From 8d272b1b6be149b9b202b1c0a86f0f52f5245bb9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Richard=20St=C3=B6ckl?= Date: Mon, 27 May 2024 12:26:51 +0200 Subject: [PATCH] chore: Add config instructions in extra README file --- README.md | 5 ++++- config/README.md | 22 ++++++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 config/README.md diff --git a/README.md b/README.md index b065118..1c40293 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,6 @@ Author: richard.stoeckl@ur.de [![Snakemake](https://img.shields.io/badge/snakemake-≥8.10.0-brightgreen.svg)](https://snakemake.github.io) -[![GitHub actions status](https://github.com/basecallNanopore/basecallNanopore/workflows/Tests/badge.svg?branch=main)](https://github.com/richardstoeckl/basecallNanopore/actions?query=branch%3Amain+workflow%3ATests) ## About @@ -31,6 +30,10 @@ For Dorado, a pipeline based on [recommendations from Nanopore](https://github.c 3. Basecall using Dorado in duplex mode but constrain to the reads for each barcode seperately ## Usage + +**[Check out the usage instructions in the snakemake workflow catalog](https://snakemake.github.io/snakemake-workflow-catalog?usage=richardstoeckl/basecallNanopore)** + +But here is a rough overview: 1. Install [conda](https://docs.conda.io/en/latest/miniconda.html) (mamba or miniconda is fine). 2. Install snakemake with: ```bash diff --git a/config/README.md b/config/README.md new file mode 100644 index 0000000..09e129b --- /dev/null +++ b/config/README.md @@ -0,0 +1,22 @@ +# General configuration + +To configure this workflow, modify `config/config.yaml` according to your needs, following the explanations provided in the file. + +## "Main" section + +Here you should provide the paths to your intermediary/results/logs directories. The `interim` directory will contain larger intermediary files. The `results` directory will contain the final output of the pipeline. The `log`directory will be used to store the log files for each step. +Here you should also write the name of your run file (see [relevant section below](#run-file-setup)). + +## "Tools" section + +Here you should give the paths to your guppy and/or dorado installation. Additionally you should change the given parameters to suit your compute setup. + + +# Run file setup + +The setup of the basecall runs is specified via comma-separated values files (`.csv`). +Missing values can be specified by empty columns. + +Depending on what you enter here, the pipeline will automatically adjust what will be done (e.g. which basecaller will be used and how many barcodes will be used). + +You can use the `config/runs_test.csv`file as a template.