nf-configs/docs/pipeline/eager/eva.md

nf-core/configs: eva eager specific configuration

Extra specific configuration for eager pipeline

Usage

To use, run the pipeline with -profile eva.

This will download and launch the eager specific eva.config which has been pre-configured with a setup suitable for the MPI-EVA cluster.

Example: nextflow run nf-core/eager -profile eva

eager specific configurations for eva

Specific configurations for eva has been made for eager.

General profiles

• The general MPI-EVA profile runs with default nf-core/eager parameters, but with modifications to account for issues SGE have with Java tools.

big_data

• This defines larger base computing resources for when working with very deep sequenced or high-endogenous samples.

Contextual profiles

Human Pop-Gen

• human: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as -l 16500, -n 0.01)

Pathogen

• pathogen_loose: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as -l 16 -n 0.01)
• pathogen_strict: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as -l 32, -n 0.1)