TrimFlow

workflow example managed with Nextflow within Singularity that run Trimgalore on fastq files

Setup

• Install Singularity : on Linux or on Windows (v2.4.1 and above required)

• Install Nextflow: HOWTO

Quick start

Choose one of the methods below:

( change path/to/reads/ to match the folder of your data. Reads folder must be in the current folder or a subdirectory -- ./data/ )

1. Let nextflow download the workflow files and the container image automatically

nextflow run mhebrard/TrimFlow  --reads 'path/to/reads/*_R{1,2}*'

2. download the workflow files and the container image manually, then run it locally

nextflow pull mhebrard/TrimFlow
singularity pull --name TrimFlow.simg shub://mhebrard/TrimFlow
nextflow run mhebrard/TrimFlow -with-singularity ./Trimflow.simg --reads 'path/to/reads/*_R{1,2}*'

Version

The first digit correspond to the version of the container image.

The other digits represent the version of the nextflow script.