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34 lines
1.1 KiB
Markdown
34 lines
1.1 KiB
Markdown
# nf-core/configs: eva eager specific configuration
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Extra specific configuration for eager pipeline
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## Usage
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To use, run the pipeline with `-profile eva`.
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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.
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Example: `nextflow run nf-core/eager -profile eva`
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## eager specific configurations for eva
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Specific configurations for eva has been made for eager.
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### General profiles
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- The general MPI-EVA profile runs with default nf-core/eager parameters, but with modifications to account for issues SGE have with Java tools.
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#### big_data
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- This defines larger base computing resources for when working with very deep sequenced or high-endogenous samples.
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### Contextual profiles
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#### Human Pop-Gen
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- `human`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 16500, -n 0.01`)
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#### Pathogen
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- `pathogen_loose`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 16 -n 0.01`)
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- `pathogen_strict`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 32, -n 0.1`)
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