Important! Template update for nf-core/tools v1.11

.github/CONTRIBUTING.md

@@ -55,7 +55,7 @@ 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/eager documentation](https://nf-co.re/eager/latest/usage) and don't hesitate to get in touch on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/eager documentation](https://nf-co.re/eager/usage) and don't hesitate to get in touch on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 # Code Contribution Guidelines
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -54,9 +54,10 @@ A clear and concise description of what you expected to happen.
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
-- version: <!-- [e.g. 2.1.0] -->
-- Image tag: <!-- [e.g. nfcore/eager:2.1.0] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
+- version: <!-- [e.g. 2.2.0] -->
+- Image tag: <!-- [e.g. nfcore/eager:2.2.0] -->
+
 
 ## Additional context
 

.github/workflows/awstest.yml

@@ -4,9 +4,6 @@ name: nf-core AWS test
 # It runs the -profile 'test' on AWS batch.
 
 on:
-  push:
-    branches:
-      - master
   workflow_dispatch:
 
 jobs:

CHANGELOG.md

@@ -1,7 +1,5 @@
 # nf-core/eager: Changelog
 
-All notable changes to this project will be documented in this file.
-
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.10.2
+FROM nfcore/base:1.11
 LABEL authors="The nf-core/eager community" \
       description="Docker image containing all software requirements for the nf-core/eager pipeline"
 

README.md

@@ -1,6 +1,6 @@
 # ![nf-core/eager](docs/images/nf-core-eager_logo.png)
 
-**A fully reproducible and state-of-the-art genomics pipeline for ancient DNA**.
+**A fully reproducible and state-of-the-art ancient DNA analysis pipeline**.
 
 [![GitHub Actions CI Status](https://github.com/nf-core/eager/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/eager/actions)
 [![GitHub Actions Linting Status](https://github.com/nf-core/eager/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/eager/actions)
@@ -83,12 +83,12 @@ Additional functionality contained by the pipeline currently includes:
 
 1. Install [`nextflow`](https://nf-co.re/usage/installation) (version >= 20.04.0)
 
-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/eager -profile test,<docker/singularity/conda/institute>
+    nextflow run nf-core/eager -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.
@@ -114,7 +114,7 @@ as described in the documentation.
 
 ## Documentation
 
-The nf-core/eager pipeline comes with documentation about the pipeline which you can read at [https://nf-co.re/eager/usage](https://nf-co.re/eager/usage) or find in the [`docs/` directory](docs).
+The nf-core/eager pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/eager/usage) and [output](https://nf-co.re/eager/output).
 
 1. [Nextflow installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration

docs/output.md

@@ -1,5 +1,9 @@
 # nf-core/eager: Output
 
+## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/eager/output](https://nf-co.re/eager/output)
+
+> _Documentation of pipeline parameters is generated automatically from the pipeline schema and these markdown files may not be up-to-date._
+
 ## Table of contents
 
 <!-- TOC depthfrom:2 depthto:3 -->

docs/usage.md

@@ -1,5 +1,9 @@
 # nf-core/eager: Usage
 
+## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/eager/usage](https://nf-co.re/eager/usage)
+
+> _Documentation of pipeline parameters is generated automatically from the pipeline schema and may not be up-to-date here._
+
 ## Table of contents
 
 <!-- TOC depthfrom:2 depthto:3 -->
@@ -173,21 +177,20 @@ software to be installed and available on the `PATH`. This is _not_ recommended.
 > *Important*: If running nf-core/eager on a cluster - ask your system
 > administrator what profile to use.
 
+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.
+
 - `docker`
-  - A generic configuration profile to be used with
-    [Docker](https://docker.com/)
-  - Pulls software from Docker Hub:
-    [`nfcore/eager`](https://hub.docker.com/r/nfcore/eager/)
+  - A generic configuration profile to be used with [Docker](https://docker.com/)
+  - Pulls software from Docker Hub: [`nfcore/eager`](https://hub.docker.com/r/nfcore/eager/)
 - `singularity`
-  - A generic configuration profile to be used with
-    [Singularity](https://sylabs.io/docs/)
-  - Pulls software from Docker Hub:
-    [`nfcore/eager`](https://hub.docker.com/r/nfcore/eager/)
+  - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
+  - Pulls software from Docker Hub: [`nfcore/eager`](https://hub.docker.com/r/nfcore/eager/)
+- `podman`
+  - A generic configuration profile to be used with [Podman](https://podman.io/)
+  - Pulls software from Docker Hub: [`nfcore/eager`](https://hub.docker.com/r/nfcore/eager/)
 - `conda`
-  - Please only use Conda as a last resort i.e. when it's not possible to run
-    the pipeline with Docker or Singularity.
-  - A generic configuration profile to be used with
-    [Conda](https://conda.io/docs/)
+  - 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`
   - A profile with a complete configuration for automated testing
@@ -230,6 +233,15 @@ Further institutions can be added at
 [nf-core/configs](https://github.com/nf-core/configs). Please ask the eager
 developers to add your institution to the list above, if you add one!
 
+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.
+
 ### `-resume`
 
 Specify this when restarting a pipeline. Nextflow will used cached results from

nextflow.config

@@ -278,6 +278,9 @@ profiles {
     singularity.enabled = true
     singularity.autoMounts = true
   }
+  podman {
+    podman.enabled = true
+  }
   test { includeConfig 'conf/test.config' }
 }
 

nextflow_schema.json

@@ -1,8 +1,8 @@
 {
-    "$schema": "https://json-schema.org/draft-07/schema",
+    "$schema": "http://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/eager/master/nextflow_schema.json",
     "title": "nf-core/eager pipeline parameters",
-    "description": "A fully reproducible and state of the art ancient DNA analysis pipeline",
+    "description": "A fully reproducible and state-of-the-art ancient DNA analysis pipeline",
     "type": "object",
     "definitions": {
         "input_options": {
@@ -169,9 +169,18 @@
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",
-                    "description": "Mode for publishing results in the output directory. Options: 'symlink', 'rellink', 'link', 'copy', 'copyNoFollow', 'move'.",
-                    "fa_icon": "fas fa-upload",
-                    "help_text": "Nextflow mode for 'publishing' final results files i.e. how to move final files into your `--outdir` from working directories. Options: 'symlink', 'rellink', 'link', 'copy', 'copyNoFollow', 'move'.  Default: 'copy'.\n\n> It is recommended to select `copy` (default) if you plan to regularly delete intermediate files from `work/`."
+                    "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"
+                    ]
                 },
                 "saveTrimmed": {
                     "type": "boolean",