modules: A Nextflow repository from sk-sahu

THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!
PLEASE BE KIND TO OUR CODE REVIEWERS AND SUBMIT ONE PULL REQUEST PER MODULE :)

A repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation.

Using existing modules
Adding a new module file
Terminology
Help
Citation

Using existing modules

The module files hosted in this repository define a set of processes for software tools such as fastqc, bwa, samtools etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.

We have written a helper command in the nf-core/tools package that uses the GitHub API to obtain the relevant information for the module files present in the software/ directory of this repository. This includes using git commit hashes to track changes for reproducibility purposes, and to download and install all of the relevant module files.

Install the latest version of nf-core/tools (>=1.10.2)

List the available modules:

$ nf-core modules list

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 1.10.2



INFO      Modules available from nf-core/modules (master):                                                                                                                  modules.py:51

bwa/index
bwa/mem
deeptools/computematrix
deeptools/plotfingerprint
deeptools/plotheatmap
deeptools/plotprofile
fastqc
..truncated..

Install the module in your pipeline directory:

$ nf-core modules install . fastqc

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 1.10.2



INFO      Installing fastqc                                                                                                                                                 modules.py:62
INFO      Downloaded 3 files to ./modules/nf-core/software/fastqc                                                                                                           modules.py:97

Import the module in your Nextflow script:

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { FASTQC } from './modules/nf-core/software/fastqc/main' addParams( options: [:] )

We have plans to add other utility commands to help developers install and maintain modules downloaded from this repository so watch this space!

$ nf-core modules --help

...truncated...

Commands:
  list     List available software modules.
  install  Add a DSL2 software wrapper module to a pipeline.
  update   Update one or all software wrapper modules.             (NOT YET IMPLEMENTED)
  remove   Remove a software wrapper from a pipeline.              (NOT YET IMPLEMENTED)
  check    Check that imported module code has not been modified.  (NOT YET IMPLEMENTED)

Adding a new module file

NB: The definition and standards for module files are still under discussion but we are now gladly accepting submissions :)

If you decide to upload a module to nf-core/modules then this will ensure that it will become available to all nf-core pipelines, and to everyone within the Nextflow community! See software/ for examples.

Module template

We have added a directory called software/TOOL/SUBTOOL/ that serves as a template with which to create your own module and tests/software/TOOL/SUBTOOL/ as an example of how to add the required CI tests. Where applicable, we have added extensive TODO statements for general information, to help guide you as to where to make the appropriate changes, and how to make them. If in doubt, have a look at how we have done things for other modules.

.
├── software
│   └── TOOL
│       └── SUBTOOL
│           ├── functions.nf    ## Utility functions imported in main module script
│           ├── main.nf         ## Main module script
│           └── meta.yml        ## Documentation for module, input, output, params, author
├── tests
│   └── software
│       └── TOOL
│           └── SUBTOOL
│               ├── main.nf     ## Minimal workflow to test module
│               └── test.yml    ## Pytest-workflow test file

Guidelines

The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in RFC 2119.

General

Software that can be piped together SHOULD be added to separate module files unless there is a run-time, storage advantage in implementing in this way. For example, using a combination of bwa and samtools to output a BAM file instead of a SAM file:
```
bwa mem | samtools view -B -T ref.fasta
```
Where applicable, the usage and generation of compressed files SHOULD be enforced as input and output, respectively:
- *.fastq.gz and NOT *.fastq
- *.bam and NOT *.sam
Where applicable, each module command MUST emit a file <SOFTWARE>.version.txt containing a single line with the software's version in the format <VERSION_NUMBER> or 0.7.17 e.g.
```
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
```
If the software is unable to output a version number on the command-line then a variable called VERSION can be manually specified to create this file e.g. homer/annotatepeaks module.
The process definition MUST NOT contain a when statement.

Naming conventions

The directory structure for the module name must be all lowercase e.g. software/bwa/mem/. The name of the software (i.e. bwa) and tool (i.e. mem) MUST be all one word.
The process name in the module file MUST be all uppercase e.g. process BWA_MEM {. The name of the software (i.e. BWA) and tool (i.e. MEM) MUST be all one word separated by an underscore.
All parameter names MUST follow the snake_case convention.
All function names MUST follow the camelCase convention.

Module parameters

A module file SHOULD only define input and output files as command-line parameters to be executed within the process.
All other parameters MUST be provided as a string i.e. options.args where options is a Groovy Map that MUST be provided via the Nextflow addParams option when including the module via include in the parent workflow.
If the tool supports multi-threading then you MUST provide the appropriate parameter using the Nextflow task variable e.g. --threads $task.cpus.
Any parameters that need to be evaluated in the context of a particular sample e.g. single-end/paired-end data MUST also be defined within the process.

Input/output options

Named file extensions MUST be emitted for ALL output channels e.g. path "*.txt", emit: txt.
Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.

Resource requirements

An appropriate resource label MUST be provided for the module as listed in the nf-core pipeline template e.g. process_low, process_medium or process_high.
If the tool supports multi-threading then you MUST provide the appropriate parameter using the Nextflow task variable e.g. --threads $task.cpus.

Software requirements

BioContainers is a registry of Docker and Singularity containers automatically created from all of the software packages on Bioconda. Where possible we will use BioContainers to fetch pre-built software containers and Bioconda to install software using Conda.

Software requirements SHOULD be declared within the module file using the Nextflow container directive. For single-tool BioContainers, the simplest method to obtain the Docker container path is to replace bwa with your tool name in this Quay.io link. You will see a list of tags sorted by the most recent. You can then use exactly the same name (e.g. bwa) version (e.g. 0.7.17) and tag (e.g. hed695b0_7) to add all of the Conda, Docker and Singularity definitions in the module.
```
conda (params.enable_conda ? "bioconda::bwa=0.7.17=hed695b0_7" : null)              // Conda package
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
    container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"  // Singularity image
} else {
    container "quay.io/biocontainers/bwa:0.7.17--hed695b0_7"                        // Docker image
}
```
If the software is available on Conda it MUST also be defined using the Nextflow conda directive. Using bioconda::bwa=0.7.17=hed695b0_7 as an example, software MUST be pinned to the channel (i.e. bioconda), version (i.e. 0.7.17) and build (i.e. hed695b0_7). This allows us to perform file output integrity CI tests on the same input test data with Docker, Singularity and Conda.
If required, multi-tool containers may also be available on BioContainers e.g. bwa and samtools. You can install and use the galaxy-tool-util package to search for both single- and multi-tool containers available in Conda, Docker and Singularity format. e.g. to search for Docker (hosted on Quay.io) and Singularity multi-tool containers with both bowtie and samtools installed you can use the following command:
```
mulled-search --destination quay singularity --channel bioconda --search bowtie samtools | grep "mulled"
```
NB: Build information for all tools within a multi-tool container can be obtained in the /usr/local/conda-meta/history file within the container.
It is also possible for a new multi-tool container to be built and added to BioContainers by submitting a pull request on their multi-package-containers repository.
If the software is not available on Bioconda a Dockerfile MUST be provided within the module directory. We will use GitHub Actions to auto-build the containers on the GitHub Packages registry.

Publishing results

The Nextflow publishDir definition is currently quite limited in terms of parameter/option evaluation. To overcome this, the publishing logic we have implemented for use with DSL2 modules attempts to minimise changing the publishDir directive (default: params.outdir) in favour of constructing and appending the appropriate output directory paths via the saveAs: statement e.g.

publishDir "${params.outdir}",
    mode: params.publish_dir_mode,
    saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

The saveFiles function can be found in the functions.nf file of utility functions that will be copied into all module directories. It uses the various publishing options specified as input to the module to construct and append the relevant output path to params.outdir.

We also use a standardised parameter called params.publish_dir_mode that can be used to alter the file publishing method (default: copy).

Testing

In order to test that each module added to nf-core/modules is actually working and to be able to track any changes to results files between module updates we have set-up a number of Github Actions CI tests to run each module on a minimal test dataset using Docker, Singularity and Conda.

Test data

All test data for nf-core/modules MUST be added to tests/data/ and organised by filename extension.
In order to keep the size of this repository as minimal as possible, pre-existing files from tests/data/ MUST be reused if at all possible.
Test files MUST be kept as tiny as possible.

Pytest workflow

Every module MUST have a test workflow utilising test data added to the appropriate directory e.g. tests/software/fastqc/main.nf
Any outputs produced by the test workflow MUST be included in the pytest-workflow for that tool e.g. tests/software/fastqc/test.yml. md5sum checks are the preferable choice of test to determine file changes, however, this may not be possible for all outputs generated by some tools e.g. if they include time stamps or command-related headers. Please do your best to avoid just checking for the file being present e.g. it may still be possible to check that the file contains the appropriate text snippets.
A filter for the module must be created in .github/filters.yml. If the test workflow you have created invokes more than one tool please include any paths specific for those tool's too e.g. bowtie build is upstream of bowtie align and they have both been chained together to test the latter.

Running Tests Locally

Install nextflow
Install any of Docker, Singularity or Conda
Install pytest-workflow

Start running your own tests!

Typical command with Docker:

cd /path/to/git/clone/of/nf-core/modules/
PROFILE=docker pytest --tag bowtie --symlink --keep-workflow-wd

Typical command with Singularity:

cd /path/to/git/clone/of/nf-core/modules/
TMPDIR=~ PROFILE=singularity pytest --tag bowtie --symlink --keep-workflow-wd

Typical command with Conda:

cd /path/to/git/clone/of/nf-core/modules/
PROFILE=conda pytest --tag bowtie --symlink --keep-workflow-wd

See docs on running pytest-workflow for more info.

Documentation

A module MUST be documented in the meta.yml file. It MUST document params, input and output. input and output MUST be a nested list.

We are aware that there is very little documentation, documenting the (Documentation)[#documentation] section. Writing more code and tests is so much cooooler! Please bear with us, we will get here eventually...

Uploading to `nf-core/modules`

Fork the nf-core/modules repository to your own GitHub account. Within the local clone of your fork add the module file to the software/ directory. Please try and keep PRs as atomic as possible to aid the reviewing process - ideally, one module addition/update per PR.

Commit and push these changes to your local clone on GitHub, and then create a pull request on the nf-core/modules GitHub repo with the appropriate information.

We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.

Terminology

The features offered by Nextflow DSL2 can be used in various ways depending on the granularity with which you would like to write pipelines. Please see the listing below for the hierarchy and associated terminology we have decided to use when referring to DSL2 components:

Module: A process that can be used within different pipelines and is as atomic as possible i.e. cannot be split into another module. An example of this would be a module file containing the process definition for a single tool such as FastQC. At present, this repository has been created to only host atomic module files that should be added to the software/ directory along with the required documentation and tests.
Sub-workflow: A chain of multiple modules that offer a higher-level of functionality within the context of a pipeline. For example, a sub-workflow to run multiple QC tools with FastQ files as input. Sub-workflows should be shipped with the pipeline implementation and if required they should be shared amongst different pipelines directly from there. As it stands, this repository will not host sub-workflows although this may change in the future since well-written sub-workflows will be the most powerful aspect of DSL2.
Workflow: What DSL1 users would consider an end-to-end pipeline. For example, from one or more inputs to a series of outputs. This can either be implemented using a large monolithic script as with DSL1, or by using a combination of DSL2 individual modules and sub-workflows.

Help

For further information or help, don't hesitate to get in touch on Slack #modules channel (you can join with this invite).

Citation

If you use the module files in this repository for your analysis please you can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

sk-sahu/modules

Table of contents

Using existing modules

Adding a new module file

Module template

Guidelines

General

Naming conventions

Module parameters

Input/output options

Resource requirements

Software requirements

Publishing results

Testing

Test data

Pytest workflow

Running Tests Locally

Documentation

Uploading to `nf-core/modules`

Terminology

Help

Citation

sk-sahu/modules

Table of contents

Using existing modules

Adding a new module file

Module template

Guidelines

General

Naming conventions

Module parameters

Input/output options

Resource requirements

Software requirements

Publishing results

Testing

Test data

Pytest workflow

Running Tests Locally

Documentation

Uploading to nf-core/modules

Terminology

Help

Citation

Uploading to `nf-core/modules`