nf-fgbio

Use various fgbio functions and classes in your Nextflow scope.

Visit us at Fulcrum Genomics to learn more about how we can power your Bioinformatics with nf-fgbio and beyond.

Quickstart

Add the plugin to your Nextflow config:

plugins { id 'nf-fgbio' }

readStructure

A Read Structure refers to a String that describes how the bases in a sequencing run should be allocated into logical reads. The readStructure function converts a string into an fgbio ReadStructure object. This function can be used to validate a read structure, as well as query and manipulate the read structure and its read segments.

For example:

include { readStructure } from 'plugin/nf-fgbio'
 
channel.of("12M138T", "4M3S12B100T")
  .map { it -> readStructure(it) }
  .map { it -> it.segments() }
  .view()

The above example creates a channel with two read structures (each as strings), converts them into a fgbio ReadStructure object, and returns a vector of read segments for each read structure.

Vector(12M, 138T)
Vector(4M, 3S, 12B, 100T)

fromSampleSheet

The fromSampleSheet factory method parses a sample sheet from a file and returns a list of fgbio Sample data objects. This allows downstream processes to operate per-sample, with sample metadata stored in the Sample object. For example:

include { fromSampleSheet } from 'plugin/nf-fgbio'
 
channel.fromSampleSheet("./plugins/nf-fgbio/build/resources/main/samplesheet.csv")
  .map { it -> it.sampleName }
  .view()

yields a channel of sample names:

Sample_Name_1
Sample_Name_2
Sample_Name_3
Sample_Name_4
Sample_Name_5
Sample_Name_6
Sample_Name_7
Sample_Name_8
Sample_Name_9
Sample_Name_10
Sample_Name_11
Sample_Name_12

The lane option can be specified to restrict to samples from a specific lane.

channel.fromSampleSheet("/path/to/samplesheet.csv", lane: 1)

Testing the Plugin Locally

Execute the following to compile and run unit tests for the plugin:

make compile
make test

To install the plugin for use in local workflows (e.g. not internet connected), execute the following:

make install-local

Developing the Plugin Locally

Execute the following to build the plugin along with Nextflow source files:

make compile-with-nextflow

Test your changes to the plugin on a Nextflow script like:

NXF_PLUGINS_DEV="${PWD}/plugins" nextflow/launch.sh run <script.nf> -plugins nf-fgbio

Publishing to GitHub

After bumping the version of the plugin in the file MANIFEST.MF, execute the following:

GITHUB_TOKEN=... GITHUB_USERNAME=... GITHUB_COMMIT_EMAIL=... make publish-to-github

Downloads

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