nf-core_modules/README.md

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

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

Table of contents

• Using existing modules
• Adding new modules
• 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 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 (>=2.0)

2. List the available modules:

   $ 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:

   $ 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:

   #!/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:

   $ 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:

   $ 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.

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 (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.