mirror of
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Harshil Patel
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README.md
293
README.md
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# 
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> DSL2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT OF THIS REPOSITORY MAY CHANGE IN THE NEAR FUTURE!
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[](https://nfcore.slack.com/channels/modules)
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A repository for hosting nextflow [`DSL2`](https://www.nextflow.io/docs/edge/dsl2.htmlhttps://www.nextflow.io/docs/edge/dsl2.html) module files containing tool-specific process definitions and their associated documentation.
|
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> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!
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||||
|
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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.
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## Table of contents
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- [Using existing modules](#using-existing-modules)
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||||
- [Configuration and parameters](#configuration-and-parameters)
|
||||
- [Offline usage](#offline-usage)
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- [Adding a new module file](#adding-a-new-module-file)
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- [Testing](#testing)
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- [Documentation](#documentation)
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- [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules)
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- [Terminology](#terminology)
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- [Help](#help)
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## Terminology
|
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The features offered by Nextflow DSL 2 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 DSL 2 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`. This repository has been created to only host atomic module files that should be added to the `tools` sub-directory along with the required documentation, software 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.
|
||||
- *Workflow*: What DSL 1 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 DSL 1, or by using a combination of DSL 2 individual modules and sub-workflows.
|
||||
- [Citation](#citation)
|
||||
|
||||
## Using existing modules
|
||||
|
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The Nextflow [`include`](https://www.nextflow.io/docs/edge/dsl2.html#modules-include) statement can be used within your pipelines in order to load module files that you have available locally.
|
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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.
|
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|
||||
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.
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1. [Install](https://github.com/nf-core/tools#installation) the latest version of `nf-core/tools` (`>=1.10.2`)
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2. List the available modules:
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|
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```console
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$ nf-core modules list
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|
||||
,--./,-.
|
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___ __ __ __ ___ /,-._.--~\
|
||||
|\ | |__ __ / ` / \ |__) |__ } {
|
||||
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
||||
`._,._,'
|
||||
|
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nf-core/tools version 1.10.2
|
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|
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|
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|
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INFO Modules available from nf-core/modules (master): modules.py:51
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|
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bwa/index
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bwa/mem
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deeptools/computematrix
|
||||
deeptools/plotfingerprint
|
||||
deeptools/plotheatmap
|
||||
deeptools/plotprofile
|
||||
fastqc
|
||||
..truncated..
|
||||
```
|
||||
|
||||
3. Install the module in your pipeline directory:
|
||||
|
||||
```console
|
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$ 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
|
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```
|
||||
|
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4. Import the module in your Nextflow script:
|
||||
|
||||
```nextflow
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { FASTQC } from './modules/nf-core/software/fastqc/main'
|
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```
|
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|
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5. We have plans to add other utility commands to help developers install and maintain modules downloaded from this repository so watch this space!
|
||||
|
||||
```console
|
||||
$ nf-core modules --help
|
||||
|
||||
...truncated...
|
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|
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Commands:
|
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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)
|
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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
|
||||
[`nf-core/modules/software`](https://github.com/nf-core/modules/tree/master/software)
|
||||
for examples.
|
||||
|
||||
### Current guidelines
|
||||
|
||||
The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in [RFC 2119](https://tools.ietf.org/html/rfc2119).
|
||||
|
||||
#### 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:
|
||||
|
||||
```bash
|
||||
bwa mem | samtools view -B -T ref.fasta
|
||||
```
|
||||
|
||||
* Where applicable, the usage/generation of compressed files SHOULD be enforced as input/output e.g. `*.fastq.gz` and NOT `*.fastq`, `*.bam` and NOT `*.sam` etc.
|
||||
* A module MUST NOT contain a `when` statement.
|
||||
* 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`:
|
||||
|
||||
```bash
|
||||
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](https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf).
|
||||
|
||||
#### 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 in the `input` section of the process.
|
||||
* 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](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config#L29) 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](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 e.g. go to the [BWA BioContainers webpage](https://biocontainers.pro/#/tools/bwa), click on the `Pacakages and Containers` tab, sort by `Version` and get the portion of the link after the `docker pull` command where `Type` is Docker. You may need to double-check that you are using the latest version of the software because you may find that containers for older versions have been rebuilt more recently.
|
||||
|
||||
* If the software is available on Conda the software should also be defined using the Nextflow `conda` directive. Software MUST be pinned to the channel (i.e. `bioconda`) and version (i.e. `0.7.17`) e.g. `bioconda::bwa=0.7.17`. Pinning the build too e.g. "bioconda::bwa=0.7.17=h9402c20_2" is not currently a requirement.
|
||||
|
||||
* If required, multi-tool containers may also be available on BioContainers e.g. [`bwa` and `samtools`](https://biocontainers.pro/#/tools/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40). It is also possible for a 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.
|
||||
|
||||
* 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).
|
||||
|
||||
### Uploading to `nf-core/modules`
|
||||
|
||||
[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 [`nf-core/modules/software`](https://github.com/nf-core/modules/tree/master/software) directory.
|
||||
|
||||
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.
|
||||
|
||||
## 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](https://nfcore.slack.com/channels/modules) (you can join with [this invite](https://nf-co.re/join/slack)).
|
||||
|
||||
## 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](https://dx.doi.org/10.1038/s41587-020-0439-x).
|
||||
> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)
|
||||
|
||||
|
||||
<!---
|
||||
|
||||
#### Publishing results
|
||||
|
||||
- The module MUST accept the parameters `params.out_dir` and `params.publish_dir` and MUST publish results into `${params.out_dir}/${params.publish_dir}`.
|
||||
- The `publishDirMode` MUST be configurable via `params.publish_dir_mode`
|
||||
- The module MUST accept a parameter `params.publish_results` accepting at least
|
||||
- `"none"`, to publish no files at all,
|
||||
- a glob pattern which is initalized to a sensible default value.
|
||||
|
||||
It MAY accept `"logs"` to publish relevant log files, or other flags, if applicable.
|
||||
|
||||
- To ensure consistent naming, files SHOULD be renamed according to the `$name` variable before returning them.
|
||||
|
||||
#### Testing
|
||||
|
||||
- Every module MUST be tested by adding a test workflow with a toy dataset.
|
||||
- Test data MUST be stored within this repo. It is RECOMMENDED to re-use generic files from `tests/data` by symlinking them into the test directory of the module. Specific files MUST be added to the test-directory directly. Test files MUST be kept as tiny as possible.
|
||||
|
||||
#### 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. [Exact detail need to be elaborated. ]
|
||||
|
||||
You should be able to get a good idea as to how other people are using module files by looking at pipelines available in nf-core e.g. [`nf-core/chipseq`](https://github.com/nf-core/chipseq/tree/dev) (work in progress)
|
||||
|
||||
### Configuration and parameters
|
||||
|
||||
|
|
@ -52,73 +246,4 @@ 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.
|
||||
|
||||
## Adding a new module file
|
||||
|
||||
If you decide to upload your module file to `nf-core/modules` then this will
|
||||
ensure that it will be automatically downloaded, and available at run-time to
|
||||
all nf-core pipelines, and to everyone within the Nextflow community! See
|
||||
[`nf-core/modules/software`](https://github.com/nf-core/modules/tree/master/software)
|
||||
for examples.
|
||||
|
||||
**The definition and standards for module files are still under discussion
|
||||
amongst the community. Currently the following points have been agreed on:**
|
||||
|
||||
The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in [RFC 2119](https://tools.ietf.org/html/rfc2119).
|
||||
|
||||
### Defining inputs, outputs and parameters
|
||||
- A module file SHOULD only define inputs and outputs as parameters. Additionally,
|
||||
- it MUST define threads or resources where required for a particular process using `task.cpus`
|
||||
- ~~it MUST be possible to pass additional parameters to the tool as a command line string via the `params.<MODULE>_args` parameter.~~
|
||||
- it MUST be possible to pass additional parameters as a [nextflow Map](https://www.nextflow.io/docs/latest/script.html#maps) through an additional input channel `val(options)` [Details require discussion].
|
||||
- All NGS modules MUST accept a triplet [name, single_end, reads] as input. The single-end boolean values MUST be specified through the input channel and not inferred from the data e.g. [here](https://github.com/nf-core/tools/blob/028a9b3f9d1ad044e879a1de13d3c3a25a06b9a7/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/modules/nf-core/fastqc.nf#L13).
|
||||
- Process names MUST be all uppercase.
|
||||
- Each process MUST emit a file `<TOOL>.version.txt` containing a single line with the software's version in the format `v<VERSION_NUMBER>`.
|
||||
- All outputs MUST be named using `emit`.
|
||||
- A Process MUST NOT contain a `when` statement.
|
||||
- Optional inputs need development on the nextflow side. In the meanwhile, "fake files" MAY be used to work around this issue.
|
||||
|
||||
### Atomicity
|
||||
- Software that can be piped together SHOULD be added to separate module files unless there is an run-time, storage advantage in implementing in this way e.g. `bwa mem | samtools view -C -T ref.fasta` to output CRAM instead of SAM.
|
||||
|
||||
### Resource requirements
|
||||
- Each module MUST define a label `process_low`, `process_medium` or `process_high` to declare resource requirements. (*These flags will be ignored outside of nf-core and the pipeline developer is free to define adequate resource requirements*)
|
||||
|
||||
### Publishing results
|
||||
- The module MUST accept the parameters `params.out_dir` and `params.publish_dir` and MUST publish results into `${params.out_dir}/${params.publish_dir}`.
|
||||
- The `publishDirMode` MUST be configurable via `params.publish_dir_mode`
|
||||
- The module MUST accept a parameter `params.publish_results` accepting at least
|
||||
- `"none"`, to publish no files at all,
|
||||
- a glob pattern which is initalized to a sensible default value.
|
||||
|
||||
It MAY accept `"logs"` to publish relevant log files, or other flags, if applicable.
|
||||
|
||||
- To ensure consistent naming, files SHOULD be renamed according to the `$name` variable before returning them.
|
||||
|
||||
### Testing
|
||||
- Every module MUST be tested by adding a test workflow with a toy dataset.
|
||||
- Test data MUST be stored within this repo. It is RECOMMENDED to re-use generic files from `tests/data` by symlinking them into the test directory of the module. Specific files MUST be added to the test-directory directly. Test files MUST be kept as tiny as possible.
|
||||
|
||||
### Software requirements
|
||||
- Software requirements SHOULD be declared in a conda `environment.yml` file, including exact version numbers. Additionally, there MUST be a `Dockerfile` that containerizes the environment, or packages the software if conda is not available.
|
||||
- Docker containers MUST BE identified by their `sha256(Dockerfile + environment.yml)`.
|
||||
- Each module must have it's own `Dockerfile` and `environment.yml` file
|
||||
- Care should be taken to maintain identical files for subcommands that use the same software. Then the hash tag will be the same and they will be implicitly re-used across subcommands.
|
||||
|
||||
### File formats
|
||||
- Wherever possible, [CRAM](https://en.wikipedia.org/wiki/CRAM_(file_format)) files SHOULD be used over BAM files.
|
||||
- Wherever possible, FASTQ files SHOULD be compressed using gzip.
|
||||
|
||||
### 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. [Exact detail need to be elaborated. ]
|
||||
|
||||
### Uploading to `nf-core/modules`
|
||||
|
||||
[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 [`nf-core/modules/software`](https://github.com/nf-core/modules/tree/master/software) directory. Please keep the naming consistent between the module and documentation files e.g. `bwa.nf` and `bwa.md`, respectively.
|
||||
|
||||
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 `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.
|
||||
|
||||
## Help
|
||||
|
||||
If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).
|
||||
-->
|
||||
|
|
|
|||
59
software/SOFTWARE/TOOL/functions.nf
Normal file
59
software/SOFTWARE/TOOL/functions.nf
Normal file
|
|
@ -0,0 +1,59 @@
|
|||
/*
|
||||
* -----------------------------------------------------
|
||||
* Utility functions used in nf-core DSL2 module files
|
||||
* -----------------------------------------------------
|
||||
*/
|
||||
|
||||
/*
|
||||
* Extract name of software tool from process name using $task.process
|
||||
*/
|
||||
def getSoftwareName(task_process) {
|
||||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
|
||||
*/
|
||||
def initOptions(Map args) {
|
||||
def Map options = [:]
|
||||
options.args = args.args ?: ''
|
||||
options.args2 = args.args2 ?: ''
|
||||
options.publish_by_id = args.publish_by_id ?: false
|
||||
options.publish_dir = args.publish_dir ?: ''
|
||||
options.publish_files = args.publish_files ?: null
|
||||
options.suffix = args.suffix ?: ''
|
||||
return options
|
||||
}
|
||||
|
||||
/*
|
||||
* Tidy up and join elements of a list to return a path string
|
||||
*/
|
||||
def getPathFromList(path_list) {
|
||||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
|
||||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
|
||||
return paths.join('/')
|
||||
}
|
||||
|
||||
/*
|
||||
* Function to save/publish module results
|
||||
*/
|
||||
def saveFiles(Map args) {
|
||||
if (!args.filename.endsWith('.version.txt')) {
|
||||
def ioptions = initOptions(args.options)
|
||||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
|
||||
if (ioptions.publish_by_id) {
|
||||
path_list.add(args.publish_id)
|
||||
}
|
||||
if (ioptions.publish_files instanceof Map) {
|
||||
for (ext in ioptions.publish_files) {
|
||||
if (args.filename.endsWith(ext.key)) {
|
||||
def ext_list = path_list.collect()
|
||||
ext_list.add(ext.value)
|
||||
return "${getPathFromList(ext_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
} else {
|
||||
return "${getPathFromList(path_list)}/$args.filename"
|
||||
}
|
||||
}
|
||||
}
|
||||
84
software/SOFTWARE/TOOL/main.nf
Normal file
84
software/SOFTWARE/TOOL/main.nf
Normal file
|
|
@ -0,0 +1,84 @@
|
|||
// Import generic module functions
|
||||
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||||
|
||||
// TODO nf-core: All of these TODO statements can be deleted after the relevant changes have been made.
|
||||
// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
|
||||
// https://github.com/nf-core/modules/tree/master/software
|
||||
// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
|
||||
// https://nf-co.re/join
|
||||
|
||||
// TODO nf-core: The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in RFC 2119 (https://tools.ietf.org/html/rfc2119).
|
||||
// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
|
||||
// All other parameters MUST be provided as a string i.e. "options.args"
|
||||
// where "options" is a Groovy Map that MUST be provided in the "input:" section of the process.
|
||||
// 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 and evaluated appropriately.
|
||||
// TODO nf-core: 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
|
||||
// e.g. bwa mem | samtools view -B -T ref.fasta to output BAM instead of SAM.
|
||||
// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.
|
||||
|
||||
// TODO nf-core: Process name MUST be all uppercase,
|
||||
// "SOFTWARE" and (ideally) "TOOL" MUST be all one word separated by an "_".
|
||||
process SOFTWARE_TOOL {
|
||||
// TODO nf-core: If a meta map of sample information is NOT provided in "input:" section
|
||||
// change tag value to another appropriate input value e.g. tag "$fasta"
|
||||
tag "$meta.id"
|
||||
// TODO nf-core: Provide appropriate resource label for process as listed in the nf-core pipeline template below:
|
||||
// https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config#L29
|
||||
label 'process_medium'
|
||||
publishDir "${params.outdir}",
|
||||
mode: params.publish_dir_mode,
|
||||
// TODO nf-core: If a meta map of sample information is NOT provided in "input:" section
|
||||
// change "publish_id:meta.id" to initialise an empty string e.g. "publish_id:''".
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
// TODO nf-core: Fetch "docker pull" address for latest BioContainer image of software: e.g. https://biocontainers.pro/#/tools/samtools
|
||||
// If required, multi-tool containers may also be available and are usually named to start with "mulled".
|
||||
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
|
||||
|
||||
// TODO nf-core: List required Conda packages.
|
||||
// Software MUST be pinned to channel (i.e. "bioconda") and version (i.e. "1.10") as in the example below.
|
||||
// Pinning the build too e.g. "bioconda::samtools=1.10=h9402c20_2" is not currently a requirement.
|
||||
conda (params.conda ? "bioconda::samtools=1.10" : null)
|
||||
|
||||
input:
|
||||
// TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
|
||||
// MUST be provided as an input via a Groovy Map called "meta".
|
||||
// This information may not be required in some instances e.g. indexing reference genome files:
|
||||
// https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
|
||||
// TODO nf-core: Where applicable please provide/convert compressed files as input/output
|
||||
// e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
|
||||
tuple val(meta), path(reads)
|
||||
// TODO nf-core: List additional required input channels/values here
|
||||
val options
|
||||
|
||||
output:
|
||||
// TODO nf-core: Named file extensions MUST be emitted for ALL output channels
|
||||
// TODO nf-core: If meta is provided in "input:" section then it MUST be added to ALL output channels (except version)
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
// TODO nf-core: List additional required output channels/values here
|
||||
path "*.version.txt", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def ioptions = initOptions(options)
|
||||
// TODO nf-core: If a meta map of sample information is NOT provided in "input:" section delete the line below
|
||||
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
||||
// TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
|
||||
// If the software is unable to output a version number on the command-line then it can be manually specified
|
||||
// e.g. https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf
|
||||
// TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
|
||||
// TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
|
||||
// using the Nextflow "task" variable e.g. "--threads $task.cpus"
|
||||
// TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
|
||||
"""
|
||||
software tool \\
|
||||
$ioptions.args \\
|
||||
--threads $task.cpus \\
|
||||
$reads \\
|
||||
> ${prefix}.bam
|
||||
|
||||
echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
42
software/SOFTWARE/TOOL/meta.yml
Normal file
42
software/SOFTWARE/TOOL/meta.yml
Normal file
|
|
@ -0,0 +1,42 @@
|
|||
name: bwa mem
|
||||
description: Performs fastq alignment to a fasta reference using the burrows-wheeler aligner
|
||||
keywords:
|
||||
- mem
|
||||
- bwa
|
||||
- alignment
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
input:
|
||||
-
|
||||
- id:
|
||||
type: val
|
||||
description: read/read pair id
|
||||
- reads:
|
||||
type: file
|
||||
description: Input fastq file
|
||||
pattern: "*.{fastq,fq}"
|
||||
- index:
|
||||
type: file
|
||||
description: bwa indexes file
|
||||
pattern: "*.{amb,ann,bwt,pac,sa}"
|
||||
- prefix:
|
||||
type: val
|
||||
description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
|
||||
output:
|
||||
-
|
||||
- bam:
|
||||
type: file
|
||||
description: Output bam file
|
||||
pattern: "*.bam"
|
||||
- bamindex:
|
||||
type: file
|
||||
description: Output bam index file
|
||||
pattern: "*.bai"
|
||||
|
||||
authors:
|
||||
- "@jeremy1805"
|
||||
15
software/SOFTWARE/TOOL/test/main.nf
Normal file
15
software/SOFTWARE/TOOL/test/main.nf
Normal file
|
|
@ -0,0 +1,15 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include '../../../../tests/functions/check_process_outputs.nf' params(params)
|
||||
include '../main.nf' params(params)
|
||||
|
||||
reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz'
|
||||
index = '../../../../test-datasets/tools/bwa/mem/index/H3N2.{amb,ann,bwt,pac,sa}'
|
||||
prefix = 'H3N2'
|
||||
|
||||
workflow {
|
||||
read_input=Channel.fromFilePairs(reads)
|
||||
bwa_mem(read_input,file(index),prefix)
|
||||
}
|
||||
2
software/SOFTWARE/TOOL/test/nextflow.config
Normal file
2
software/SOFTWARE/TOOL/test/nextflow.config
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
docker.enabled = true
|
||||
params.outdir = './results'
|
||||
Loading…
Reference in a new issue