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Linting fixes

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James Fellows Yates 2021-02-14 17:58:50 +01:00
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docs/eva.md
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@ -2,7 +2,7 @@
All nf-core pipelines have been successfully configured for use on the Department of Genetics and Archaeogenetic's clusters at the [Max Planck Institute for Evolutionary Anthropology (MPI-EVA)](http://eva.mpg.de). All nf-core pipelines have been successfully configured for use on the Department of Genetics and Archaeogenetic's clusters at the [Max Planck Institute for Evolutionary Anthropology (MPI-EVA)](http://eva.mpg.de).
To use, run the pipeline with `-profile eva`. You can further with optimise submissions by specifying which cluster queue you are using e,g, `-profile eva,archgen`. This will download and launch the [`eva.config`](../conf/eva.config) which has been pre-configured with a setup suitable for the `all.q` queue. The number of parallel jobs that run is currently limited to 8. To use, run the pipeline with `-profile eva`. You can further with optimise submissions by specifying which cluster queue you are using e,g, `-profile eva,archgen`. This will download and launch the [`eva.config`](../conf/eva.config) which has been pre-configured with a setup suitable for the `all.q` queue. The number of parallel jobs that run is currently limited to 8.
Using this profile, a docker image containing all of the required software will be downloaded, and converted to a `singularity` image before execution of the pipeline. The image will currently be centrally stored here: Using this profile, a docker image containing all of the required software will be downloaded, and converted to a `singularity` image before execution of the pipeline. The image will currently be centrally stored here:
@ -26,4 +26,3 @@ 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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@ -26,9 +26,9 @@ Specific configurations for eva has been made for eager.
#### Human Pop-Gen #### Human Pop-Gen
* `human`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 16500, -n 0.01`) - `human`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 16500, -n 0.01`)
#### 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`)