Added to the nf-core guidelines

markdown/adding_pipelines.md

@@ -28,6 +28,9 @@ and copy over your code in the relevant places.
 If you really don't want to use the template it should possible to work without it.
 Please see the [manual synchronisation](/sync) documentation.
 
+> Note that workflow names should be all lower-case and contain no punctuation.
+> This is to allow consistent names between platforms (eg. GitHub + Docker Hub).
+
 ## Push to GitHub
 Create a repository on GitHub for your new pipeline under your personal account.
 Make sure _not_ to initialise it with `README` file - you just want an empty repository.

markdown/developer_docs.md

@@ -1,80 +1,57 @@
+# Requirements for nf-core pipelines
+If you're thinking of adding a new pipeline to nf-core, please read the documentation
+about [adding a new pipeline](/adding_pipelines).
 
-# Introduction
-Welcome to the nf-core developer documentation!
+## Workflow size
+We aim to have a _"not too big, not too small"_ rule with nf-core pipelines.
+This is a little fuzzy, but as a rule of thumb workflows should contain at
+least three different processes and be simple enough to run that a new user
+can realistically run the pipeline after spending ten minutes reading the docs.
 
-Some quick links to help you find your way around:
-
-* Getting Help
-    * The quickest place to get help is on the nf-core Gitter channel: [https://gitter.im/nf-core/](https://gitter.im/nf-core/Lobby) - a free chat interface that integrates nicely with GitHub.
-    * If you've found a bug in a pipeline, please create a GitHub issue in that pipeline repository.
-* [Lint test error codes](errors)
-* [Pipeline syncing](sync)
-
-# Guidelines for nf-core pipelines
-For now, the guidelines are pretty simple. The below gives an outline of what is required.
-For more detail, please see the [**list of lint test error codes**](errors).
-
-**We highly recommend using the [`nf-core create`](tools#creating-a-new-workflow) command** to begin your project.
-This tool builds a skeleton pipeline from scratch with all of the features required to pass the below tests.
-It also makes it trivial to keep your pipeline in sync with core updates to the nf-core pipeline template (this will be automated, see [pipeline syncing](sync)).
-
-## Features
-All pipelines must adhere to the following:
+## Minimum requirements
+All nf-core pipelines _must_ adhere to the following:
 
 * Be built using Nextflow
 * Have an [MIT licence](https://choosealicense.com/licenses/mit/)
 * Have software bundled using [Docker](https://www.docker.com/)
 * Continuous integration testing
 * Stable release tags
 * Common pipeline structure and usage
-* Excellent documentation
+* Run in a single command (not multiple sub-workflows)
+    * It is ok to have workflows that use the output of _another_ nf-core pipeline as input
+* Excellent documentation and GitHub repository keywords
 * A responsible contact person / GitHub username
     * This will typically be the main person behind the pipeline development
     * This person should be responsible for basic maintenance and questions
 * The pipeline must not have any failures in the `nf-core lint` tests
     * These tests are run by the [nf-core/tools](https://github.com/nf-core/tools) package and validate the requirements listed on this page.
     * You can see the list of tests and how to pass them on the [error codes page](errors).
 
-_(any point can be skipped, given a good enough reason...)_
-
+## Recommended features
 If possible, it's great if pipelines can also have:
 
 * All software bundled using [bioconda](https://bioconda.github.io/)
-    * See below for how to use a bioconda env script automatically build docker and singularity containers, meaning you have a single file to maintain.
+    * Nearly all nf-core pipelines use a conda `env` script to list their software requirements.
+    The pipeline Docker images are then built using this, meaning that with a single file your pipeline can support nextflow users running with conda, docker or singularity.
+    * The [nf-core template](/tools#creating-a-new-workflow) comes with all required code to support this setup.
 * Optimised output file formats
     * Pipelines should generate `CRAM` alignment files by default, but have a `--bam` option to generate `BAM` outputs if required by the user.
 * Explicit support for running in cloud environments
     * For example, use of [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) and aws-batch
+    * The [nf-core template](/tools#creating-a-new-workflow) comes with all required code to support this setup.
 * Benchmarks from running on cloud environments such as [AWS](https://aws.amazon.com/)
 
-## Pipeline organisation
-It's highly recommended that pipelines are built using the [`nf-core create`](tools#creating-a-new-workflow) command, as this will ensure future community updates to be propagated to your pipeline (read more [here](sync)).
-
 ## Coding style
 The nf-core style requirements are growing and maturing over time.
 Typically, as we agree on a new standard we try to build a test for it into the `nf-core lint` command.
 As such, to get a feel for what's expected, please read the [lint test error codes](errors).
 
 However, in general, pipelines must:
 
-* Use config profiles to organise anything that is not common for all users
+* Use [config profiles](https://www.nextflow.io/docs/latest/config.html) to organise hardware-specific options
 * Run with as little input as possible
     * Metadata (eg. be able to run with just FastQ files, where possible)
     * Reference files (eg. auto-generate missing reference files, where possible)
 * Keep only code for the latest stable on the main `master` branch.
     * The main development code should be kept in a branch called `dev`
 * Use GitHub releases and keep a detailed changelog file
-
-# Plans for the future
-There's always more cool stuff we want to do!
-
-Currently, our focus is on setting up [automatic syncing](sync) for all pipelines so that we can keep core pipeline structure and boilerplate code up to date across all pipelines. This is a huge task, but we made excellent progress at the first nf-core hackathon and hope to get it running soon.
-
-We of course continue to pursue the core aim of nf-core: to assemble a large collection of high quality analysis pipelines covering a wide range of different applications.
-
-Other big and as-yet unstarted pipe dreams include:
-* Automated [@nf_core twitter](https://twitter.com/nf_core) tweets when pipelines are released
-* A graphical user interface and API to launch pipelines (see [tools#61](https://github.com/nf-core/tools/issues/61))
-* A web-based monitoring tool to listen to nextflow pipeline event broadcasts and visualise running workflows
-
-Just about every nf-core repository has a healthy list of GitHub issues listing planned improvements, so if you're hungry for more, go and have an explore!

public_html/developer_docs.php

@@ -1,6 +1,7 @@
 <?php
-$title = 'Developers';
-$subtitle = 'Learn how to develop pipelines that adhere to the nf-core guidelines.';
+$title = 'Guidelines';
+$subtitle = 'Guidelines and requirements for nf-core pipelines.';
+
 $markdown_fn = '../markdown/developer_docs.md';
 include('../includes/header.php');
 include('../includes/footer.php');