cast MemoryUnit to String
+            if (p['value'].getClass() == nextflow.util.MemoryUnit) {
+                new_params.replace(p.key, p['value'].toString())
+            }
+            // Cast Duration to String
+            if (p['value'].getClass() == nextflow.util.Duration) {
+                new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
+            }
+            // Cast LinkedHashMap to String
+            if (p['value'].getClass() == LinkedHashMap) {
+                new_params.replace(p.key, p['value'].toString())
+            }
+        }
+        return new_params
+    }
+
+    //
+    // This function tries to read a JSON params file
+    //
+    private static LinkedHashMap paramsLoad(String json_schema) {
+        def params_map = new LinkedHashMap()
+        try {
+            params_map = paramsRead(json_schema)
+        } catch (Exception e) {
+            println "Could not read parameters settings from JSON. $e"
+            params_map = new LinkedHashMap()
+        }
+        return params_map
+    }
+
+    //
+    // Method to actually read in JSON file using Groovy.
+    // Group (as Key), values are all parameters
+    //    - Parameter1 as Key, Description as Value
+    //    - Parameter2 as Key, Description as Value
+    //    ....
+    // Group
+    //    -
+    private static LinkedHashMap paramsRead(String json_schema) throws Exception {
+        def json = new File(json_schema).text
+        def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions')
+        def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties')
+        /* Tree looks like this in nf-core schema
+        * definitions <- this is what the first get('definitions') gets us
+                group 1
+                    title
+                    description
+                        properties
+                        parameter 1
+                            type
+                            description
+                        parameter 2
+                            type
+                            description
+                group 2
+                    title
+                    description
+                        properties
+                        parameter 1
+                            type
+                            description
+        * properties <- parameters can also be ungrouped, outside of definitions
+                parameter 1
+                    type
+                    description
+        */
+
+        // Grouped params
+        def params_map = new LinkedHashMap()
+        schema_definitions.each { key, val ->
+            def Map group = schema_definitions."$key".properties // Gets the property object of the group
+            def title = schema_definitions."$key".title
+            def sub_params = new LinkedHashMap()
+            group.each { innerkey, value ->
+                sub_params.put(innerkey, value)
+            }
+            params_map.put(title, sub_params)
+        }
+
+        // Ungrouped params
+        def ungrouped_params = new LinkedHashMap()
+        schema_properties.each { innerkey, value ->
+            ungrouped_params.put(innerkey, value)
+        }
+        params_map.put("Other parameters", ungrouped_params)
+
+        return params_map
+    }
+
+    //
+    // Get maximum number of characters across all parameter names
+    //
+    private static Integer paramsMaxChars(params_map) {
+        Integer max_chars = 0
+        for (group in params_map.keySet()) {
+            def group_params = params_map.get(group)  // This gets the parameters of that particular group
+            for (param in group_params.keySet()) {
+                if (param.size() > max_chars) {
+                    max_chars = param.size()
+                }
+            }
+        }
+        return max_chars
+    }
 }
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
new file mode 100755
index 0000000000000000000000000000000000000000..b6e689ec883ee85fd1f884c7d9c4960062ba5db8
--- /dev/null
+++ b/lib/NfcoreTemplate.groovy
@@ -0,0 +1,266 @@
+//
+// This file holds several functions used within the nf-core pipeline template.
+//
+
+import org.yaml.snakeyaml.Yaml
+
+class NfcoreTemplate {
+
+    //
+    // Check AWS Batch related parameters have been specified correctly
+    //
+    public static void awsBatch(workflow, params) {
+        if (workflow.profile.contains('awsbatch')) {
+            // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
+            assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
+            // Check outdir paths to be S3 buckets if running on AWSBatch
+            assert params.outdir.startsWith('s3:')       : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
+        }
+    }
+
+    //
+    // Check params.hostnames
+    //
+    public static void hostName(workflow, params, log) {
+        Map colors = logColours(params.monochrome_logs)
+        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.info "=${colors.yellow}====================================================${colors.reset}=\n" +
+                            "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
+                            "      but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
+                            "      ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
+                            "=${colors.yellow}====================================================${colors.reset}="
+                    }
+                }
+            }
+        }
+    }
+
+    //
+    // Construct and send completion email
+    //
+    public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
+
+        // Set up the e-mail variables
+        def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+        if (!workflow.success) {
+            subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        }
+
+        def summary = [:]
+        for (group in summary_params.keySet()) {
+            summary << summary_params[group]
+        }
+
+        def misc_fields = [:]
+        misc_fields['Date Started']              = workflow.start
+        misc_fields['Date Completed']            = workflow.complete
+        misc_fields['Pipeline script file path'] = workflow.scriptFile
+        misc_fields['Pipeline script hash ID']   = workflow.scriptId
+        if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
+        if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+        if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
+        misc_fields['Nextflow Version']           = workflow.nextflow.version
+        misc_fields['Nextflow Build']             = workflow.nextflow.build
+        misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+        def email_fields = [:]
+        email_fields['version']      = workflow.manifest.version
+        email_fields['runName']      = workflow.runName
+        email_fields['success']      = workflow.success
+        email_fields['dateComplete'] = workflow.complete
+        email_fields['duration']     = workflow.duration
+        email_fields['exitStatus']   = workflow.exitStatus
+        email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+        email_fields['errorReport']  = (workflow.errorReport ?: 'None')
+        email_fields['commandLine']  = workflow.commandLine
+        email_fields['projectDir']   = workflow.projectDir
+        email_fields['summary']      = summary << misc_fields
+
+        // On success try attach the multiqc report
+        def mqc_report = null
+        try {
+            if (workflow.success) {
+                mqc_report = multiqc_report.getVal()
+                if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+                    if (mqc_report.size() > 1) {
+                        log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    }
+                    mqc_report = mqc_report[0]
+                }
+            }
+        } catch (all) {
+            if (multiqc_report) {
+                log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            }
+        }
+
+        // Check if we are only sending emails on failure
+        def email_address = params.email
+        if (!params.email && params.email_on_fail && !workflow.success) {
+            email_address = params.email_on_fail
+        }
+
+        // Render the TXT template
+        def engine       = new groovy.text.GStringTemplateEngine()
+        def tf           = new File("$projectDir/assets/email_template.txt")
+        def txt_template = engine.createTemplate(tf).make(email_fields)
+        def email_txt    = txt_template.toString()
+
+        // Render the HTML template
+        def hf            = new File("$projectDir/assets/email_template.html")
+        def html_template = engine.createTemplate(hf).make(email_fields)
+        def email_html    = html_template.toString()
+
+        // Render the sendmail template
+        def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit
+        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+        def sf                     = new File("$projectDir/assets/sendmail_template.txt")
+        def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+        def sendmail_html          = sendmail_template.toString()
+
+        // Send the HTML e-mail
+        Map colors = logColours(params.monochrome_logs)
+        if (email_address) {
+            try {
+                if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+                // Try to send HTML e-mail using sendmail
+                [ 'sendmail', '-t' ].execute() << sendmail_html
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+            } catch (all) {
+                // Catch failures and try with plaintext
+                def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
+                    mail_cmd += [ '-A', mqc_report ]
+                }
+                mail_cmd.execute() << email_html
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            }
+        }
+
+        // Write summary e-mail HTML to a file
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+        def output_hf = new File(output_d, "pipeline_report.html")
+        output_hf.withWriter { w -> w << email_html }
+        def output_tf = new File(output_d, "pipeline_report.txt")
+        output_tf.withWriter { w -> w << email_txt }
+    }
+
+    //
+    // Print pipeline summary on completion
+    //
+    public static void summary(workflow, params, log) {
+        Map colors = logColours(params.monochrome_logs)
+        if (workflow.success) {
+            if (workflow.stats.ignoredCount == 0) {
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
+            } else {
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            }
+        } else {
+            hostName(workflow, params, log)
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+        }
+    }
+
+    //
+    // ANSII Colours used for terminal logging
+    //
+    public static Map logColours(Boolean monochrome_logs) {
+        Map colorcodes = [:]
+
+        // Reset / Meta
+        colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
+        colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
+        colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
+        colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+        colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
+        colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
+        colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
+
+        // Regular Colors
+        colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
+        colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
+        colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
+        colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
+        colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
+        colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
+        colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
+        colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+
+        // Bold
+        colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
+        colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
+        colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
+        colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
+        colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
+        colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
+        colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
+        colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+
+        // Underline
+        colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
+        colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
+        colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
+        colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
+        colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
+        colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
+        colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
+        colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+
+        // High Intensity
+        colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
+        colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
+        colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
+        colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
+        colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
+        colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
+        colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
+        colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+
+        // Bold High Intensity
+        colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
+        colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
+        colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
+        colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
+        colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
+        colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
+        colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
+        colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+
+        return colorcodes
+    }
+
+    //
+    // Does what is says on the tin
+    //
+    public static String dashedLine(monochrome_logs) {
+        Map colors = logColours(monochrome_logs)
+        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+    }
+
+    //
+    // nf-core logo
+    //
+    public static String logo(workflow, monochrome_logs) {
+        Map colors = logColours(monochrome_logs)
+        String.format(
+            """\n
+            ${dashedLine(monochrome_logs)}
+                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                    ${colors.green}`._,._,\'${colors.reset}
+            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+            ${dashedLine(monochrome_logs)}
+            """.stripIndent()
+        )
+    }
+}
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
new file mode 100755
index 0000000000000000000000000000000000000000..18173e98503206c71e7cfc1615bfbfb6202c1198
--- /dev/null
+++ b/lib/Utils.groovy
@@ -0,0 +1,47 @@
+//
+// This file holds several Groovy functions that could be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+
+class Utils {
+
+    //
+    // When running with -profile conda, warn if channels have not been set-up appropriately
+    //
+    public static void checkCondaChannels(log) {
+        Yaml parser = new Yaml()
+        def channels = []
+        try {
+            def config = parser.load("conda config --show channels".execute().text)
+            channels = config.channels
+        } catch(NullPointerException | IOException e) {
+            log.warn "Could not verify conda channel configuration."
+            return
+        }
+
+        // Check that all channels are present
+        def required_channels = ['conda-forge', 'bioconda', 'defaults']
+        def conda_check_failed = !required_channels.every { ch -> ch in channels }
+
+        // Check that they are in the right order
+        conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
+        conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
+
+        if (conda_check_failed) {
+            log.warn "=============================================================================\n" +
+                "  There is a problem with your Conda configuration!\n\n" +
+                "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
+                "  Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
+                "  NB: The order of the channels matters!\n" +
+                "==================================================================================="
+        }
+    }
+
+    //
+    // Join module args with appropriate spacing
+    //
+    public static String joinModuleArgs(args_list) {
+        return ' ' + args_list.join(' ')
+    }
+}
diff --git a/lib/WorkflowHic.groovy b/lib/WorkflowHic.groovy
new file mode 100755
index 0000000000000000000000000000000000000000..5381157ff81cd224ecdeebb857b5f68332145fb5
--- /dev/null
+++ b/lib/WorkflowHic.groovy
@@ -0,0 +1,59 @@
+//
+// This file holds several functions specific to the workflow/hic.nf in the nf-core/hic pipeline
+//
+
+class WorkflowHic {
+
+    //
+    // Check and validate parameters
+    //
+    public static void initialise(params, log) {
+        genomeExistsError(params, log)
+
+        if (!params.fasta) {
+            log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
+            System.exit(1)
+        }
+    }
+
+    //
+    // Get workflow summary for MultiQC
+    //
+    public static String paramsSummaryMultiqc(workflow, summary) {
+        String summary_section = ''
+        for (group in summary.keySet()) {
+            def group_params = summary.get(group)  // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                for (param in group_params.keySet()) {
+                    summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                }
+                summary_section += "    </dl>\n"
+            }
+        }
+
+        String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+        yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
+        yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+        yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+        yaml_file_text        += "plot_type: 'html'\n"
+        yaml_file_text        += "data: |\n"
+        yaml_file_text        += "${summary_section}"
+        return yaml_file_text
+    }
+
+    //
+    // Exit pipeline if incorrect --genome key provided
+    //
+    private static void genomeExistsError(params, log) {
+        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+            log.error "=============================================================================\n" +
+                "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
+                "  Currently, the available genome keys are:\n" +
+                "  ${params.genomes.keySet().join(", ")}\n" +
+                "==================================================================================="
+            System.exit(1)
+        }
+    }
+}
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
new file mode 100755
index 0000000000000000000000000000000000000000..92eb1766e1d7763ccc40bcefc92b56a28544a4b1
--- /dev/null
+++ b/lib/WorkflowMain.groovy
@@ -0,0 +1,94 @@
+//
+// This file holds several functions specific to the main.nf workflow in the nf-core/hic pipeline
+//
+
+class WorkflowMain {
+
+    //
+    // Citation string for pipeline
+    //
+    public static String citation(workflow) {
+        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+            // TODO nf-core: Add Zenodo DOI for pipeline after first release
+            //"* The pipeline\n" +
+            //"  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
+            "* The nf-core framework\n" +
+            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+            "* Software dependencies\n" +
+            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    }
+
+    //
+    // Print help to screen if required
+    //
+    public static String help(workflow, params, log) {
+        def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+        def help_string = ''
+        help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
+        help_string += NfcoreSchema.paramsHelp(workflow, params, command)
+        help_string += '\n' + citation(workflow) + '\n'
+        help_string += NfcoreTemplate.dashedLine(params.monochrome_logs)
+        return help_string
+    }
+
+    //
+    // Print parameter summary log to screen
+    //
+    public static String paramsSummaryLog(workflow, params, log) {
+        def summary_log = ''
+        summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
+        summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
+        summary_log += '\n' + citation(workflow) + '\n'
+        summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
+        return summary_log
+    }
+
+    //
+    // Validate parameters and print summary to screen
+    //
+    public static void initialise(workflow, params, log) {
+        // Print help to screen if required
+        if (params.help) {
+            log.info help(workflow, params, log)
+            System.exit(0)
+        }
+
+        // Validate workflow parameters via the JSON schema
+        if (params.validate_params) {
+            NfcoreSchema.validateParameters(workflow, params, log)
+        }
+
+        // Print parameter summary log to screen
+        log.info paramsSummaryLog(workflow, params, log)
+
+        // Check that conda channels are set-up correctly
+        if (params.enable_conda) {
+            Utils.checkCondaChannels(log)
+        }
+
+        // Check AWS batch settings
+        NfcoreTemplate.awsBatch(workflow, params)
+
+        // Check the hostnames against configured profiles
+        NfcoreTemplate.hostName(workflow, params, log)
+
+        // Check input has been provided
+        if (!params.input) {
+            log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
+            System.exit(1)
+        }
+    }
+
+    //
+    // Get attribute from genome config file e.g. fasta
+    //
+    public static String getGenomeAttribute(params, attribute) {
+        def val = ''
+        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+            if (params.genomes[ params.genome ].containsKey(attribute)) {
+                val = params.genomes[ params.genome ][ attribute ]
+            }
+        }
+        return val
+    }
+}
diff --git a/main.nf b/main.nf
index 806b8a3c43d13cbc5fe448d82f8851d7580941e7..59b966325e9decf9ccb8b91afa014ac82cb8dd86 100644
--- a/main.nf
+++ b/main.nf
@@ -1,390 +1,63 @@
 #!/usr/bin/env nextflow
 /*
 ========================================================================================
-                         nf-core/hic
+    nf-core/hic
 ========================================================================================
- nf-core/hic Analysis Pipeline.
- #### Homepage / Documentation
- https://github.com/nf-core/hic
+    Github : https://github.com/nf-core/hic
+    Website: https://nf-co.re/hic
+    Slack  : https://nfcore.slack.com/channels/hic
 ----------------------------------------------------------------------------------------
 */
 
-log.info Headers.nf_core(workflow, params.monochrome_logs)
-
-////////////////////////////////////////////////////
-/* --               PRINT HELP                 -- */
-////////////////////////////////////////////////////+
-def json_schema = "$projectDir/nextflow_schema.json"
-if (params.help) {
-    def command = "nextflow run nf-core/hic --input '*_R{1,2}.fastq.gz' -profile docker"
-    log.info NfcoreSchema.params_help(workflow, params, json_schema, command)
-    exit 0
-}
-
-////////////////////////////////////////////////////
-/* --         VALIDATE PARAMETERS              -- */
-////////////////////////////////////////////////////+
-if (params.validate_params) {
-    NfcoreSchema.validateParameters(params, json_schema, log)
-}
-
-////////////////////////////////////////////////////
-/* --     Collect configuration parameters     -- */
-////////////////////////////////////////////////////
-
-// Check if genome exists in the config file
-if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-    exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(', ')}"
-}
-
-// TODO nf-core: Add any reference files that are needed
-// Configurable reference genomes
-//
-// NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
-// If you want to use the channel below in a process, define the following:
-//   input:
-//   file fasta from ch_fasta
-//
-params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
-if (params.fasta) { ch_fasta = file(params.fasta, checkIfExists: true) }
-
-// Check AWS batch settings
-if (workflow.profile.contains('awsbatch')) {
-    // AWSBatch sanity checking
-    if (!params.awsqueue || !params.awsregion) exit 1, 'Specify correct --awsqueue and --awsregion parameters on AWSBatch!'
-    // Check outdir paths to be S3 buckets if running on AWSBatch
-    // related: https://github.com/nextflow-io/nextflow/issues/813
-    if (!params.outdir.startsWith('s3:')) exit 1, 'Outdir not on S3 - specify S3 Bucket to run on AWSBatch!'
-    // Prevent trace files to be stored on S3 since S3 does not support rolling files.
-    if (params.tracedir.startsWith('s3:')) exit 1, 'Specify a local tracedir or run without trace! S3 cannot be used for tracefiles.'
-}
-
-// Stage config files
-ch_multiqc_config = file("$projectDir/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("$projectDir/docs/output.md", checkIfExists: true)
-ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
+nextflow.enable.dsl = 2
 
 /*
- * Create a channel for input read files
- */
-if (params.input_paths) {
-    if (params.single_end) {
-        Channel
-            .from(params.input_paths)
-            .map { row -> [ row[0], [ file(row[1][0], checkIfExists: true) ] ] }
-            .ifEmpty { exit 1, 'params.input_paths was empty - no input files supplied' }
-            .into { ch_read_files_fastqc; ch_read_files_trimming }
-    } else {
-        Channel
-            .from(params.input_paths)
-            .map { row -> [ row[0], [ file(row[1][0], checkIfExists: true), file(row[1][1], checkIfExists: true) ] ] }
-            .ifEmpty { exit 1, 'params.input_paths was empty - no input files supplied' }
-            .into { ch_read_files_fastqc; ch_read_files_trimming }
-    }
-} else {
-    Channel
-        .fromFilePairs(params.input, size: params.single_end ? 1 : 2)
-        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.input}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --single_end on the command line." }
-        .into { ch_read_files_fastqc; ch_read_files_trimming }
-}
-
-////////////////////////////////////////////////////
-/* --         PRINT PARAMETER SUMMARY          -- */
-////////////////////////////////////////////////////
-log.info NfcoreSchema.params_summary_log(workflow, params, json_schema)
-
-// Header log info
-def summary = [:]
-if (workflow.revision) summary['Pipeline Release'] = workflow.revision
-summary['Run Name']         = workflow.runName
-// TODO nf-core: Report custom parameters here
-summary['Input']            = params.input
-summary['Fasta Ref']        = params.fasta
-summary['Data Type']        = params.single_end ? 'Single-End' : 'Paired-End'
-summary['Max Resources']    = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
-if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
-summary['Output dir']       = params.outdir
-summary['Launch dir']       = workflow.launchDir
-summary['Working dir']      = workflow.workDir
-summary['Script dir']       = workflow.projectDir
-summary['User']             = workflow.userName
-if (workflow.profile.contains('awsbatch')) {
-    summary['AWS Region']   = params.awsregion
-    summary['AWS Queue']    = params.awsqueue
-    summary['AWS CLI']      = params.awscli
-}
-summary['Config Profile'] = workflow.profile
-if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description
-if (params.config_profile_contact)     summary['Config Profile Contact']     = params.config_profile_contact
-if (params.config_profile_url)         summary['Config Profile URL']         = params.config_profile_url
-summary['Config Files'] = workflow.configFiles.join(', ')
-if (params.email || params.email_on_fail) {
-    summary['E-mail Address']    = params.email
-    summary['E-mail on failure'] = params.email_on_fail
-    summary['MultiQC maxsize']   = params.max_multiqc_email_size
-}
-
-// Check the hostnames against configured profiles
-checkHostname()
-
-Channel.from(summary.collect{ [it.key, it.value] })
-    .map { k,v -> "<dt>$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'
-    section_href: 'https://github.com/nf-core/hic'
-    plot_type: 'html'
-    data: |
-        <dl class=\"dl-horizontal\">
-            $x
-        </dl>
-    """.stripIndent() }
-    .set { ch_workflow_summary }
-
-/*
- * Parse software version numbers
- */
-process get_software_versions {
-    publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode,
-        saveAs: { filename ->
-                      if (filename.indexOf('.csv') > 0) filename
-                      else null
-        }
-
-    output:
-    file 'software_versions_mqc.yaml' into ch_software_versions_yaml
-    file 'software_versions.csv'
+========================================================================================
+    GENOME PARAMETER VALUES
+========================================================================================
+*/
 
-    script:
-    // TODO nf-core: Get all tools to print their version number here
-    """
-    echo $workflow.manifest.version > v_pipeline.txt
-    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
-    """
-}
+params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
 
 /*
- * STEP 1 - FastQC
- */
-process fastqc {
-    tag "$name"
-    label 'process_medium'
-    publishDir "${params.outdir}/fastqc", mode: params.publish_dir_mode,
-        saveAs: { filename ->
-                      filename.indexOf('.zip') > 0 ? "zips/$filename" : "$filename"
-        }
-
-    input:
-    set val(name), file(reads) from ch_read_files_fastqc
-
-    output:
-    file '*_fastqc.{zip,html}' into ch_fastqc_results
+========================================================================================
+    VALIDATE & PRINT PARAMETER SUMMARY
+========================================================================================
+*/
 
-    script:
-    """
-    fastqc --quiet --threads $task.cpus $reads
-    """
-}
+WorkflowMain.initialise(workflow, params, log)
 
 /*
- * STEP 2 - MultiQC
- */
-process multiqc {
-    publishDir "${params.outdir}/MultiQC", mode: params.publish_dir_mode
-
-    input:
-    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 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")
+========================================================================================
+    NAMED WORKFLOW FOR PIPELINE
+========================================================================================
+*/
 
-    output:
-    file "*multiqc_report.html" into ch_multiqc_report
-    file "*_data"
-    file "multiqc_plots"
+include { HIC } from './workflows/hic'
 
-    script:
-    rtitle = ''
-    rfilename = ''
-    if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
-        rtitle = "--title \"${workflow.runName}\""
-        rfilename = "--filename " + workflow.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 $custom_config_file .
-    """
+//
+// WORKFLOW: Run main nf-core/hic analysis pipeline
+//
+workflow NFCORE_HIC {
+    HIC ()
 }
 
 /*
- * STEP 3 - Output Description HTML
- */
-process output_documentation {
-    publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode
-
-    input:
-    file output_docs from ch_output_docs
-    file images from ch_output_docs_images
-
-    output:
-    file 'results_description.html'
+========================================================================================
+    RUN ALL WORKFLOWS
+========================================================================================
+*/
 
-    script:
-    """
-    markdown_to_html.py $output_docs -o results_description.html
-    """
+//
+// WORKFLOW: Execute a single named workflow for the pipeline
+// See: https://github.com/nf-core/rnaseq/issues/619
+//
+workflow {
+    NFCORE_HIC ()
 }
 
 /*
- * Completion e-mail notification
- */
-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"
-    }
-    def email_fields = [:]
-    email_fields['version'] = workflow.manifest.version
-    email_fields['runName'] = workflow.runName
-    email_fields['success'] = workflow.success
-    email_fields['dateComplete'] = workflow.complete
-    email_fields['duration'] = workflow.duration
-    email_fields['exitStatus'] = workflow.exitStatus
-    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-    email_fields['errorReport'] = (workflow.errorReport ?: 'None')
-    email_fields['commandLine'] = workflow.commandLine
-    email_fields['projectDir'] = workflow.projectDir
-    email_fields['summary'] = summary
-    email_fields['summary']['Date Started'] = workflow.start
-    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
-    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("$projectDir/assets/email_template.txt")
-    def txt_template = engine.createTemplate(tf).make(email_fields)
-    def email_txt = txt_template.toString()
-
-    // Render the HTML template
-    def hf = new File("$projectDir/assets/email_template.html")
-    def html_template = engine.createTemplate(hf).make(email_fields)
-    def email_html = html_template.toString()
-
-    // Render the sendmail template
-    def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
-    def sf = new File("$projectDir/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 (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 $email_address (sendmail)"
-        } catch (all) {
-            // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-            if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
-              mail_cmd += [ '-A', mqc_report ]
-            }
-            mail_cmd.execute() << email_html
-            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}/pipeline_info/")
-    if (!output_d.exists()) {
-        output_d.mkdirs()
-    }
-    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")
-    output_tf.withWriter { w -> w << email_txt }
-
-    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${c_reset}-"
-    }
-
-}
-
-workflow.onError {
-    // Print unexpected parameters - easiest is to just rerun validation
-    NfcoreSchema.validateParameters(params, json_schema, log)
-}
-
-def checkHostname() {
-    def c_reset = params.monochrome_logs ? '' : "\033[0m"
-    def c_white = params.monochrome_logs ? '' : "\033[0;37m"
-    def c_red = params.monochrome_logs ? '' : "\033[1;91m"
-    def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m"
-    if (params.hostnames) {
-        def hostname = 'hostname'.execute().text.trim()
-        params.hostnames.each { prof, hnames ->
-            hnames.each { hname ->
-                if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
-                    log.error "${c_red}====================================================${c_reset}\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" +
-                            "${c_red}====================================================${c_reset}\n"
-                }
-            }
-        }
-    }
-}
+========================================================================================
+    THE END
+========================================================================================
+*/
diff --git a/modules.json b/modules.json
new file mode 100644
index 0000000000000000000000000000000000000000..a68b1c1a6a7a5f41f235094a0055e1f1751c98de
--- /dev/null
+++ b/modules.json
@@ -0,0 +1,14 @@
+{
+    "name": "nf-core/hic",
+    "homePage": "https://github.com/nf-core/hic",
+    "repos": {
+        "nf-core/modules": {
+            "fastqc": {
+                "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+            },
+            "multiqc": {
+                "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+            }
+        }
+    }
+}
diff --git a/modules/local/functions.nf b/modules/local/functions.nf
new file mode 100644
index 0000000000000000000000000000000000000000..da9da093d3f6025e328759a12adc2c1c9ede0d03
--- /dev/null
+++ b/modules/local/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
new file mode 100644
index 0000000000000000000000000000000000000000..9dc52498ede5820f4590cc1199e1fef34083ef65
--- /dev/null
+++ b/modules/local/get_software_versions.nf
@@ -0,0 +1,33 @@
+// Import generic module functions
+include { saveFiles } from './functions'
+
+params.options = [:]
+
+process GET_SOFTWARE_VERSIONS {
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
+
+    cache false
+
+    input:
+    path versions
+
+    output:
+    path "software_versions.tsv"     , emit: tsv
+    path 'software_versions_mqc.yaml', emit: yaml
+
+    script: // This script is bundled with the pipeline, in nf-core/hic/bin/
+    """
+    echo $workflow.manifest.version > pipeline.version.txt
+    echo $workflow.nextflow.version > nextflow.version.txt
+    scrape_software_versions.py &> software_versions_mqc.yaml
+    """
+}
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
new file mode 100644
index 0000000000000000000000000000000000000000..760a42609b4490aeb7e3edf9186ed7930e9913c1
--- /dev/null
+++ b/modules/local/samplesheet_check.nf
@@ -0,0 +1,31 @@
+// Import generic module functions
+include { saveFiles } from './functions'
+
+params.options = [:]
+
+process SAMPLESHEET_CHECK {
+    tag "$samplesheet"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
+
+    input:
+    path samplesheet
+
+    output:
+    path '*.csv'
+
+    script: // This script is bundled with the pipeline, in nf-core/hic/bin/
+    """
+    check_samplesheet.py \\
+        $samplesheet \\
+        samplesheet.valid.csv
+    """
+}
diff --git a/modules/nf-core/modules/fastqc/functions.nf b/modules/nf-core/modules/fastqc/functions.nf
new file mode 100644
index 0000000000000000000000000000000000000000..da9da093d3f6025e328759a12adc2c1c9ede0d03
--- /dev/null
+++ b/modules/nf-core/modules/fastqc/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..39c327b261f7a590f48f64b6dd0eaf24f44ef926
--- /dev/null
+++ b/modules/nf-core/modules/fastqc/main.nf
@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process FASTQC {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+    } else {
+        container "quay.io/biocontainers/fastqc:0.11.9--0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), path("*.zip") , emit: zip
+    path  "*.version.txt"          , emit: version
+
+    script:
+    // Add soft-links to original FastQs for consistent naming in pipeline
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        """
+        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
+        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
+        """
+    } else {
+        """
+        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
+        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
+        """
+    }
+}
diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml
new file mode 100644
index 0000000000000000000000000000000000000000..8eb9953dce50e37c6ead461861bc39a1436308f2
--- /dev/null
+++ b/modules/nf-core/modules/fastqc/meta.yml
@@ -0,0 +1,51 @@
+name: fastqc
+description: Run FastQC on sequenced reads
+keywords:
+    - quality control
+    - qc
+    - adapters
+    - fastq
+tools:
+    - fastqc:
+        description: |
+            FastQC gives general quality metrics about your reads.
+            It provides information about the quality score distribution
+            across your reads, the per base sequence content (%A/C/G/T).
+            You get information about adapter contamination and other
+            overrepresented sequences.
+        homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+            List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+            respectively.
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - html:
+        type: file
+        description: FastQC report
+        pattern: "*_{fastqc.html}"
+    - zip:
+        type: file
+        description: FastQC report archive
+        pattern: "*_{fastqc.zip}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"
+    - "@grst"
+    - "@ewels"
+    - "@FelixKrueger"
diff --git a/modules/nf-core/modules/multiqc/functions.nf b/modules/nf-core/modules/multiqc/functions.nf
new file mode 100644
index 0000000000000000000000000000000000000000..da9da093d3f6025e328759a12adc2c1c9ede0d03
--- /dev/null
+++ b/modules/nf-core/modules/multiqc/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..da78080024721aee1d944f954150fa9352352aca
--- /dev/null
+++ b/modules/nf-core/modules/multiqc/main.nf
@@ -0,0 +1,35 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process MULTIQC {
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0"
+    } else {
+        container "quay.io/biocontainers/multiqc:1.10.1--py_0"
+    }
+
+    input:
+    path multiqc_files
+
+    output:
+    path "*multiqc_report.html", emit: report
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
+    path "*.version.txt"       , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    multiqc -f $options.args .
+    multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
+    """
+}
diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/modules/multiqc/meta.yml
new file mode 100644
index 0000000000000000000000000000000000000000..532a8bb1eff7f38e4f38dc1e36f2ce1f6c6657d1
--- /dev/null
+++ b/modules/nf-core/modules/multiqc/meta.yml
@@ -0,0 +1,39 @@
+name: MultiQC
+description: Aggregate results from bioinformatics analyses across many samples into a single report
+keywords:
+    - QC
+    - bioinformatics tools
+    - Beautiful stand-alone HTML report
+tools:
+    - multiqc:
+        description: |
+            MultiQC searches a given directory for analysis logs and compiles a HTML report.
+            It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+        homepage: https://multiqc.info/
+        documentation: https://multiqc.info/docs/
+input:
+    - multiqc_files:
+        type: file
+        description: |
+            List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+output:
+    - report:
+        type: file
+        description: MultiQC report file
+        pattern: "multiqc_report.html"
+    - data:
+        type: dir
+        description: MultiQC data dir
+        pattern: "multiqc_data"
+    - plots:
+        type: file
+        description: Plots created by MultiQC
+        pattern: "*_data"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@abhi18av"
+    - "@bunop"
+    - "@drpatelh"
diff --git a/nextflow.config b/nextflow.config
index b1736d02ca90f89bdadda219a961008a015a5512..8c5d7ac6beffe20a5979f989d71d6737a5c87c55 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,130 +1,136 @@
 /*
- * -------------------------------------------------
- *  nf-core/hic Nextflow config file
- * -------------------------------------------------
- * Default config options for all environments.
- */
+========================================================================================
+    nf-core/hic Nextflow config file
+========================================================================================
+    Default config options for all compute environments
+----------------------------------------------------------------------------------------
+*/
 
 // Global default params, used in configs
 params {
 
-  // Workflow flags
-  // TODO nf-core: Specify your pipeline's command line flags
-  genome = false
-  input = null
-  input_paths = null
-  single_end = false
-  outdir = './results'
-  publish_dir_mode = 'copy'
-
-  // Boilerplate options
-  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 = 's3://ngi-igenomes/igenomes'
-  tracedir = "${params.outdir}/pipeline_info"
-  igenomes_ignore = false
-  custom_config_version = 'master'
-  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-  hostnames = false
-  config_profile_name = null
-  config_profile_description = false
-  config_profile_contact = false
-  config_profile_url = false
-  validate_params = true
-  show_hidden_params = false
-  schema_ignore_params = 'genomes,input_paths'
-
-  // Defaults only, expecting to be overwritten
-  max_memory = 128.GB
-  max_cpus = 16
-  max_time = 240.h
+    // TODO nf-core: Specify your pipeline's command line flags
+    // Input options
+    input                      = null
 
-}
+    // References
+    genome                     = null
+    igenomes_base              = 's3://ngi-igenomes/igenomes'
+    igenomes_ignore            = false
+
+    // MultiQC options
+    multiqc_config             = null
+    multiqc_title              = null
+    max_multiqc_email_size     = '25.MB'
+
+    // Boilerplate options
+    outdir                     = './results'
+    tracedir                   = "${params.outdir}/pipeline_info"
+    publish_dir_mode           = 'copy'
+    email                      = null
+    email_on_fail              = null
+    plaintext_email            = false
+    monochrome_logs            = false
+    help                       = false
+    validate_params            = true
+    show_hidden_params         = false
+    schema_ignore_params       = 'genomes,modules'
+    enable_conda               = false
+    singularity_pull_docker_container = false
 
-// Container slug. Stable releases should specify release tag!
-// Developmental code should specify :dev
-process.container = 'nfcore/hic:dev'
+    // Config options
+    custom_config_version      = 'master'
+    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+    hostnames                  = [:]
+    config_profile_description = null
+    config_profile_contact     = null
+    config_profile_url         = null
+    config_profile_name        = null
+
+    // Max resource options
+    // Defaults only, expecting to be overwritten
+    max_memory                 = '128.GB'
+    max_cpus                   = 16
+    max_time                   = '240.h'
+
+}
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+
 // Load nf-core custom profiles from different Institutions
 try {
-  includeConfig "${params.custom_config_base}/nfcore_custom.config"
+    includeConfig "${params.custom_config_base}/nfcore_custom.config"
 } catch (Exception e) {
-  System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
-
-profiles {
-  conda {
-    docker.enabled = false
-    singularity.enabled = false
-    podman.enabled = false
-    shifter.enabled = false
-    charliecloud.enabled = false
-    process.conda = "$projectDir/environment.yml"
-  }
-  debug { process.beforeScript = 'echo $HOSTNAME' }
-  docker {
-    docker.enabled = true
-    singularity.enabled = false
-    podman.enabled = false
-    shifter.enabled = false
-    charliecloud.enabled = false
-    // 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 {
-    docker.enabled = false
-    singularity.enabled = true
-    podman.enabled = false
-    shifter.enabled = false
-    charliecloud.enabled = false
-    singularity.autoMounts = true
-  }
-  podman {
-    singularity.enabled = false
-    docker.enabled = false
-    podman.enabled = true
-    shifter.enabled = false
-    charliecloud.enabled = false
-  }
-  shifter {
-    singularity.enabled = false
-    docker.enabled = false
-    podman.enabled = false
-    shifter.enabled = true
-    charliecloud.enabled = false
-  }
-  charliecloud {
-    singularity.enabled = false
-    docker.enabled = false
-    podman.enabled = false
-    shifter.enabled = false
-    charliecloud.enabled = true
-  }
-  test { includeConfig 'conf/test.config' }
-  test_full { includeConfig 'conf/test_full.config' }
+    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
 // Load igenomes.config if required
 if (!params.igenomes_ignore) {
-  includeConfig 'conf/igenomes.config'
+    includeConfig 'conf/igenomes.config'
+} else {
+    params.genomes = [:]
+}
+
+profiles {
+    debug { process.beforeScript = 'echo $HOSTNAME' }
+    conda {
+        params.enable_conda    = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
+    docker {
+        docker.enabled         = true
+        docker.userEmulation   = true
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
+    singularity {
+        singularity.enabled    = true
+        singularity.autoMounts = true
+        docker.enabled         = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
+    podman {
+        podman.enabled         = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
+    shifter {
+        shifter.enabled        = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        charliecloud.enabled   = false
+    }
+    charliecloud {
+        charliecloud.enabled   = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+    }
+    test      { includeConfig 'conf/test.config'      }
+    test_full { includeConfig 'conf/test_full.config' }
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 env {
-  PYTHONNOUSERSITE = 1
-  R_PROFILE_USER = "/.Rprofile"
-  R_ENVIRON_USER = "/.Renviron"
+    PYTHONNOUSERSITE = 1
+    R_PROFILE_USER   = "/.Rprofile"
+    R_ENVIRON_USER   = "/.Renviron"
 }
 
 // Capture exit codes from upstream processes when piping
@@ -132,61 +138,61 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
-  enabled = true
-  file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
+    enabled = true
+    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
 }
 report {
-  enabled = true
-  file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+    enabled = true
+    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
 }
 trace {
-  enabled = true
-  file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+    enabled = true
+    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
 }
 dag {
-  enabled = true
-  file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
+    enabled = true
+    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
 }
 
 manifest {
-  name = 'nf-core/hic'
-  author = 'Nicolas Servant'
-  homePage = 'https://github.com/nf-core/hic'
-  description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
-  mainScript = 'main.nf'
-  nextflowVersion = '>=20.04.0'
-  version = '1.3.0dev'
+    name            = 'nf-core/hic'
+    author          = 'Nicolas Servant'
+    homePage        = 'https://github.com/nf-core/hic'
+    description     = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
+    mainScript      = 'main.nf'
+    nextflowVersion = '!>=21.04.0'
+    version         = '1.3.0'
 }
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {
-  if (type == 'memory') {
-    try {
-      if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-        return params.max_memory as nextflow.util.MemoryUnit
-      else
-        return obj
-    } catch (all) {
-      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-      return obj
-    }
-  } else if (type == 'time') {
-    try {
-      if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-        return params.max_time as nextflow.util.Duration
-      else
-        return obj
-    } catch (all) {
-      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-      return obj
-    }
-  } else if (type == 'cpus') {
-    try {
-      return Math.min( obj, params.max_cpus as int )
-    } catch (all) {
-      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-      return obj
+    if (type == 'memory') {
+        try {
+            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+                return params.max_memory as nextflow.util.MemoryUnit
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'time') {
+        try {
+            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+                return params.max_time as nextflow.util.Duration
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'cpus') {
+        try {
+            return Math.min( obj, params.max_cpus as int )
+        } catch (all) {
+            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+            return obj
+        }
     }
-  }
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index fa1428978cb58f5d4f118b52ac40ec46f399f8fb..c04fb92dbaf1d7b015a4c77b961cdd23c1d6c76a 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -16,19 +16,17 @@
             "properties": {
                 "input": {
                     "type": "string",
-                    "fa_icon": "fas fa-dna",
-                    "description": "Input FastQ files.",
-                    "help_text": "Use this to specify the location of your input FastQ files. For example:\n\n```bash\n--input 'path/to/data/sample_*_{1,2}.fastq'\n```\n\nPlease note the following requirements:\n\n1. The path must be enclosed in quotes\n2. The path must have at least one `*` wildcard character\n3. When using the pipeline with paired end data, the path must use `{1,2}` notation to specify read pairs.\n\nIf left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`"
-                },
-                "single_end": {
-                    "type": "boolean",
-                    "description": "Specifies that the input is single-end reads.",
-                    "fa_icon": "fas fa-align-center",
-                    "help_text": "By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--single_end` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--input`. For example:\n\n```bash\n--single_end --input '*.fastq'\n```\n\nIt is not possible to run a mixture of single-end and paired-end files in one run."
+                    "format": "file-path",
+                    "mimetype": "text/csv",
+                    "pattern": "\\.csv$",
+                    "schema": "assets/schema_input.json",
+                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
+                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/hic/usage#samplesheet-input).",
+                    "fa_icon": "fas fa-file-csv"
                 },
                 "outdir": {
                     "type": "string",
-                    "description": "The output directory where the results will be saved.",
+                    "description": "Path to the output directory where the results will be saved.",
                     "default": "./results",
                     "fa_icon": "fas fa-folder-open"
                 },
@@ -38,6 +36,11 @@
                     "fa_icon": "fas fa-envelope",
                     "help_text": "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.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
+                },
+                "multiqc_title": {
+                    "type": "string",
+                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
+                    "fa_icon": "fas fa-file-signature"
                 }
             }
         },
@@ -45,22 +48,26 @@
             "title": "Reference genome options",
             "type": "object",
             "fa_icon": "fas fa-dna",
-            "description": "Options for the reference genome indices used to align reads.",
+            "description": "Reference genome related files and options required for the workflow.",
             "properties": {
                 "genome": {
                     "type": "string",
                     "description": "Name of iGenomes reference.",
                     "fa_icon": "fas fa-book",
-                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`.\n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
+                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
                 },
                 "fasta": {
                     "type": "string",
-                    "fa_icon": "fas fa-font",
+                    "format": "file-path",
+                    "mimetype": "text/plain",
+                    "pattern": "\\.fn?a(sta)?(\\.gz)?$",
                     "description": "Path to FASTA genome file.",
-                    "help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible."
+                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
+                    "fa_icon": "far fa-file-code"
                 },
                 "igenomes_base": {
                     "type": "string",
+                    "format": "directory-path",
                     "description": "Directory / URL base for iGenomes references.",
                     "default": "s3://ngi-igenomes/igenomes",
                     "fa_icon": "fas fa-cloud-download-alt",
@@ -75,91 +82,57 @@
                 }
             }
         },
-        "generic_options": {
-            "title": "Generic options",
+        "institutional_config_options": {
+            "title": "Institutional config options",
             "type": "object",
-            "fa_icon": "fas fa-file-import",
-            "description": "Less common options for the pipeline, typically set in a config file.",
-            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+            "fa_icon": "fas fa-university",
+            "description": "Parameters used to describe centralised config profiles. These should not be edited.",
+            "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
             "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-question-circle"
-                },
-                "publish_dir_mode": {
+                "custom_config_version": {
                     "type": "string",
-                    "default": "copy",
+                    "description": "Git commit id for Institutional configs.",
+                    "default": "master",
                     "hidden": true,
-                    "description": "Method used to save pipeline results to output directory.",
-                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
-                    "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ]
-                },
-                "validate_params": {
-                    "type": "boolean",
-                    "description": "Boolean whether to validate parameters against the schema at runtime",
-                    "default": true,
-                    "fa_icon": "fas fa-check-square",
-                    "hidden": true
+                    "fa_icon": "fas fa-users-cog"
                 },
-                "email_on_fail": {
+                "custom_config_base": {
                     "type": "string",
-                    "description": "Email address for completion summary, only when pipeline fails.",
-                    "fa_icon": "fas fa-exclamation-triangle",
-                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
+                    "description": "Base directory for Institutional configs.",
+                    "default": "https://raw.githubusercontent.com/nf-core/configs/master",
                     "hidden": true,
-                    "help_text": "This works exactly as with `--email`, except emails are only sent if the workflow is not successful."
+                    "help_text": "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 this parameter.",
+                    "fa_icon": "fas fa-users-cog"
                 },
-                "plaintext_email": {
-                    "type": "boolean",
-                    "description": "Send plain-text email instead of HTML.",
-                    "fa_icon": "fas fa-remove-format",
+                "hostnames": {
+                    "type": "string",
+                    "description": "Institutional configs hostname.",
                     "hidden": true,
-                    "help_text": "Set to receive plain-text e-mails instead of HTML formatted."
+                    "fa_icon": "fas fa-users-cog"
                 },
-                "max_multiqc_email_size": {
+                "config_profile_name": {
                     "type": "string",
-                    "description": "File size limit when attaching MultiQC reports to summary emails.",
-                    "default": "25.MB",
-                    "fa_icon": "fas fa-file-upload",
+                    "description": "Institutional config name.",
                     "hidden": true,
-                    "help_text": "If file generated by pipeline exceeds the threshold, it will not be attached."
+                    "fa_icon": "fas fa-users-cog"
                 },
-                "monochrome_logs": {
-                    "type": "boolean",
-                    "description": "Do not use coloured log outputs.",
-                    "fa_icon": "fas fa-palette",
+                "config_profile_description": {
+                    "type": "string",
+                    "description": "Institutional config description.",
                     "hidden": true,
-                    "help_text": "Set to disable colourful command line output and live life in monochrome."
+                    "fa_icon": "fas fa-users-cog"
                 },
-                "multiqc_config": {
+                "config_profile_contact": {
                     "type": "string",
-                    "description": "Custom config file to supply to MultiQC.",
-                    "fa_icon": "fas fa-cog",
-                    "hidden": true
+                    "description": "Institutional config contact information.",
+                    "hidden": true,
+                    "fa_icon": "fas fa-users-cog"
                 },
-                "tracedir": {
+                "config_profile_url": {
                     "type": "string",
-                    "description": "Directory to keep pipeline Nextflow logs and reports.",
-                    "default": "${params.outdir}/pipeline_info",
-                    "fa_icon": "fas fa-cogs",
-                    "hidden": true
-                },
-                "show_hidden_params": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
+                    "description": "Institutional config URL link.",
                     "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
+                    "fa_icon": "fas fa-users-cog"
                 }
             }
         },
@@ -172,7 +145,7 @@
             "properties": {
                 "max_cpus": {
                     "type": "integer",
-                    "description": "Maximum number of CPUs that can be requested    for any single job.",
+                    "description": "Maximum number of CPUs that can be requested for any single job.",
                     "default": 16,
                     "fa_icon": "fas fa-microchip",
                     "hidden": true,
@@ -198,58 +171,102 @@
                 }
             }
         },
-        "institutional_config_options": {
-            "title": "Institutional config options",
+        "generic_options": {
+            "title": "Generic options",
             "type": "object",
-            "fa_icon": "fas fa-university",
-            "description": "Parameters used to describe centralised config profiles. These should not be edited.",
-            "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
+            "fa_icon": "fas fa-file-import",
+            "description": "Less common options for the pipeline, typically set in a config file.",
+            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
             "properties": {
-                "custom_config_version": {
+                "help": {
+                    "type": "boolean",
+                    "description": "Display help text.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
+                "publish_dir_mode": {
                     "type": "string",
-                    "description": "Git commit id for Institutional configs.",
-                    "default": "master",
-                    "hidden": true,
-                    "fa_icon": "fas fa-users-cog",
-                    "help_text": "Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default: `master`.\n\n```bash\n## Download and use config file with following git commit id\n--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96\n```"
+                    "default": "copy",
+                    "description": "Method used to save pipeline results to output directory.",
+                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
+                    "fa_icon": "fas fa-copy",
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
+                    "hidden": true
                 },
-                "custom_config_base": {
+                "email_on_fail": {
                     "type": "string",
-                    "description": "Base directory for Institutional configs.",
-                    "default": "https://raw.githubusercontent.com/nf-core/configs/master",
-                    "hidden": true,
-                    "help_text": "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:\n\n```bash\n## Download and unzip the config files\ncd /path/to/my/configs\nwget https://github.com/nf-core/configs/archive/master.zip\nunzip master.zip\n\n## Run the pipeline\ncd /path/to/my/data\nnextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/\n```\n\n> 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.",
-                    "fa_icon": "fas fa-users-cog"
+                    "description": "Email address for completion summary, only when pipeline fails.",
+                    "fa_icon": "fas fa-exclamation-triangle",
+                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
+                    "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
+                    "hidden": true
                 },
-                "hostnames": {
+                "plaintext_email": {
+                    "type": "boolean",
+                    "description": "Send plain-text email instead of HTML.",
+                    "fa_icon": "fas fa-remove-format",
+                    "hidden": true
+                },
+                "max_multiqc_email_size": {
                     "type": "string",
-                    "description": "Institutional configs hostname.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-users-cog"
+                    "description": "File size limit when attaching MultiQC reports to summary emails.",
+                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
+                    "default": "25.MB",
+                    "fa_icon": "fas fa-file-upload",
+                    "hidden": true
                 },
-                "config_profile_name": {
+                "monochrome_logs": {
+                    "type": "boolean",
+                    "description": "Do not use coloured log outputs.",
+                    "fa_icon": "fas fa-palette",
+                    "hidden": true
+                },
+                "multiqc_config": {
                     "type": "string",
-                    "description": "Institutional config name.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-users-cog"
+                    "description": "Custom config file to supply to MultiQC.",
+                    "fa_icon": "fas fa-cog",
+                    "hidden": true
                 },
-                "config_profile_description": {
+                "tracedir": {
                     "type": "string",
-                    "description": "Institutional config description.",
+                    "description": "Directory to keep pipeline Nextflow logs and reports.",
+                    "default": "${params.outdir}/pipeline_info",
+                    "fa_icon": "fas fa-cogs",
+                    "hidden": true
+                },
+                "validate_params": {
+                    "type": "boolean",
+                    "description": "Boolean whether to validate parameters against the schema at runtime",
+                    "default": true,
+                    "fa_icon": "fas fa-check-square",
+                    "hidden": true
+                },
+                "show_hidden_params": {
+                    "type": "boolean",
+                    "fa_icon": "far fa-eye-slash",
+                    "description": "Show all params when using `--help`",
                     "hidden": true,
-                    "fa_icon": "fas fa-users-cog"
+                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
                 },
-                "config_profile_contact": {
-                    "type": "string",
-                    "description": "Institutional config contact information.",
+                "enable_conda": {
+                    "type": "boolean",
+                    "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
                     "hidden": true,
-                    "fa_icon": "fas fa-users-cog"
+                    "fa_icon": "fas fa-bacon"
                 },
-                "config_profile_url": {
-                    "type": "string",
-                    "description": "Institutional config URL link.",
+                "singularity_pull_docker_container": {
+                    "type": "boolean",
+                    "description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.",
                     "hidden": true,
-                    "fa_icon": "fas fa-users-cog"
+                    "fa_icon": "fas fa-toolbox",
+                    "help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues."
                 }
             }
         }
@@ -262,13 +279,13 @@
             "$ref": "#/definitions/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/definitions/institutional_config_options"
         },
         {
             "$ref": "#/definitions/max_job_request_options"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/definitions/generic_options"
         }
     ]
 }
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
new file mode 100644
index 0000000000000000000000000000000000000000..b664bc8caf10c1ee8b810f3108e0eedefc6b398b
--- /dev/null
+++ b/subworkflows/local/input_check.nf
@@ -0,0 +1,42 @@
+//
+// Check input samplesheet and get read channels
+//
+
+params.options = [:]
+
+include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' addParams( options: params.options )
+
+workflow INPUT_CHECK {
+    take:
+    samplesheet // file: /path/to/samplesheet.csv
+
+    main:
+    SAMPLESHEET_CHECK ( samplesheet )
+        .splitCsv ( header:true, sep:',' )
+        .map { create_fastq_channels(it) }
+        .set { reads }
+
+    emit:
+    reads // channel: [ val(meta), [ reads ] ]
+}
+
+// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
+def create_fastq_channels(LinkedHashMap row) {
+    def meta = [:]
+    meta.id           = row.sample
+    meta.single_end   = row.single_end.toBoolean()
+
+    def array = []
+    if (!file(row.fastq_1).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
+    }
+    if (meta.single_end) {
+        array = [ meta, [ file(row.fastq_1) ] ]
+    } else {
+        if (!file(row.fastq_2).exists()) {
+            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
+        }
+        array = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
+    }
+    return array
+}
diff --git a/workflows/hic.nf b/workflows/hic.nf
new file mode 100644
index 0000000000000000000000000000000000000000..7e9a39cb112804fb87c7c740290e873e41bc56a7
--- /dev/null
+++ b/workflows/hic.nf
@@ -0,0 +1,141 @@
+/*
+========================================================================================
+    VALIDATE INPUTS
+========================================================================================
+*/
+
+def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+
+// Validate input parameters
+WorkflowHic.initialise(params, log)
+
+// TODO nf-core: Add all file path parameters for the pipeline to the list below
+// Check input path parameters to see if they exist
+def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ]
+for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
+
+// Check mandatory parameters
+if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
+
+/*
+========================================================================================
+    CONFIG FILES
+========================================================================================
+*/
+
+ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
+ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
+
+/*
+========================================================================================
+    IMPORT LOCAL MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+// Don't overwrite global params.modules, create a copy instead and use that within the main script.
+def modules = params.modules.clone()
+
+//
+// MODULE: Local to the pipeline
+//
+include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions' addParams( options: [publish_files : ['tsv':'']] )
+
+//
+// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
+//
+include { INPUT_CHECK } from '../subworkflows/local/input_check' addParams( options: [:] )
+
+/*
+========================================================================================
+    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+def multiqc_options   = modules['multiqc']
+multiqc_options.args += params.multiqc_title ? Utils.joinModuleArgs(["--title \"$params.multiqc_title\""]) : ''
+
+//
+// MODULE: Installed directly from nf-core/modules
+//
+include { FASTQC  } from '../modules/nf-core/modules/fastqc/main'  addParams( options: modules['fastqc'] )
+include { MULTIQC } from '../modules/nf-core/modules/multiqc/main' addParams( options: multiqc_options   )
+
+/*
+========================================================================================
+    RUN MAIN WORKFLOW
+========================================================================================
+*/
+
+// Info required for completion email and summary
+def multiqc_report = []
+
+workflow HIC {
+
+    ch_software_versions = Channel.empty()
+
+    //
+    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
+    //
+    INPUT_CHECK (
+        ch_input
+    )
+
+    //
+    // MODULE: Run FastQC
+    //
+    FASTQC (
+        INPUT_CHECK.out.reads
+    )
+    ch_software_versions = ch_software_versions.mix(FASTQC.out.version.first().ifEmpty(null))
+
+    //
+    // MODULE: Pipeline reporting
+    //
+    ch_software_versions
+        .map { it -> if (it) [ it.baseName, it ] }
+        .groupTuple()
+        .map { it[1][0] }
+        .flatten()
+        .collect()
+        .set { ch_software_versions }
+
+    GET_SOFTWARE_VERSIONS (
+        ch_software_versions.map { it }.collect()
+    )
+
+    //
+    // MODULE: MultiQC
+    //
+    workflow_summary    = WorkflowHic.paramsSummaryMultiqc(workflow, summary_params)
+    ch_workflow_summary = Channel.value(workflow_summary)
+
+    ch_multiqc_files = Channel.empty()
+    ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(GET_SOFTWARE_VERSIONS.out.yaml.collect())
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+
+    MULTIQC (
+        ch_multiqc_files.collect()
+    )
+    multiqc_report       = MULTIQC.out.report.toList()
+    ch_software_versions = ch_software_versions.mix(MULTIQC.out.version.ifEmpty(null))
+}
+
+/*
+========================================================================================
+    COMPLETION EMAIL AND SUMMARY
+========================================================================================
+*/
+
+workflow.onComplete {
+    NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+    NfcoreTemplate.summary(workflow, params, log)
+}
+
+/*
+========================================================================================
+    THE END
+========================================================================================
+*/