diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 538f355cedd9809e4bd3ac8067cb00832e5385b1..62ad6c259efad78784730845c6e83ac9e7b158ab 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -59,4 +59,4 @@ For further information/help, please consult the [nf-core/hic documentation](htt
 don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel
 ([join our Slack here](https://nf-co.re/join/slack)).
 
-For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/docs) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/usage) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index dea18053f8ab41016fc4e427dbbc48cf56709781..baf9343cd03e2d5e64918be1d49cdc79c6f5c72f 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -35,7 +35,7 @@ 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 8344dc5156a7da39aaed1a21d6a27c11855c628d..d5cef6aca217882a56da77f50ff8c2f96ea535b5 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 94bca240004c28e2608c4e1a8c2a82bb054ce428..b91b9269f62a65f9a450f3b1a8af35604acdd523 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:
@@ -36,4 +35,4 @@ 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 719ea08ec239f9d45b9ecfafba5fb63ff4e7426a..201b5c94015b12cbcc1c7b4198246dbf7e49cb31 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 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).
 
+## v1.2.3dev
+
+* Template update for nf-core/tools v1.11
+
 ## v1.2.2 - 2020-09-02
 
 ### `Added`
diff --git a/Dockerfile b/Dockerfile
index 3c8d019dc4fb85111fe16279257c734d8aeafd43..70ba2d7b13acc7835c8d4bfd3ba0022b336350e9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +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"
 
diff --git a/README.md b/README.md
index 4ffcce8a79bc79ce52c5396597c289a63c886011..cd476c6432b7b1f9290d41a939c268c1de296d04 100644
--- a/README.md
+++ b/README.md
@@ -42,18 +42,14 @@ sites (bowtie2)
 
 ## Quick Start
 
-i. Install [`nextflow`](https://nf-co.re/usage/installation)
+1. Install [`nextflow`](https://nf-co.re/usage/installation)
 
-ii. Install either [`Docker`](https://docs.docker.com/engine/installation/)
-or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/)
-for full pipeline reproducibility (please only use [`Conda`](https://conda.io/miniconda.html)
-as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))
+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))_
 
-iii. Download the pipeline and test it on a minimal dataset with a single command
-
-```bash
-nextflow run nf-core/hic -profile test,<docker/singularity/conda/institute>
-```
+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/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.
@@ -61,35 +57,18 @@ If so, you can simply use `-profile <institute>` in your command.
 This will enable either `docker` or `singularity` and set the appropriate execution
 settings for your local compute environment.
 
-iv. Start running your own analysis!
-
-```bash
-nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
-```
+4. Start running your own analysis!
+    ```bash
+    nextflow run nf-core/hic -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
+    ```
 
-See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running
-the pipeline.
+See [usage docs](https://nf-co.re/hic/usage) for all of the available options when running the pipeline.
 
 ## Documentation
 
-The nf-core/hic pipeline comes with documentation about the pipeline,
-found in the `docs/` directory:
-
-1. [Installation](https://nf-co.re/usage/installation)
-2. Pipeline configuration
-    * [Local installation](https://nf-co.re/usage/local_installation)
-    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
-    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
-3. [Running the pipeline](docs/usage.md)
-4. [Output and how to interpret the results](docs/output.md)
-5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
-
-The nf-core/hic pipeline comes with documentation about the pipeline which
-you can read at [https://nf-co.re/hic/usage](https://nf-co.re/hic/usage) or
-find in the [`docs/` directory](docs).
+The nf-core/hic pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/hic/usage) and [output](https://nf-co.re/hic/output).
 
-For further information or help, don't hesitate to get in touch on
-[Slack](https://nfcore.slack.com/channels/hic).
+For further information or help, don't hesitate to get in touch on [Slack](https://nfcore.slack.com/channels/hic).
 You can join with [this invite](https://nf-co.re/join/slack).
 
 ## Credits
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/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 95aca423a2f44853e03c8ed443f6eb8ac43b9019..895a4f2a16d75e7ca0dfb21c13d0cccc7ea3a322 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -1,8 +1,12 @@
 # nf-core/hic: Output
 
-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.
+## :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
@@ -191,12 +195,16 @@ reported in the MultiQC output for future traceability.
 
 **Output files:**
 
-* `Project_multiqc_report.html`
-  * MultiQC report - a standalone HTML file that can be viewed in your
-web browser
-* `Project_multiqc_data/`
-  * Directory containing parsed statistics from the different tools used
-in the pipeline
+* `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.
+
+## Pipeline information
+
+[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.
+
+**Output files:**
 
 * `pipeline_info/`
   * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`,
diff --git a/docs/usage.md b/docs/usage.md
index 11b065386fdcd684ef7d12de906b4c963b180c1a..31eabe9fb8044a14de7319c5824c18a53b06936e 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1,5 +1,11 @@
 # 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
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:
@@ -74,9 +80,7 @@ fails after three times then the pipeline is stopped.
 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.
@@ -104,9 +108,11 @@ installed and available on the `PATH`. This is _not_ recommended.
 * `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`
@@ -151,15 +157,7 @@ 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
@@ -215,7 +213,7 @@ A normal glob pattern, enclosed in quotation marks, can then be used for `--inpu
 For example:
 
 ```bash
---single_end --reads '*.fastq'
+--single_end --input '*.fastq'
 ```
 
 It is not possible to run a mixture of single-end and paired-end files in one run.
diff --git a/nextflow.config b/nextflow.config
index c765a4a7e242e7da17ae4f1efbb86a39a5fe7a72..341e2a52fda6ba43db1a497be24b7d6643be6c7b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -108,6 +108,9 @@ profiles {
     singularity.enabled = true
     singularity.autoMounts = true
   }
+  podman {
+    podman.enabled = true
+  }
   test { includeConfig 'conf/test.config' }
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 9071bd2454457a3c914a00271a047790a3dc366d..84bb558fd02002db37df4755daa2dff36d09d89f 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)",
@@ -295,7 +295,7 @@
                         "link",
                         "copy",
                         "copyNoFollow",
-                        "mov"
+                        "move"
                     ]
                 },
                 "name": {