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Add software dependencies and version string to requirements list

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Gregor Sturm 2020-07-14 12:07:41 +02:00
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README.md
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@ -7,12 +7,12 @@ A repository for hosting nextflow [`DSL2`](https://www.nextflow.io/docs/edge/dsl
## Table of contents ## Table of contents
- [Using existing modules](#using-existing-modules) - [Using existing modules](#using-existing-modules)
- [Configuration and parameters](#configuration-and-parameters) - [Configuration and parameters](#configuration-and-parameters)
- [Offline usage](#offline-usage) - [Offline usage](#offline-usage)
- [Adding a new module file](#adding-a-new-module-file) - [Adding a new module file](#adding-a-new-module-file)
- [Testing](#testing) - [Testing](#testing)
- [Documentation](#documentation) - [Documentation](#documentation)
- [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules) - [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules)
- [Help](#help) - [Help](#help)
## Terminology ## Terminology
@ -27,7 +27,7 @@ The features offered by Nextflow DSL 2 can be used in various ways depending on
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. 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.
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/rnaseq`](https://github.com/nf-core/rnaseq/pull/162) 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 ### Configuration and parameters
@ -54,21 +54,34 @@ nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf
## Adding a new module file ## 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/nf`](https://github.com/nf-core/modules/tree/master/nf) for examples. 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. The definition and standards for module files are still under discussion amongst the community.
Currently the following points have been agreed on: Currently the following points have been agreed on:
- Module file should only define inputs/outputs as parameters and have the ability to use `params.MODULENAME_options` as an additional parameter to add any additional settings via pipelines. - Module file should only define inputs/outputs as parameters and have the
- Specify single-end boolean values within the input channel and not be 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) ability to use `params.MODULENAME_options` as an additional parameter to add
- Define threads or resources where required for a particular process using `task.cpus` any additional settings via pipelines.
- 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` to output BAM instead of SAM - Specify single-end boolean values
- Process names should be all uppercase within the input channel and not be 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)
- Define threads or resources where required for a particular process using
`task.cpus`
- 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` to output BAM instead of SAM -
Process names should be all uppercase
- The `publishDirMode` should be configurable - The `publishDirMode` should be configurable
- Test data is stored within this repo. Re-use generic files from `tests/data` by - Test data is stored within this repo. Re-use generic files
symlinking them into the test directory of the module. Add specific files from `tests/data` by symlinking them into the test directory of the module.
to the test-directory directly. Keep test files as tiny as possible. Add specific files to the test-directory directly. Keep test files as tiny as
possible.
- Software requirements should be declared in a conda `environment.yml` file,
including exact version numbers. Additionally, there should be a `Dockerfile`
that containerizes the environment.
- Each process should emit a file `TOOL.version.txt` containing a single line
with the software's version in the format `vX.X.X`.
### Testing ### Testing
@ -80,7 +93,7 @@ Please add some documentation to the top of the module file in the form of nativ
### Uploading to `nf-core/modules` ### 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/nf`](https://github.com/nf-core/modules/tree/master/nf) directory. Please keep the naming consistent between the module and documentation files e.g. `bwa.nf` and `bwa.md`, respectively. [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. 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.