[](https://nfcore.slack.com/channels/modules)
A repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation.
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 [`modules/`](modules/) 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.
We have plans to add other utility commands to help developers install and maintain modules downloaded from this repository so watch this space e.g. `nf-core modules update` command to automatically check and update modules installed within the pipeline.
- Please create a [new issue](https://github.com/nf-core/modules/issues/new?assignees=&labels=new%20module&template=new_nodule.md&title=new%20module:) before adding it
- Set an appropriate subject for the issue e.g. `new module: fastqc`
- Add yourself to the `Assignees` so we can track who is working on the module
### nf-core modules create
We have implemented a number of commands in the `nf-core/tools` package to make it incredibly easy for you to create and contribute your own modules to nf-core/modules.
3. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Conda`](https://conda.io/miniconda.html)
4. [Fork and clone this repo locally](#uploading-to-nf-coremodules)
All of the files required to add the module to `nf-core/modules` will be created/edited in the appropriate places. The 4 files you will need to change are:
This is the main script containing the `process` definition for the module. You will see an extensive number of `TODO` statements to help guide you to fill in the appropriate sections and to ensure that you adhere to the guidelines we have set for module submissions.
This file will be used to store general information about the module and author details - the majority of which will already be auto-filled. However, you will need to add a brief description of the files defined in the `input` and `output` section of the main script since these will be unique to each module.
Every module MUST have a test workflow. This file will define one or more Nextflow `workflow` definitions that will be used to unit test the output files created by the module. By default, one `workflow` definition will be added but please feel free to add as many as possible so we can ensure that the module works on different data types / parameters e.g. separate `workflow` for single-end and paired-end data.
Minimal test data required for your module may already exist within this repository, in which case you may just have to change a couple of paths in this file - see the [Test data](#test-data) section for more info and guidelines for adding new standardised data if required.
This file will contain all of the details required to unit test the main script in the point above using [pytest-workflow](https://pytest-workflow.readthedocs.io/). If possible, any outputs produced by the test workflow(s) MUST be included and listed in this file along with an appropriate check e.g. md5sum. The different test options are listed in the [pytest-workflow docs](https://pytest-workflow.readthedocs.io/en/stable/#test-options).
As highlighted in the next point, we have added a command to make it much easier to test the workflow(s) defined for the module and to automatically create the `test.yml` with the md5sum hashes for all of the outputs generated by the module.
`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.
9. Once ready, the code can be pushed and a pull request (PR) created
On a regular basis you can pull upstream changes into this branch and it is recommended to do so before pushing and creating a pull request - see below. Rather than merging changes directly from upstream the rebase strategy is recommended so that your changes are applied on top of the latest master branch from the nf-core repo. This can be performed as follows
```bash
git pull --rebase upstream master
```
Once you are ready you can push the code and create a PR
```bash
git push -u origin fastqc
```
Once the PR has been accepted you should delete the branch and checkout master again.
```bash
git checkout master
git branch -d fastqc
```
In case there are commits on the local branch that didn't make it into the PR (usually commits made after the PR), git will warn about this and not delete the branch. If you are sure you want to delete, use the following command
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.
- All test data for `nf-core/modules` MUST be added to the `modules` branch of [`nf-core/test-datasets`](https://github.com/nf-core/test-datasets/tree/modules/data) and organised by filename extension.
- In order to keep the size of this repository as minimal as possible, pre-existing files from [`nf-core/test-datasets`](https://github.com/nf-core/test-datasets/tree/modules/data) MUST be reused if at all possible.
- If the appropriate test data doesn't exist in the `modules` branch of [`nf-core/test-datasets`](https://github.com/nf-core/test-datasets/tree/modules/data) please contact us on the [nf-core Slack `#modules` channel](https://nfcore.slack.com/channels/modules) (you can join with [this invite](https://nf-co.re/join/slack)) to discuss possible options.
As outlined in the [nf-core modules create](#nf-core-modules-create) section we have made it quite trivial to create an initial yaml file (via the `nf-core modules create-test-yml` command) containing a listing of all of the module output files and their associated md5sums. However, md5sum checks may not be appropriate for all output files if for example they contain timestamps. This is why it is a good idea to re-run the tests locally with `pytest-workflow` before you create your pull request adding the module. If your files do indeed have timestamps or other issues that prevent you from using the md5sum check, then you can edit the `test.yml` file to instead check that the file contains some specific content or as a last resort, if it exists. The different test options are listed in the [pytest-workflow docs](https://pytest-workflow.readthedocs.io/en/stable/#test-options).
2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Conda`](https://conda.io/miniconda.html)
4. Start running your own tests using the appropriate [`tag`](https://github.com/nf-core/modules/blob/3d720a24fd3c766ba56edf3d4e108a1c45d353b2/tests/modules/fastqc/test.yml#L3-L5) defined in the `test.yml`:
> :warning: if you have a module named `build` this can conflict with some pytest internal behaviour. This results in no tests being run (i.e. recieving a message of `collected 0 items`). In this case rename the `tests/<module>/build` directry to `tests/<module>/build_test`, and update the corresponding `test.yml` accordingly. An example can be seen with the [`bowtie2/build` module tests](https://github.com/nf-core/modules/tree/master/tests/modules/bowtie2/build_test).
[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/modules` repository to your own GitHub account. Within the local clone of your fork add the module file to the [`modules/`](modules) 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](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) 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.
- All non-mandatory command-line tool options 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.
- 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.
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](https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf).
- The directory structure for the module name must be all lowercase e.g. [`modules/bwa/mem/`](modules/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.
- Input channel declarations MUST be defined for all _possible_ input files (i.e. both required and optional files).
- Directly associated auxiliary files to an input file MAY be defined within the same input channel alongside the main input channel (e.g. [BAM and BAI](https://github.com/nf-core/modules/blob/e937c7950af70930d1f34bb961403d9d2aa81c7d/modules/samtools/flagstat/main.nf#L22)).
- Other generic auxiliary files used across different input files (e.g. common reference sequences) MAY be defined using a dedicated input channel (e.g. [reference files](https://github.com/nf-core/modules/blob/3cabc95d0ed8a5a4e07b8f9b1d1f7ff9a70f61e1/modules/bwa/mem/main.nf#L21-L23)).
- 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, passing an empty list (`[]`) instead of a file as a module parameter can be used to work around this issue.
- All `params` within the module MUST be initialised and used in the local context of the module. In other words, named `params` defined in the parent workflow MUST NOT be assumed to be passed to the module to allow developers to call their parameters whatever they want. In general, it may be more suitable to use additional `input` value channels to cater for such scenarios.
- 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.
- An appropriate resource `label` MUST be provided for the module as listed in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config#L29-L46) e.g. `process_low`, `process_medium` or `process_high`.
- If a module contains _multiple_ tools that supports multi-threading (e.g. [piping output into a samtools command](https://github.com/nf-core/modules/blob/28b023e6f4d0d2745406d9dc6e38006882804e67/modules/bowtie2/align/main.nf#L32-L46)), you MUST assign cpus per tool such that the total number of used CPUs does not exceed `task.cpus`.
- For example, combining two (or more) tools that both (all) have multi-threading, this can be assigned to the variable [`split_cpus`](https://github.com/nf-core/modules/blob/28b023e6f4d0d2745406d9dc6e38006882804e67/modules/bowtie2/align/main.nf#L32)
- If one tool is multi-threaded and another uses a single thread, you can specify directly in the command itself e.g. with [`${task.cpus - 1}`](https://github.com/nf-core/modules/blob/6e68c1af9a514bb056c0513ebba6764efd6750fc/modules/bwa/sampe/main.nf#L42-L43)
[BioContainers](https://biocontainers.pro/#/) is a registry of Docker and Singularity containers automatically created from all of the software packages on [Bioconda](https://bioconda.github.io/). 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 `nf-core modules create` command will automatically fetch and fill-in the appropriate Conda / Docker / Singularity definitions by parsing the information provided in the first part of the module name:
- If the software is available on Conda it MUST also be defined using the Nextflow `conda` directive. Using `bioconda::bwa=0.7.17` as an example, software MUST be pinned to the channel (i.e. `bioconda`) and version (i.e. `0.7.17`). Conda packages MUST not be pinned to a build because they can vary on different platforms.
- If required, multi-tool containers may also be available on BioContainers e.g. [`bwa` and `samtools`](https://biocontainers.pro/#/tools/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40). You can install and use the [`galaxy-tool-util`](https://anaconda.org/bioconda/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:
- 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`](https://github.com/BioContainers/multi-package-containers) repository.
- Fork the [multi-package-containers repository](https://github.com/BioContainers/multi-package-containers)
- Make a change to the `hash.tsv` file in the `combinations` directory see [here](https://github.com/aunderwo/multi-package-containers/blob/master/combinations/hash.tsv#L124) for an example where `pysam=0.16.0.1,biopython=1.78` was added.
- Commit the code and then make a pull request to the original repo, for [example](https://github.com/BioContainers/multi-package-containers/pull/1661)
- Once the PR has been accepted a container will get built and you can find it using a search tool in the `galaxy-tool-util conda` package
- 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](https://github.com/features/packages).
The [Nextflow `publishDir`](https://www.nextflow.io/docs/latest/process.html#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.
The `saveFiles` function can be found in the [`functions.nf`](modules/fastqc/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`.
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 [`modules/`](modules/) 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.
For further information or help, don't hesitate to get in touch on [Slack `#modules` channel](https://nfcore.slack.com/channels/modules) (you can join with [this invite](https://nf-co.re/join/slack)).
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](https://dx.doi.org/10.1038/s41587-020-0439-x).
If you want to use an existing module file available in `nf-core/modules`, and you're running on a system that has no internet connection, you'll need to download the repository (e.g. `git clone https://github.com/nf-core/modules.git`) and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline by creating a custom config file called e.g. `custom_module.conf` containing the following information:
```bash
include /path/to/downloaded/modules/directory/
```
Then you can run the pipeline by directly passing the additional config file with the `-c` parameter:
```bash
nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf
```
> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
> files + singularity containers + institutional configs + modules in one go for you, to make this process easier.
