nf-microbe/modules

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 nf-microbe modules
• Adding nf-core modules to nf-microbe
• Adding new modules to nf-microbe
• Help
• Citation

Using nf-microbe 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:

```console $ nf-core modules -g https://github.com/nf-microbe/modules.git 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.. ```

1. Install the module in your pipeline directory:

```console $ nf-core modules -g https://github.com/nf-microbe/modules.git install fastqc

                                     ,--./,-.
     ___     __   __   __   ___     /,-._.--~\

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

nf-core/tools version 2.0

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

1. 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' ```

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

```console $ nf-core modules -g https://github.com/nf-microbe/modules.git remove fastqc

                                     ,--./,-.
     ___     __   __   __   ___     /,-._.--~\

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

nf-core/tools version 2.0

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

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

```console $ nf-core modules -g https://github.com/nf-microbe/modules.git 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 nf-core modules to nf-microbe

1. Run the nf-microbe/add_nfcore_modules.py script

python nf-microbe/add_nfcore_modules.py --module <module_name>

Adding new modules to nf-microbe

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.