mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-22 08:29:54 +00:00
34 lines
1.1 KiB
Markdown
34 lines
1.1 KiB
Markdown
# 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`](../../../conf/pipeline/eager/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`)
|