Template update for nf-core/tools version 1.11

.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)).

.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] -->
 

.github/workflows/awsfulltest.yml

 name: nf-core AWS full size tests
-# This workflow is triggered on push to the master branch.
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   release:
     types: [published]
+  workflow_dispatch:
 
 jobs:
   run-awstest:

.github/workflows/awstest.yml

 name: nf-core AWS test
 # This workflow is triggered on push to the master branch.
-# It runs the -profile 'test' on AWS batch
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It runs the -profile 'test' on AWS batch.
 
 on:
-  push:
-    branches:
-      - master
+  workflow_dispatch:
 
 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"'"}]}'

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.
 

Dockerfile

-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

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 -->
 

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)

docs/output.md

 # 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.

docs/usage.md

 # 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).
 

environment.yml

 # 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

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

nextflow_schema.json

 {
-    "$schema": "https://json-schema.org/draft-07/schema",
+    "$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": {