From b2f4ec5d68d85a8001232461af85e2fbbfd1aabb Mon Sep 17 00:00:00 2001 From: Philip Smith Date: Thu, 2 Nov 2023 17:02:32 +0000 Subject: [PATCH] Update README.md --- README.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index b50eccb..0ba2279 100644 --- a/README.md +++ b/README.md @@ -23,8 +23,7 @@ Samples passing all filtering criteria then undergo read downsampling to the spe * [Pipeline setup](#pipeline-setup) + [Step 1 Clone the repo](#step-1-clone-the-repo) + [Step 2 Install conda](#step-2-install-conda) - - [For those with Conda already installed](#for-those-with-conda-already-installed) - + [Step 3 Installing additional dependencies](#step-3-installing-additional-dependencies) + + [Step 3 Installing environment](#step-3-installing-environment) + [Step 4 Preparing the input files](#step-4-preparing-the-input-files) - [Sample sheet](#sample-sheet) - [config.yaml](#configyaml) @@ -65,7 +64,7 @@ Our recommendation is to use micromamba or, ideally, the installed conda version See installing [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) or [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) for more information. -### Step 3 Installing environment & additional dependencies +### Step 3 Installing environment From within the repository directory, run the `install_env.sh` script to generate a conda environment and install custom packages: @@ -203,5 +202,5 @@ To confirm the quality of newly generated downsampled absolute copy number profi ## Citation -Please cite this pipeline using the following zenodo repository `10.5281/zenodo.10040893` +Please cite this pipeline using the publication ["The copy-number landscape of recurrent ovarian high grade serous carcinoma"](https://doi.org/10.1038/s41467-023-39867-7) Smith & Bradley et al. 2023 - _Nature Communications_ and/or the version controlled zenodo repository [10.5281/zenodo.10040893](https://zenodo.org/doi/10.5281/zenodo.10040893).