hoelzer / wuhan

Workflow template

Maintainer: Martin

Email: [e-mail]

Automated Syntax check Setup

• First: for a new Workflow edit the badge in the Readme and replace wf_template with the new reponame
• Info: The file .github/workflows/nextflow-test.yml contains the script name e.g. main.nf, change this if you have another script name

Installation

One time installation only, to use private nextflow repos

• create git access token here
  • repo <- click on this option
  • give it a name (e.g. nextflow) and Generate token
• do nano ~/.nextflow/scm and include

providers {
    github {
        user = 'username'
        password = 'Personal API token'  } }

Input examples

• one .fastq file per sample: --nano 'sample1.fastq'
• paired end illumina: --illumina 'S_41_17_Cf*.R{1,2}.fastq.gz'

Execution example

nextflow run main.nf

Flowchart