From a78aac327dde8ca0cdb84a011ccfc96c3e3a509e Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sun, 14 Feb 2021 17:58:50 +0100 Subject: [PATCH] Linting fixes --- docs/eva.md | 3 +-- docs/pipeline/eager/eva.md | 6 +++--- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/docs/eva.md b/docs/eva.md index d69ef03..42575b2 100644 --- a/docs/eva.md +++ b/docs/eva.md @@ -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). -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: @@ -26,4 +26,3 @@ Note the following characteristics of this profile: ### 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` - diff --git a/docs/pipeline/eager/eva.md b/docs/pipeline/eager/eva.md index 4537182..a8dc563 100644 --- a/docs/pipeline/eager/eva.md +++ b/docs/pipeline/eager/eva.md @@ -26,9 +26,9 @@ Specific configurations for eva has been made for eager. #### 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_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`) \ No newline at end of file +- `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`)