Running nf-core pipelines

Software requirements for nf-core pipelines

In order to run nf-core pipelines, you need to have Nextflow installed (https://www.nextflow.io). The only other requirement is a software packaging tool: Conda, Docker or Singularity. On Genotoul, we use Singularity.

Usage instructions and documentation

Each pipeline has its own webpage at https://nf-co.re/PIPELINE. See online documentation for rnaseq pipeline

In addition to this documentation, each pipeline comes with basic command line reference. This can be seen by running the pipeline with the --help flag, for example:

$ nextflow run nf-core/rnaseq --help

General informations

Genomes with nf-core:

• We do not provide igenome
• You can use genome from /bank in genologin
• As we are not sure about software used to generate indexes we recommand to
  • Run one time workflow with --fasta and --gtf (or more if required) and --save_reference
  • Indexes will be available in results/genome
  • Create a genome.config file and use it while rerun analysis with --genome GenomeName. More info in genome