diff --git a/docs/usage.md b/docs/usage.md index c073e3a..1bc5066 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -9,7 +9,7 @@ This document describes the parameter options used by the pipeline. * [`--bed`](#--bed-arg-required) * [`--output`](#--output-arg-required) * [Workflow modifying parameters](#workflow-modifying-parameters) - * [`--subsampling`](#--subsampling) + * [`--subsampling`](#--subsampling)https://github.com/genepi/umi-pipeline-nf/blob/medaka_GPU/docs/usage.md * [`--call_variants`](#--call_variants) * [Read filtering parameters](#read-filtering-parameters) * [`--min_read_length`](#--min_read_length-arg) @@ -158,14 +158,14 @@ Specify if secondary mappings should be included in the analysis. [default: fals ### `--balance_strands ` Specify if the number of forward and reverse reads per cluster should be equalized. [default: true] -### `--use_gpu` +### `--use_gpu ` Specify if GPU acceleration for Medaka should be enabled. [default: false] Note: GPU acceleration is only available with the `docker` profile and has been tested with an RTX 4080 SUPER GPU (16 GB). - -### `--gpu_driver` -Specify the path to the GPU driver. The NVIDIA toolkit (https://developer.nvidia.com/cuda-toolkit) and NVIDIA container toolkit (https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html) must be installed for GPU usage. +### `--gpu_memory ` +Specify the available GPU memory in GB. [default: 16] + ### `--medaka_model ` Specify the medaka model that is used for cluster polishing. [default: "r1041_e82_400bps_hac_g615"] Note: The models are specific for Chemistry, basecalling algorithm and sequencing speed.