diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 078248e142a984d938145ff04fd4e14a7e5ba4e8..53f847861047be018e469f25039e10383cce8071 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -54,4 +54,4 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/docs) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/usage) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index a97d3399b3697abad1ad812c27acd09479fae26b..14a7e8bffa54880834ad505addf8c91b875e5992 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -36,7 +36,7 @@ Steps to reproduce the behaviour:
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/hic:1.0.0] -->
 
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 26d2e7e9f9223900ddc066163f442f821d1a62f3..76e9d3891314a04fafb23117045e4116a9deef03 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,10 +1,12 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on push to the master branch.
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   release:
     types: [published]
+  workflow_dispatch:
 
 jobs:
   run-awstest:
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 78ee5bc67a2ad5565bca78f0de19cb639bf51998..cd8579f8ae0390fa28d40a0579e2ad57f7801b29 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -1,11 +1,10 @@
 name: nf-core AWS test
 # This workflow is triggered on push to the master branch.
-# It runs the -profile 'test' on AWS batch
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It runs the -profile 'test' on AWS batch.
 
 on:
-  push:
-    branches:
-      - master
+  workflow_dispatch:
 
 jobs:
   run-awstest:
@@ -37,4 +36,4 @@ jobs:
           --job-name nf-core-hic \
           --job-queue $AWS_JOB_QUEUE \
           --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e1f95fb60e0b075d09055fab82cbfe0d7174887..62f0e5f1fcfb257028ff9bade4edf1fab723e1ff 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).
 
-## v1.2.1 - [date]
+## v1.2.2 - [date]
 
 Initial release of nf-core/hic, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/Dockerfile b/Dockerfile
index f7e704c8df0c2008f3647406381ee8225ed1eeb0..d7a7b246dedf0b81e5d9be40a0de0e5b1dbdcf7a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nfcore/base:1.10.2
+FROM nfcore/base:1.11
 LABEL authors="Nicolas Servant" \
       description="Docker image containing all software requirements for the nf-core/hic pipeline"
 
@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-hic-1.2.1/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-hic-1.2.2/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-hic-1.2.1 > nf-core-hic-1.2.1.yml
+RUN conda env export --name nf-core-hic-1.2.2 > nf-core-hic-1.2.2.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile
diff --git a/README.md b/README.md
index 8ef1c645c0854a57ad80dd219e1b7aba68ee9668..13e8e7c3a9d88a6ee06c43cf72cb11fa77f06c3c 100644
--- a/README.md
+++ b/README.md
@@ -18,12 +18,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 1. Install [`nextflow`](https://nf-co.re/usage/installation)
 
-2. Install either [`Docker`](https://docs.docker.com/engine/installation/) or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
+2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```bash
-    nextflow run nf-core/hic -profile test,<docker/singularity/conda/institute>
+    nextflow run nf-core/hic -profile test,<docker/singularity/podman/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.
@@ -33,14 +33,14 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
     <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
     ```bash
-    nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
+    nextflow run nf-core/hic -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
     ```
 
-See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
+See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running the pipeline.
 
 ## Documentation
 
-The nf-core/hic pipeline comes with documentation about the pipeline which you can read at [https://nf-core/hic/docs](https://nf-core/hic/docs) or find in the [`docs/` directory](docs).
+The nf-core/hic pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/hic/usage) and [output](https://nf-co.re/hic/output).
 
 <!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works -->
 
diff --git a/assets/nf-core-hic_logo.png b/assets/nf-core-hic_logo.png
index 6b364161664e70224fac3a83fb9f02ed0acbd9f8..dee3db82069b61e9a5380d940355f47ff565057c 100644
Binary files a/assets/nf-core-hic_logo.png and b/assets/nf-core-hic_logo.png differ
diff --git a/docs/README.md b/docs/README.md
index 67df846ef262b9918e55dff0147baf0d3cc03a9e..a6889549c7f27bda0aed81947685713781fe2d1b 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -2,8 +2,6 @@
 
 The nf-core/hic documentation is split into the following pages:
 
-<!-- TODO nf-core: If you write more documentation pages, add them to the docs index page here -->
-
 * [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.
 * [Output](output.md)
diff --git a/docs/images/nf-core-hic_logo.png b/docs/images/nf-core-hic_logo.png
index e5fead372861ff430d7f1428e15dad9b045523e8..dee3db82069b61e9a5380d940355f47ff565057c 100644
Binary files a/docs/images/nf-core-hic_logo.png and b/docs/images/nf-core-hic_logo.png differ
diff --git a/docs/output.md b/docs/output.md
index 77bc6bf828ceaa772f633a4f3ea8640c9ad82b4b..4a7372e92d17cf7897c93fb403d6bd41c2bc2f29 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -1,5 +1,11 @@
 # nf-core/hic: Output
 
+## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/hic/output](https://nf-co.re/hic/output)
+
+> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
+
+## Introduction
+
 This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
@@ -40,7 +46,7 @@ For more information about how to use MultiQC reports, see [https://multiqc.info
 
 **Output files:**
 
-* `multiqc/`  
+* `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.
diff --git a/docs/usage.md b/docs/usage.md
index 21419157b7c30126ec0eca6b8188284dcbb7325a..76803ddcd3e60bf2dc060ced21e610abf5cff261 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1,5 +1,9 @@
 # nf-core/hic: Usage
 
+## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/hic/usage](https://nf-co.re/hic/usage)
+
+> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
+
 ## Introduction
 
 <!-- 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. -->
@@ -47,7 +51,7 @@ 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, 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, Conda) - see below.
 
 > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
@@ -64,8 +68,11 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 * `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/)
+* `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/)
 * `conda`
-  * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker or Singularity.
+  * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity or Podman.
   * A generic configuration profile to be used with [Conda](https://conda.io/docs/)
   * Pulls most software from [Bioconda](https://bioconda.github.io/)
 * `test`
@@ -98,7 +105,7 @@ process {
 
 See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information.
 
-If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition below). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
+If you 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.
 
 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).
 
diff --git a/environment.yml b/environment.yml
index bda1cbfc9ab83de16e65c77354b2894dc4a83237..5762739c27540ed6cbb8a9e7314ced9561435abe 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-hic-1.2.1
+name: nf-core-hic-1.2.2
 channels:
   - conda-forge
   - bioconda
diff --git a/nextflow.config b/nextflow.config
index 7c450f1bd889a56e840e32960fdb22de4251d6c1..42d1074af186e50964cd7f73df138920d933d2d7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -71,6 +71,9 @@ profiles {
     singularity.enabled = true
     singularity.autoMounts = true
   }
+  podman {
+    podman.enabled = true
+  }
   test { includeConfig 'conf/test.config' }
 }
 
@@ -113,7 +116,7 @@ manifest {
   description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '1.2.1'
+  version = '1.2.2'
 }
 
 // Function to ensure that resource requirements don't go beyond
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ccbfe4b5162528808d9ffb5289a826e15ece76e7..21e29d7e5fc226e377bef6fa7e4d9b498d281eed 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "https://json-schema.org/draft-07/schema",
+    "$schema": "http://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/hic/master/nextflow_schema.json",
     "title": "nf-core/hic pipeline parameters",
     "description": "Analysis of Chromosome Conformation Capture data (Hi-C)",
@@ -101,7 +101,7 @@
                         "link",
                         "copy",
                         "copyNoFollow",
-                        "mov"
+                        "move"
                     ]
                 },
                 "name": {