nf-core_modules/README.md

# ![nf-core/modules](docs/images/nfcore-modules_logo.png)

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> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!

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.

## Table of contents

- [Using existing modules](#using-existing-modules)
- [Adding new modules](#adding-new-modules)
- [Help](#help)
- [Citation](#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 [`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.

1. Install the latest version of [`nf-core/tools`](https://github.com/nf-core/tools#installation) (`>=2.0`)
2. List the available modules:

    ```console
    $ nf-core modules list remote

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

    nf-core/tools version 2.0

    INFO     Modules available from nf-core/modules (master):                       pipeline_modules.py:164

    ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
    ┃ Module Name                    ┃
    ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
    │ bandage/image                  │
    │ bcftools/consensus             │
    │ bcftools/filter                │
    │ bcftools/isec                  │
    ..truncated..
    ```

3. Install the module in your pipeline directory:

    ```console
    $ nf-core modules install fastqc

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

    nf-core/tools version 2.0

    INFO     Installing fastqc                                                      pipeline_modules.py:213
    INFO     Downloaded 3 files to ./modules/nf-core/modules/fastqc                 pipeline_modules.py:236
    ```

4. Import the module in your Nextflow script:

    ```nextflow
    #!/usr/bin/env nextflow

    nextflow.enable.dsl = 2

    include { FASTQC } from './modules/nf-core/modules/fastqc/main'
    ```

5. Remove the module from the pipeline repository if required:

    ```console
    $ nf-core modules remove fastqc

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

    nf-core/tools version 2.0

    INFO     Removing fastqc                                                        pipeline_modules.py:271
    INFO     Successfully removed fastqc                                            pipeline_modules.py:285
    ```

6. Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:

    ```console
    $ nf-core modules lint fastqc

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

    nf-core/tools version 2.0

    INFO     Linting pipeline: .                                                    lint.py:104
    INFO     Linting module: fastqc                                                 lint.py:106

    ╭─────────────────────────────────────────────────────────────────────────────────╮
    │ [!] 1 Test Warning                                                              │
    ╰─────────────────────────────────────────────────────────────────────────────────╯
    ╭──────────────┬───────────────────────────────┬──────────────────────────────────╮
    │ Module name  │ Test message                  │ File path                        │
    ├──────────────┼───────────────────────────────┼──────────────────────────────────┤
    │ fastqc       │ Local copy of module outdated │ modules/nf-core/modules/fastqc/  │
    ╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯
    ╭──────────────────────╮
    │ LINT RESULTS SUMMARY │
    ├──────────────────────┤
    │ [✔]  15 Tests Passed │
    │ [!]   1 Test Warning │
    │ [✗]   0 Test Failed  │
    ╰──────────────────────╯
    ```

## Adding new modules

If you wish to contribute a new module, please see the documentation on the [nf-core website](https://nf-co.re/developers/adding_modules).

> Please be kind to our code reviewers and submit one pull request per module :)

## 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).

<!---

### Offline usage

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.

# New test data created for the module- sequenzautils/bam2seqz
The new test data is an output from another module- sequenzautils/bcwiggle- (which uses sarscov2 genome fasta file as an input).
-->