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James Fellows Yates 2021-04-06 17:53:27 +02:00
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docs/eva.md
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@ -25,4 +25,4 @@ Note the following characteristics of this profile:
### debug ### debug
This simple profile just turns off automatic clean up of intermediate files. This can be useful for debugging. Specify e.g. with `-profile eva,archgen` This simple profile just turns off automatic clean up of intermediate files. This can be useful for debugging. Specify e.g. with `-profile eva,archgen`.

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docs/pipeline/eager/eva.md
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@ -31,4 +31,4 @@ Specific configurations for eva has been made for eager.
#### Pathogen #### Pathogen
- `pathogen_loose`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 16 -n 0.01`) - `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`) - `pathogen_strict`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 32, -n 0.1`)